Starting phenix.real_space_refine on Fri Mar 6 11:37:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jpu_9871/03_2026/6jpu_9871_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpu_9871/03_2026/6jpu_9871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jpu_9871/03_2026/6jpu_9871_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpu_9871/03_2026/6jpu_9871_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jpu_9871/03_2026/6jpu_9871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpu_9871/03_2026/6jpu_9871.map" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.011 sd= 0.371 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 132 5.16 5 C 17778 2.51 5 N 4734 2.21 5 O 5124 1.98 5 H 2610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30378 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "B" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "C" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "D" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "E" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "F" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 5063 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Time building chain proxies: 6.24, per 1000 atoms: 0.21 Number of scatterers: 30378 At special positions: 0 Unit cell: (154.76, 145.22, 142.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 O 5124 8.00 N 4734 7.00 C 17778 6.00 H 2610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 18 sheets defined 46.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 282 through 288 removed outlier: 4.262A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 314 through 326 removed outlier: 4.210A pdb=" N SER A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU A 592 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.730A pdb=" N TRP A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 720' Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE A1139 " --> pdb=" O LYS A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU A1150 " --> pdb=" O THR A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1174 through 1185 removed outlier: 3.624A pdb=" N MET A1185 " --> pdb=" O VAL A1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 282 through 288 removed outlier: 4.262A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 386 through 401 removed outlier: 3.759A pdb=" N SER B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 495 Processing helix chain 'B' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU B 592 " --> pdb=" O TYR B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.022A pdb=" N LEU B 623 " --> pdb=" O GLY B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 646 through 658 Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'B' and resid 715 through 720 removed outlier: 3.731A pdb=" N TRP B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 715 through 720' Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 743 through 748 Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE B1139 " --> pdb=" O LYS B1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU B1150 " --> pdb=" O THR B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1167 No H-bonds generated for 'chain 'B' and resid 1165 through 1167' Processing helix chain 'B' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET B1185 " --> pdb=" O VAL B1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 282 through 288 removed outlier: 4.262A pdb=" N LEU C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 362 removed outlier: 3.881A pdb=" N ALA C 349 " --> pdb=" O TRP C 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 removed outlier: 4.050A pdb=" N HIS C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 495 Processing helix chain 'C' and resid 515 through 526 removed outlier: 4.222A pdb=" N MET C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU C 551 " --> pdb=" O PRO C 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP C 555 " --> pdb=" O GLU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 Processing helix chain 'C' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU C 592 " --> pdb=" O TYR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU C 623 " --> pdb=" O GLY C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 640 Processing helix chain 'C' and resid 646 through 658 Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 715 through 720 removed outlier: 3.729A pdb=" N TRP C 719 " --> pdb=" O GLN C 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 720 " --> pdb=" O LEU C 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 715 through 720' Processing helix chain 'C' and resid 722 through 724 No H-bonds generated for 'chain 'C' and resid 722 through 724' Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 743 through 748 Processing helix chain 'C' and resid 750 through 755 Processing helix chain 'C' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE C1139 " --> pdb=" O LYS C1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1164 removed outlier: 3.742A pdb=" N LEU C1150 " --> pdb=" O THR C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1167 No H-bonds generated for 'chain 'C' and resid 1165 through 1167' Processing helix chain 'C' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET C1185 " --> pdb=" O VAL C1181 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 282 through 288 removed outlier: 4.263A pdb=" N LEU D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA D 349 " --> pdb=" O TRP D 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER D 390 " --> pdb=" O GLN D 386 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS D 451 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 452 " --> pdb=" O ILE D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 495 Processing helix chain 'D' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 564 removed outlier: 6.154A pdb=" N GLU D 551 " --> pdb=" O PRO D 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 578 Processing helix chain 'D' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU D 592 " --> pdb=" O TYR D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 4.022A pdb=" N LEU D 623 " --> pdb=" O GLY D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 646 through 658 Processing helix chain 'D' and resid 679 through 692 Processing helix chain 'D' and resid 715 through 720 removed outlier: 3.730A pdb=" N TRP D 719 " --> pdb=" O GLN D 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 715 through 720' Processing helix chain 'D' and resid 722 through 724 No H-bonds generated for 'chain 'D' and resid 722 through 724' Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 743 through 748 Processing helix chain 'D' and resid 750 through 755 Processing helix chain 'D' and resid 1131 through 1139 removed outlier: 3.653A pdb=" N ILE D1139 " --> pdb=" O LYS D1135 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU D1150 " --> pdb=" O THR D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1165 through 1167 No H-bonds generated for 'chain 'D' and resid 1165 through 1167' Processing helix chain 'D' and resid 1174 through 1185 removed outlier: 3.624A pdb=" N MET D1185 " --> pdb=" O VAL D1181 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 282 through 288 removed outlier: 4.261A pdb=" N LEU E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 314 through 326 removed outlier: 4.210A pdb=" N SER E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 362 removed outlier: 3.881A pdb=" N ALA E 349 " --> pdb=" O TRP E 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER E 390 " --> pdb=" O GLN E 386 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR E 452 " --> pdb=" O ILE E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 495 Processing helix chain 'E' and resid 515 through 526 removed outlier: 4.222A pdb=" N MET E 526 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU E 551 " --> pdb=" O PRO E 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP E 555 " --> pdb=" O GLU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 578 Processing helix chain 'E' and resid 586 through 595 removed outlier: 3.589A pdb=" N LEU E 592 " --> pdb=" O TYR E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU E 623 " --> pdb=" O GLY E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'E' and resid 646 through 658 Processing helix chain 'E' and resid 679 through 692 Processing helix chain 'E' and resid 715 through 720 removed outlier: 3.730A pdb=" N TRP E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE E 720 " --> pdb=" O LEU E 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 715 through 720' Processing helix chain 'E' and resid 722 through 724 No H-bonds generated for 'chain 'E' and resid 722 through 724' Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 743 through 748 Processing helix chain 'E' and resid 750 through 755 Processing helix chain 'E' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE E1139 " --> pdb=" O LYS E1135 " (cutoff:3.500A) Processing helix chain 'E' and resid 1146 through 1164 removed outlier: 3.743A pdb=" N LEU E1150 " --> pdb=" O THR E1146 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1167 No H-bonds generated for 'chain 'E' and resid 1165 through 1167' Processing helix chain 'E' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET E1185 " --> pdb=" O VAL E1181 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 282 through 288 removed outlier: 4.261A pdb=" N LEU F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 314 through 326 removed outlier: 4.211A pdb=" N SER F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 362 removed outlier: 3.882A pdb=" N ALA F 349 " --> pdb=" O TRP F 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 377 Processing helix chain 'F' and resid 386 through 401 removed outlier: 3.758A pdb=" N SER F 390 " --> pdb=" O GLN F 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET F 399 " --> pdb=" O LEU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 453 removed outlier: 4.049A pdb=" N HIS F 451 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR F 452 " --> pdb=" O ILE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 495 Processing helix chain 'F' and resid 515 through 526 removed outlier: 4.221A pdb=" N MET F 526 " --> pdb=" O SER F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 564 removed outlier: 6.153A pdb=" N GLU F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP F 555 " --> pdb=" O GLU F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 578 Processing helix chain 'F' and resid 586 through 595 removed outlier: 3.588A pdb=" N LEU F 592 " --> pdb=" O TYR F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 4.023A pdb=" N LEU F 623 " --> pdb=" O GLY F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 640 Processing helix chain 'F' and resid 646 through 658 Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 715 through 720 removed outlier: 3.729A pdb=" N TRP F 719 " --> pdb=" O GLN F 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 720 " --> pdb=" O LEU F 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 715 through 720' Processing helix chain 'F' and resid 722 through 724 No H-bonds generated for 'chain 'F' and resid 722 through 724' Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 743 through 748 Processing helix chain 'F' and resid 750 through 755 Processing helix chain 'F' and resid 1131 through 1139 removed outlier: 3.652A pdb=" N ILE F1139 " --> pdb=" O LYS F1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1146 through 1164 removed outlier: 3.742A pdb=" N LEU F1150 " --> pdb=" O THR F1146 " (cutoff:3.500A) Processing helix chain 'F' and resid 1165 through 1167 No H-bonds generated for 'chain 'F' and resid 1165 through 1167' Processing helix chain 'F' and resid 1174 through 1185 removed outlier: 3.623A pdb=" N MET F1185 " --> pdb=" O VAL F1181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER A 332 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 369 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A 334 " --> pdb=" O PHE A 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 664 through 668 Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AA5, first strand: chain 'B' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER B 332 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE B 369 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 334 " --> pdb=" O PHE B 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 664 through 668 Processing sheet with id=AA7, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'C' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER C 332 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE C 369 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR C 334 " --> pdb=" O PHE C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 664 through 668 Processing sheet with id=AB1, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AB2, first strand: chain 'D' and resid 332 through 336 removed outlier: 6.380A pdb=" N SER D 332 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE D 369 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR D 334 " --> pdb=" O PHE D 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 664 through 668 Processing sheet with id=AB4, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'E' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER E 332 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE E 369 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR E 334 " --> pdb=" O PHE E 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 664 through 668 Processing sheet with id=AB7, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AB8, first strand: chain 'F' and resid 332 through 336 removed outlier: 6.381A pdb=" N SER F 332 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE F 369 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR F 334 " --> pdb=" O PHE F 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 664 through 668 966 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 2610 1.09 - 1.27: 4560 1.27 - 1.45: 8095 1.45 - 1.63: 15515 1.63 - 1.81: 234 Bond restraints: 31014 Sorted by residual: bond pdb=" CG2 ILE B 652 " pdb="HG21 ILE B 652 " ideal model delta sigma weight residual 0.970 1.060 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CB VAL F 379 " pdb=" CG2 VAL F 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.75e+01 bond pdb=" CB VAL E 379 " pdb=" CG2 VAL E 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.75e+01 bond pdb=" CB VAL B 379 " pdb=" CG2 VAL B 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.74e+01 bond pdb=" CB VAL A 379 " pdb=" CG2 VAL A 379 " ideal model delta sigma weight residual 1.521 1.659 -0.138 3.30e-02 9.18e+02 1.74e+01 ... (remaining 31009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.21: 43833 9.21 - 18.42: 44 18.42 - 27.63: 16 27.63 - 36.84: 25 36.84 - 46.05: 2 Bond angle restraints: 43920 Sorted by residual: angle pdb="HG12 ILE B 652 " pdb=" CG1 ILE B 652 " pdb="HG13 ILE B 652 " ideal model delta sigma weight residual 110.00 63.95 46.05 3.00e+00 1.11e-01 2.36e+02 angle pdb=" CB ILE B 652 " pdb=" CG1 ILE B 652 " pdb="HG12 ILE B 652 " ideal model delta sigma weight residual 109.00 146.10 -37.10 3.00e+00 1.11e-01 1.53e+02 angle pdb="HG22 VAL E 379 " pdb=" CG2 VAL E 379 " pdb="HG23 VAL E 379 " ideal model delta sigma weight residual 110.00 74.08 35.92 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CB VAL E 379 " pdb=" CG2 VAL E 379 " pdb="HG22 VAL E 379 " ideal model delta sigma weight residual 109.00 144.27 -35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb="HG11 VAL D 408 " pdb=" CG1 VAL D 408 " pdb="HG12 VAL D 408 " ideal model delta sigma weight residual 110.00 78.34 31.66 3.00e+00 1.11e-01 1.11e+02 ... (remaining 43915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15774 17.47 - 34.95: 1813 34.95 - 52.42: 470 52.42 - 69.90: 182 69.90 - 87.37: 61 Dihedral angle restraints: 18300 sinusoidal: 8136 harmonic: 10164 Sorted by residual: dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N GLY F 258 " pdb=" CA GLY F 258 " ideal model delta harmonic sigma weight residual 180.00 124.14 55.86 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA LEU A 257 " pdb=" C LEU A 257 " pdb=" N GLY A 258 " pdb=" CA GLY A 258 " ideal model delta harmonic sigma weight residual 180.00 124.15 55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA LEU C 257 " pdb=" C LEU C 257 " pdb=" N GLY C 258 " pdb=" CA GLY C 258 " ideal model delta harmonic sigma weight residual 180.00 124.15 55.85 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 18297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3238 0.060 - 0.119: 917 0.119 - 0.179: 111 0.179 - 0.238: 18 0.238 - 0.298: 18 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CB VAL C 282 " pdb=" CA VAL C 282 " pdb=" CG1 VAL C 282 " pdb=" CG2 VAL C 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL F 282 " pdb=" CA VAL F 282 " pdb=" CG1 VAL F 282 " pdb=" CG2 VAL F 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB VAL B 282 " pdb=" CA VAL B 282 " pdb=" CG1 VAL B 282 " pdb=" CG2 VAL B 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4299 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 345 " -0.017 2.00e-02 2.50e+03 1.35e-02 4.56e+00 pdb=" CG TRP C 345 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 345 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 345 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 345 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 345 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 345 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 345 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 345 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 345 " -0.016 2.00e-02 2.50e+03 1.35e-02 4.53e+00 pdb=" CG TRP F 345 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 345 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 345 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 345 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 345 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 345 " -0.016 2.00e-02 2.50e+03 1.35e-02 4.53e+00 pdb=" CG TRP D 345 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 345 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 345 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 345 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 345 " -0.002 2.00e-02 2.50e+03 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.47: 1023 2.47 - 3.00: 25827 3.00 - 3.53: 47036 3.53 - 4.07: 65533 4.07 - 4.60: 93316 Nonbonded interactions: 232735 Sorted by model distance: nonbonded pdb=" OG1 THR A 311 " pdb="HG21 THR A 311 " model vdw 1.933 2.096 nonbonded pdb=" OG1 THR C 314 " pdb=" OD2 ASP C 371 " model vdw 1.984 2.800 nonbonded pdb=" OG1 THR B 314 " pdb=" OD2 ASP B 371 " model vdw 1.984 2.800 nonbonded pdb=" OG1 THR D 314 " pdb=" OD2 ASP D 371 " model vdw 1.984 2.800 nonbonded pdb=" OG1 THR A 314 " pdb=" OD2 ASP A 371 " model vdw 1.984 2.800 ... (remaining 232730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.290 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 28404 Z= 0.303 Angle : 1.032 11.344 38466 Z= 0.578 Chirality : 0.056 0.298 4302 Planarity : 0.005 0.043 4950 Dihedral : 17.266 86.200 10962 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 70.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.77 % Favored : 90.05 % Rotamer: Outliers : 9.58 % Allowed : 8.62 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.12), residues: 3438 helix: -2.72 (0.11), residues: 1392 sheet: -1.82 (0.29), residues: 288 loop : -2.70 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 432 TYR 0.022 0.002 TYR C 274 PHE 0.025 0.003 PHE A 295 TRP 0.037 0.003 TRP C 345 HIS 0.009 0.002 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00665 (28404) covalent geometry : angle 1.03212 (38466) hydrogen bonds : bond 0.17372 ( 966) hydrogen bonds : angle 8.87298 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 967 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 667 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7711 (t) REVERT: A 370 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8621 (t80) REVERT: A 373 ILE cc_start: 0.6376 (tt) cc_final: 0.6115 (tt) REVERT: A 411 ILE cc_start: 0.8054 (mp) cc_final: 0.7320 (tp) REVERT: A 432 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.5424 (ptt-90) REVERT: A 521 MET cc_start: 0.9815 (mmt) cc_final: 0.9613 (mtp) REVERT: A 564 MET cc_start: 0.9601 (tpp) cc_final: 0.9352 (tpp) REVERT: A 575 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8572 (tp30) REVERT: A 622 ILE cc_start: 0.9320 (pt) cc_final: 0.9027 (tp) REVERT: A 691 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8877 (mm-30) REVERT: A 729 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 1156 PHE cc_start: 0.9191 (m-80) cc_final: 0.8796 (m-80) REVERT: B 263 LEU cc_start: 0.5001 (OUTLIER) cc_final: 0.4798 (tp) REVERT: B 370 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7204 (t80) REVERT: B 418 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6815 (p0) REVERT: B 584 ASN cc_start: 0.9042 (t0) cc_final: 0.8651 (m-40) REVERT: B 636 MET cc_start: 0.8063 (mpp) cc_final: 0.7606 (mpp) REVERT: B 1152 HIS cc_start: 0.8927 (m90) cc_final: 0.8720 (m-70) REVERT: B 1154 HIS cc_start: 0.8488 (t70) cc_final: 0.8136 (t70) REVERT: C 318 ARG cc_start: 0.9473 (mpt180) cc_final: 0.9074 (mmm160) REVERT: C 336 ARG cc_start: 0.8914 (tpm170) cc_final: 0.8422 (mmm160) REVERT: C 370 PHE cc_start: 0.9735 (OUTLIER) cc_final: 0.9487 (t80) REVERT: C 386 GLN cc_start: 0.3089 (OUTLIER) cc_final: 0.2031 (pm20) REVERT: C 455 TRP cc_start: 0.6040 (m-90) cc_final: 0.5697 (m-90) REVERT: C 489 ASN cc_start: 0.9016 (m-40) cc_final: 0.8425 (m110) REVERT: C 654 LEU cc_start: 0.9021 (tp) cc_final: 0.8649 (tp) REVERT: C 1165 LYS cc_start: 0.9180 (ttpp) cc_final: 0.8589 (tptp) REVERT: D 370 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8771 (t80) REVERT: D 372 GLU cc_start: 0.9134 (tp30) cc_final: 0.8746 (tm-30) REVERT: D 498 LEU cc_start: 0.8854 (mt) cc_final: 0.8555 (mt) REVERT: D 575 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (tp30) REVERT: D 656 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.8324 (mt) REVERT: D 691 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8967 (mm-30) REVERT: D 729 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9068 (tp) REVERT: E 260 ASP cc_start: 0.1344 (OUTLIER) cc_final: 0.1111 (t0) REVERT: E 304 LEU cc_start: 0.9473 (mm) cc_final: 0.9223 (mp) REVERT: E 342 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6139 (tp) REVERT: E 370 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8277 (t80) REVERT: E 386 GLN cc_start: -0.0250 (OUTLIER) cc_final: -0.0837 (mt0) REVERT: E 409 ILE cc_start: 0.8361 (mp) cc_final: 0.7825 (mp) REVERT: E 416 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7701 (pmt170) REVERT: E 432 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.5437 (mtm180) REVERT: E 466 MET cc_start: 0.9343 (ptm) cc_final: 0.8956 (ppp) REVERT: E 582 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7397 (tptp) REVERT: E 595 PHE cc_start: 0.9328 (m-80) cc_final: 0.9126 (m-80) REVERT: E 691 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8726 (mm-30) REVERT: E 713 HIS cc_start: 0.8452 (m-70) cc_final: 0.7645 (m170) REVERT: F 260 ASP cc_start: 0.0661 (OUTLIER) cc_final: -0.0222 (t0) REVERT: F 370 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7657 (t80) REVERT: F 386 GLN cc_start: -0.2462 (OUTLIER) cc_final: -0.3021 (mt0) REVERT: F 416 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5941 (pmt170) REVERT: F 440 ASP cc_start: 0.9103 (p0) cc_final: 0.8902 (p0) REVERT: F 469 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9057 (pt0) REVERT: F 482 LEU cc_start: 0.9432 (mt) cc_final: 0.9137 (mt) REVERT: F 545 LEU cc_start: 0.9325 (mt) cc_final: 0.9119 (mt) REVERT: F 560 LEU cc_start: 0.9454 (pp) cc_final: 0.9219 (pp) REVERT: F 674 TRP cc_start: 0.8739 (t60) cc_final: 0.7744 (t60) REVERT: F 689 MET cc_start: 0.8957 (mmm) cc_final: 0.8733 (mmm) REVERT: F 697 ASP cc_start: 0.9177 (m-30) cc_final: 0.8892 (t70) REVERT: F 713 HIS cc_start: 0.8388 (m-70) cc_final: 0.7937 (m170) REVERT: F 1154 HIS cc_start: 0.8814 (t70) cc_final: 0.7101 (t70) REVERT: F 1158 TYR cc_start: 0.8664 (m-10) cc_final: 0.8031 (m-10) outliers start: 300 outliers final: 90 residues processed: 893 average time/residue: 0.2090 time to fit residues: 284.5594 Evaluate side-chains 592 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 477 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN B 615 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN D 615 GLN D 624 GLN D 742 GLN ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 742 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.109824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.074981 restraints weight = 157899.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.077237 restraints weight = 113805.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079011 restraints weight = 87893.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080395 restraints weight = 71452.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.081398 restraints weight = 60274.458| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28404 Z= 0.128 Angle : 0.591 6.056 38466 Z= 0.314 Chirality : 0.042 0.173 4302 Planarity : 0.004 0.050 4950 Dihedral : 6.125 48.394 3762 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 69.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.12 % Favored : 91.77 % Rotamer: Outliers : 0.22 % Allowed : 3.19 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.13), residues: 3438 helix: -1.47 (0.12), residues: 1524 sheet: -1.71 (0.29), residues: 294 loop : -2.46 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 336 TYR 0.024 0.001 TYR B 601 PHE 0.031 0.002 PHE F1184 TRP 0.014 0.001 TRP A 455 HIS 0.007 0.001 HIS E 306 Details of bonding type rmsd covalent geometry : bond 0.00275 (28404) covalent geometry : angle 0.59126 (38466) hydrogen bonds : bond 0.04184 ( 966) hydrogen bonds : angle 6.74972 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 593 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 586 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LEU cc_start: 0.9720 (pp) cc_final: 0.9447 (pp) REVERT: A 641 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9208 (tm-30) REVERT: A 691 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9101 (mm-30) REVERT: A 692 ARG cc_start: 0.9379 (tpm170) cc_final: 0.9106 (mmm160) REVERT: A 701 PHE cc_start: 0.9695 (t80) cc_final: 0.8922 (t80) REVERT: A 1154 HIS cc_start: 0.9425 (t70) cc_final: 0.8657 (t-90) REVERT: A 1156 PHE cc_start: 0.9438 (m-80) cc_final: 0.9074 (m-80) REVERT: B 335 MET cc_start: 0.7278 (mmp) cc_final: 0.6749 (mmp) REVERT: B 499 TYR cc_start: 0.8538 (p90) cc_final: 0.8227 (p90) REVERT: B 535 ILE cc_start: 0.6869 (mt) cc_final: 0.5972 (mp) REVERT: B 584 ASN cc_start: 0.9129 (t0) cc_final: 0.8890 (m-40) REVERT: B 591 ARG cc_start: 0.9669 (mmt180) cc_final: 0.9176 (mtm180) REVERT: B 632 GLN cc_start: 0.8890 (tp40) cc_final: 0.8592 (tp40) REVERT: B 636 MET cc_start: 0.7957 (mpp) cc_final: 0.7543 (mpp) REVERT: B 727 TYR cc_start: 0.9422 (t80) cc_final: 0.9161 (t80) REVERT: B 1152 HIS cc_start: 0.9273 (m90) cc_final: 0.8839 (m-70) REVERT: B 1154 HIS cc_start: 0.9093 (t70) cc_final: 0.8761 (t70) REVERT: C 318 ARG cc_start: 0.9420 (mpt180) cc_final: 0.9125 (mmm160) REVERT: C 334 TYR cc_start: 0.8877 (m-80) cc_final: 0.8668 (m-80) REVERT: C 489 ASN cc_start: 0.8962 (m-40) cc_final: 0.8666 (m-40) REVERT: C 591 ARG cc_start: 0.9754 (mmt180) cc_final: 0.9538 (mtt-85) REVERT: C 641 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8737 (tm-30) REVERT: C 678 LEU cc_start: 0.7857 (mm) cc_final: 0.7376 (mm) REVERT: C 691 GLU cc_start: 0.8883 (mp0) cc_final: 0.8683 (mp0) REVERT: C 741 PHE cc_start: 0.9144 (m-80) cc_final: 0.8942 (m-80) REVERT: C 1152 HIS cc_start: 0.9277 (m90) cc_final: 0.8958 (m-70) REVERT: D 372 GLU cc_start: 0.9219 (tp30) cc_final: 0.8989 (tp30) REVERT: D 498 LEU cc_start: 0.9153 (mt) cc_final: 0.8731 (mt) REVERT: D 519 PHE cc_start: 0.9689 (m-80) cc_final: 0.9486 (m-80) REVERT: D 595 PHE cc_start: 0.8339 (m-80) cc_final: 0.8033 (m-80) REVERT: D 691 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9141 (mm-30) REVERT: D 715 GLN cc_start: 0.9708 (mm110) cc_final: 0.9453 (mp10) REVERT: D 754 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8724 (tp30) REVERT: E 562 LYS cc_start: 0.9517 (mttt) cc_final: 0.9299 (mttt) REVERT: E 582 LYS cc_start: 0.8503 (mtmm) cc_final: 0.7718 (tptp) REVERT: E 713 HIS cc_start: 0.8630 (m-70) cc_final: 0.7799 (m170) REVERT: E 1154 HIS cc_start: 0.9412 (t70) cc_final: 0.8436 (t70) REVERT: E 1158 TYR cc_start: 0.9455 (m-10) cc_final: 0.9220 (m-10) REVERT: F 466 MET cc_start: 0.7987 (ptt) cc_final: 0.7267 (ppp) REVERT: F 499 TYR cc_start: 0.9175 (p90) cc_final: 0.8765 (p90) REVERT: F 545 LEU cc_start: 0.9653 (mt) cc_final: 0.9359 (mt) REVERT: F 630 HIS cc_start: 0.8762 (t-170) cc_final: 0.8529 (t-170) REVERT: F 654 LEU cc_start: 0.9241 (tp) cc_final: 0.9029 (tp) REVERT: F 674 TRP cc_start: 0.9318 (t60) cc_final: 0.8428 (t60) REVERT: F 693 LEU cc_start: 0.9168 (mt) cc_final: 0.8609 (mt) REVERT: F 713 HIS cc_start: 0.8517 (m-70) cc_final: 0.7866 (m-70) REVERT: F 1154 HIS cc_start: 0.9090 (t70) cc_final: 0.8793 (t70) outliers start: 7 outliers final: 7 residues processed: 593 average time/residue: 0.1981 time to fit residues: 182.8546 Evaluate side-chains 482 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 475 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 207 optimal weight: 0.6980 chunk 270 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 102 optimal weight: 0.0170 chunk 73 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 86 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.106782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.072372 restraints weight = 165061.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074411 restraints weight = 118020.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.076021 restraints weight = 91944.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.077241 restraints weight = 75423.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.078182 restraints weight = 64465.413| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28404 Z= 0.142 Angle : 0.585 6.704 38466 Z= 0.308 Chirality : 0.041 0.161 4302 Planarity : 0.004 0.042 4950 Dihedral : 5.541 42.297 3762 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 75.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 3438 helix: -1.15 (0.12), residues: 1536 sheet: -1.69 (0.27), residues: 324 loop : -2.23 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.024 0.001 TYR B 601 PHE 0.026 0.002 PHE A 369 TRP 0.019 0.001 TRP B 674 HIS 0.008 0.001 HIS C1154 Details of bonding type rmsd covalent geometry : bond 0.00303 (28404) covalent geometry : angle 0.58471 (38466) hydrogen bonds : bond 0.03622 ( 966) hydrogen bonds : angle 6.34170 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 534 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.9174 (mmp) cc_final: 0.8954 (mmp) REVERT: A 373 ILE cc_start: 0.7716 (tt) cc_final: 0.6917 (tt) REVERT: A 399 MET cc_start: 0.6282 (mmt) cc_final: 0.6016 (mmt) REVERT: A 521 MET cc_start: 0.9849 (mtm) cc_final: 0.9634 (mtp) REVERT: A 691 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9146 (mm-30) REVERT: A 692 ARG cc_start: 0.9448 (tpm170) cc_final: 0.9117 (mmm160) REVERT: A 701 PHE cc_start: 0.9693 (t80) cc_final: 0.8966 (t80) REVERT: A 1156 PHE cc_start: 0.9381 (m-10) cc_final: 0.9002 (m-80) REVERT: A 1184 PHE cc_start: 0.9078 (t80) cc_final: 0.8864 (t80) REVERT: B 297 MET cc_start: 0.7148 (pmm) cc_final: 0.6919 (pmm) REVERT: B 298 GLN cc_start: 0.9197 (pm20) cc_final: 0.8257 (pp30) REVERT: B 335 MET cc_start: 0.7516 (mmp) cc_final: 0.6897 (mmp) REVERT: B 584 ASN cc_start: 0.9170 (t0) cc_final: 0.8819 (m-40) REVERT: B 591 ARG cc_start: 0.9703 (mmt180) cc_final: 0.9278 (mtm180) REVERT: B 632 GLN cc_start: 0.8995 (tp40) cc_final: 0.8604 (tp40) REVERT: B 727 TYR cc_start: 0.9461 (t80) cc_final: 0.9165 (t80) REVERT: B 1154 HIS cc_start: 0.9006 (t70) cc_final: 0.8585 (t-90) REVERT: C 318 ARG cc_start: 0.9442 (mpt180) cc_final: 0.9157 (mmm160) REVERT: C 334 TYR cc_start: 0.8784 (m-80) cc_final: 0.8147 (m-80) REVERT: C 489 ASN cc_start: 0.9066 (m-40) cc_final: 0.8750 (m-40) REVERT: C 641 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8877 (tm-30) REVERT: C 654 LEU cc_start: 0.9236 (tp) cc_final: 0.8955 (tp) REVERT: C 678 LEU cc_start: 0.8015 (mm) cc_final: 0.7418 (mm) REVERT: C 692 ARG cc_start: 0.9368 (tpp80) cc_final: 0.8788 (ttp80) REVERT: D 316 MET cc_start: 0.8024 (ptp) cc_final: 0.7821 (ptp) REVERT: D 372 GLU cc_start: 0.9240 (tp30) cc_final: 0.8969 (tp30) REVERT: D 689 MET cc_start: 0.9713 (mmm) cc_final: 0.9494 (mmp) REVERT: D 691 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9145 (mm-30) REVERT: E 577 MET cc_start: 0.8751 (ttp) cc_final: 0.8426 (ptm) REVERT: E 595 PHE cc_start: 0.9412 (m-80) cc_final: 0.9045 (m-80) REVERT: E 640 LEU cc_start: 0.8986 (mt) cc_final: 0.8758 (mp) REVERT: E 689 MET cc_start: 0.9654 (mmp) cc_final: 0.9437 (mmm) REVERT: E 691 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8900 (mm-30) REVERT: E 695 PHE cc_start: 0.9500 (p90) cc_final: 0.9213 (p90) REVERT: E 713 HIS cc_start: 0.8562 (m-70) cc_final: 0.7775 (m90) REVERT: F 283 MET cc_start: 0.8947 (tmm) cc_final: 0.8697 (tmm) REVERT: F 466 MET cc_start: 0.7661 (ptt) cc_final: 0.7368 (ppp) REVERT: F 499 TYR cc_start: 0.9184 (p90) cc_final: 0.8735 (p90) REVERT: F 545 LEU cc_start: 0.9622 (mt) cc_final: 0.9328 (mt) REVERT: F 674 TRP cc_start: 0.9395 (t60) cc_final: 0.8512 (t60) REVERT: F 713 HIS cc_start: 0.8585 (m-70) cc_final: 0.7931 (m-70) REVERT: F 1154 HIS cc_start: 0.9053 (t70) cc_final: 0.8723 (t70) outliers start: 0 outliers final: 0 residues processed: 534 average time/residue: 0.2016 time to fit residues: 167.8331 Evaluate side-chains 444 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 88 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS B 276 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 HIS ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS D 454 ASN ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 GLN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.097204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.064537 restraints weight = 180991.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066343 restraints weight = 128731.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067739 restraints weight = 99756.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068761 restraints weight = 82206.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069478 restraints weight = 70742.423| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28404 Z= 0.284 Angle : 0.832 13.622 38466 Z= 0.430 Chirality : 0.045 0.205 4302 Planarity : 0.006 0.064 4950 Dihedral : 6.025 42.413 3762 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 113.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.14), residues: 3438 helix: -1.58 (0.12), residues: 1578 sheet: -2.18 (0.24), residues: 396 loop : -2.12 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 591 TYR 0.037 0.003 TYR B 601 PHE 0.033 0.003 PHE C 295 TRP 0.044 0.003 TRP B 674 HIS 0.015 0.002 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00551 (28404) covalent geometry : angle 0.83187 (38466) hydrogen bonds : bond 0.04302 ( 966) hydrogen bonds : angle 6.61953 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 474 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 PHE cc_start: 0.9022 (t80) cc_final: 0.8626 (t80) REVERT: A 470 LYS cc_start: 0.9553 (pttm) cc_final: 0.9334 (pttm) REVERT: A 519 PHE cc_start: 0.9831 (m-80) cc_final: 0.9275 (t80) REVERT: A 521 MET cc_start: 0.9852 (mtm) cc_final: 0.9642 (mtp) REVERT: A 691 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9222 (mm-30) REVERT: B 283 MET cc_start: 0.9062 (tmm) cc_final: 0.8639 (tmm) REVERT: B 284 LEU cc_start: 0.9788 (mm) cc_final: 0.9475 (mm) REVERT: B 288 TYR cc_start: 0.9441 (m-10) cc_final: 0.9159 (m-10) REVERT: B 298 GLN cc_start: 0.9226 (pm20) cc_final: 0.8475 (pp30) REVERT: B 334 TYR cc_start: 0.8215 (m-80) cc_final: 0.7790 (m-80) REVERT: B 336 ARG cc_start: 0.8171 (tpt90) cc_final: 0.7832 (tpp-160) REVERT: B 466 MET cc_start: 0.9473 (ptp) cc_final: 0.9202 (ptp) REVERT: B 584 ASN cc_start: 0.9352 (t0) cc_final: 0.9033 (m-40) REVERT: B 691 GLU cc_start: 0.9619 (mm-30) cc_final: 0.9265 (mm-30) REVERT: B 1154 HIS cc_start: 0.9278 (t70) cc_final: 0.8511 (t70) REVERT: B 1158 TYR cc_start: 0.8667 (m-80) cc_final: 0.8093 (m-80) REVERT: C 283 MET cc_start: 0.9565 (tpt) cc_final: 0.9340 (tpp) REVERT: C 284 LEU cc_start: 0.9698 (mm) cc_final: 0.9492 (mm) REVERT: C 334 TYR cc_start: 0.8861 (m-80) cc_final: 0.8450 (m-80) REVERT: C 336 ARG cc_start: 0.9001 (tpm170) cc_final: 0.8721 (tpp-160) REVERT: C 489 ASN cc_start: 0.9126 (m-40) cc_final: 0.8829 (m-40) REVERT: C 641 GLN cc_start: 0.9419 (tm-30) cc_final: 0.9133 (tm-30) REVERT: C 689 MET cc_start: 0.9656 (mmm) cc_final: 0.9342 (mmm) REVERT: C 692 ARG cc_start: 0.9403 (tpp80) cc_final: 0.8968 (tpp80) REVERT: D 316 MET cc_start: 0.7487 (ptp) cc_final: 0.6907 (ptp) REVERT: D 372 GLU cc_start: 0.9056 (tp30) cc_final: 0.8824 (tp30) REVERT: D 658 VAL cc_start: 0.9577 (t) cc_final: 0.9158 (t) REVERT: D 691 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9144 (mm-30) REVERT: E 595 PHE cc_start: 0.9423 (m-80) cc_final: 0.9071 (m-80) REVERT: E 598 LEU cc_start: 0.9497 (mp) cc_final: 0.9251 (mp) REVERT: E 689 MET cc_start: 0.9768 (mmp) cc_final: 0.9540 (mmm) REVERT: E 691 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8892 (mm-30) REVERT: E 1154 HIS cc_start: 0.9219 (t-90) cc_final: 0.8275 (t-90) REVERT: E 1158 TYR cc_start: 0.9444 (m-10) cc_final: 0.9210 (m-10) REVERT: F 283 MET cc_start: 0.9040 (tmm) cc_final: 0.8714 (tmm) REVERT: F 316 MET cc_start: 0.9493 (ptp) cc_final: 0.9281 (ptp) REVERT: F 466 MET cc_start: 0.8454 (ptt) cc_final: 0.7801 (ppp) REVERT: F 596 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9156 (mm-30) REVERT: F 689 MET cc_start: 0.9374 (mmm) cc_final: 0.9052 (mmm) REVERT: F 713 HIS cc_start: 0.8477 (m-70) cc_final: 0.7815 (m-70) REVERT: F 716 LEU cc_start: 0.9549 (mt) cc_final: 0.9348 (mt) REVERT: F 1154 HIS cc_start: 0.8999 (t70) cc_final: 0.8589 (t70) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.1924 time to fit residues: 141.7471 Evaluate side-chains 391 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 323 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 283 optimal weight: 6.9990 chunk 337 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 454 ASN A 489 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 306 HIS ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.102798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070331 restraints weight = 169178.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072577 restraints weight = 115054.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074279 restraints weight = 85846.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.075465 restraints weight = 68009.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076222 restraints weight = 56673.459| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28404 Z= 0.112 Angle : 0.564 7.376 38466 Z= 0.296 Chirality : 0.041 0.206 4302 Planarity : 0.005 0.079 4950 Dihedral : 5.403 37.308 3762 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 80.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.10 % Allowed : 2.17 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.14), residues: 3438 helix: -0.97 (0.12), residues: 1578 sheet: -1.97 (0.25), residues: 396 loop : -2.11 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 659 TYR 0.025 0.001 TYR E1158 PHE 0.016 0.001 PHE B 595 TRP 0.021 0.002 TRP D 674 HIS 0.013 0.001 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00239 (28404) covalent geometry : angle 0.56425 (38466) hydrogen bonds : bond 0.03302 ( 966) hydrogen bonds : angle 5.91792 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 527 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 524 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 PHE cc_start: 0.8868 (t80) cc_final: 0.8402 (t80) REVERT: A 521 MET cc_start: 0.9822 (mtm) cc_final: 0.9619 (mtp) REVERT: A 689 MET cc_start: 0.9670 (mmp) cc_final: 0.9401 (mmm) REVERT: A 691 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9146 (mm-30) REVERT: A 692 ARG cc_start: 0.9580 (tpp80) cc_final: 0.9137 (mmm160) REVERT: A 693 LEU cc_start: 0.9352 (mm) cc_final: 0.9012 (mm) REVERT: A 701 PHE cc_start: 0.9702 (t80) cc_final: 0.9296 (t80) REVERT: A 1154 HIS cc_start: 0.9211 (t-90) cc_final: 0.8666 (t-90) REVERT: A 1156 PHE cc_start: 0.9297 (m-10) cc_final: 0.9082 (m-80) REVERT: A 1184 PHE cc_start: 0.9135 (t80) cc_final: 0.8811 (t80) REVERT: B 283 MET cc_start: 0.9039 (tmm) cc_final: 0.8726 (tmm) REVERT: B 284 LEU cc_start: 0.9769 (mm) cc_final: 0.9420 (mm) REVERT: B 288 TYR cc_start: 0.9472 (m-10) cc_final: 0.9217 (m-10) REVERT: B 297 MET cc_start: 0.6685 (pmm) cc_final: 0.6260 (pmm) REVERT: B 316 MET cc_start: 0.7923 (mtm) cc_final: 0.7487 (mtm) REVERT: B 334 TYR cc_start: 0.8198 (m-80) cc_final: 0.7704 (m-80) REVERT: B 336 ARG cc_start: 0.7981 (tpt90) cc_final: 0.7624 (tpp-160) REVERT: B 584 ASN cc_start: 0.9345 (t0) cc_final: 0.9042 (m-40) REVERT: B 667 TYR cc_start: 0.8907 (t80) cc_final: 0.8540 (t80) REVERT: B 691 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9226 (mm-30) REVERT: C 283 MET cc_start: 0.9581 (tpt) cc_final: 0.9339 (tpp) REVERT: C 284 LEU cc_start: 0.9699 (mm) cc_final: 0.9475 (mm) REVERT: C 334 TYR cc_start: 0.8696 (m-80) cc_final: 0.8387 (m-80) REVERT: C 489 ASN cc_start: 0.9007 (m-40) cc_final: 0.8720 (m-40) REVERT: C 641 GLN cc_start: 0.9340 (tm-30) cc_final: 0.9036 (tm-30) REVERT: C 654 LEU cc_start: 0.9264 (tp) cc_final: 0.9012 (tp) REVERT: C 659 ARG cc_start: 0.9064 (tpp-160) cc_final: 0.8378 (tpp-160) REVERT: C 683 ILE cc_start: 0.9507 (mt) cc_final: 0.9238 (mt) REVERT: C 692 ARG cc_start: 0.9393 (tpp80) cc_final: 0.8896 (ttp80) REVERT: C 741 PHE cc_start: 0.9289 (m-80) cc_final: 0.9013 (m-80) REVERT: D 316 MET cc_start: 0.7409 (ptp) cc_final: 0.7060 (ptp) REVERT: D 372 GLU cc_start: 0.9134 (tp30) cc_final: 0.8841 (tp30) REVERT: D 575 GLU cc_start: 0.8823 (tp30) cc_final: 0.8545 (tp30) REVERT: D 598 LEU cc_start: 0.9688 (mp) cc_final: 0.9472 (mp) REVERT: D 658 VAL cc_start: 0.9369 (t) cc_final: 0.9077 (t) REVERT: D 729 LEU cc_start: 0.9430 (tp) cc_final: 0.9072 (tp) REVERT: D 741 PHE cc_start: 0.9400 (m-10) cc_final: 0.9100 (m-10) REVERT: D 1153 LEU cc_start: 0.9550 (mm) cc_final: 0.9308 (mm) REVERT: D 1165 LYS cc_start: 0.9378 (ttpt) cc_final: 0.8900 (tptp) REVERT: E 595 PHE cc_start: 0.9410 (m-80) cc_final: 0.9071 (m-80) REVERT: E 598 LEU cc_start: 0.9549 (mp) cc_final: 0.9338 (mp) REVERT: E 641 GLN cc_start: 0.9483 (tm-30) cc_final: 0.9264 (tm-30) REVERT: E 657 GLU cc_start: 0.9676 (mm-30) cc_final: 0.9454 (mm-30) REVERT: E 689 MET cc_start: 0.9731 (mmp) cc_final: 0.9443 (mmm) REVERT: E 691 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9040 (mm-30) REVERT: E 1154 HIS cc_start: 0.9236 (t-90) cc_final: 0.8324 (t-90) REVERT: E 1184 PHE cc_start: 0.9144 (t80) cc_final: 0.8938 (t80) REVERT: F 283 MET cc_start: 0.8984 (tmm) cc_final: 0.8747 (tmm) REVERT: F 358 GLU cc_start: 0.9496 (mp0) cc_final: 0.9028 (pp20) REVERT: F 466 MET cc_start: 0.8255 (ptt) cc_final: 0.7907 (ppp) REVERT: F 596 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9101 (mm-30) REVERT: F 659 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8056 (ttp80) REVERT: F 713 HIS cc_start: 0.8412 (m-70) cc_final: 0.7621 (m90) REVERT: F 716 LEU cc_start: 0.9502 (mt) cc_final: 0.9203 (mt) REVERT: F 1154 HIS cc_start: 0.8944 (t70) cc_final: 0.8462 (t70) outliers start: 3 outliers final: 0 residues processed: 525 average time/residue: 0.1943 time to fit residues: 159.6230 Evaluate side-chains 426 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.0270 chunk 99 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 327 optimal weight: 0.6980 chunk 163 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 188 optimal weight: 0.2980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 HIS B 306 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 306 HIS ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 730 GLN ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.105051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071541 restraints weight = 163671.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073705 restraints weight = 112479.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.075355 restraints weight = 85182.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.076568 restraints weight = 68655.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.077539 restraints weight = 58176.550| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28404 Z= 0.088 Angle : 0.531 8.311 38466 Z= 0.277 Chirality : 0.041 0.164 4302 Planarity : 0.004 0.077 4950 Dihedral : 4.919 34.678 3762 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 71.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.15), residues: 3438 helix: -0.28 (0.13), residues: 1584 sheet: -1.77 (0.25), residues: 390 loop : -1.75 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 453 TYR 0.024 0.001 TYR E1158 PHE 0.012 0.001 PHE E 595 TRP 0.022 0.001 TRP D 674 HIS 0.016 0.001 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00195 (28404) covalent geometry : angle 0.53105 (38466) hydrogen bonds : bond 0.03132 ( 966) hydrogen bonds : angle 5.55546 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 541 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.8712 (t-90) cc_final: 0.8503 (t70) REVERT: A 370 PHE cc_start: 0.8874 (t80) cc_final: 0.8422 (t80) REVERT: A 521 MET cc_start: 0.9828 (mtm) cc_final: 0.9555 (mtp) REVERT: A 560 LEU cc_start: 0.9598 (pp) cc_final: 0.9167 (pp) REVERT: A 596 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8937 (mm-30) REVERT: A 598 LEU cc_start: 0.9077 (tp) cc_final: 0.8760 (tp) REVERT: A 634 PHE cc_start: 0.8784 (m-10) cc_final: 0.8531 (m-10) REVERT: A 689 MET cc_start: 0.9684 (mmp) cc_final: 0.9457 (mmm) REVERT: A 691 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9101 (mm-30) REVERT: A 692 ARG cc_start: 0.9700 (tpp80) cc_final: 0.9499 (mmm-85) REVERT: A 693 LEU cc_start: 0.9353 (mm) cc_final: 0.9056 (mm) REVERT: A 1156 PHE cc_start: 0.9219 (m-10) cc_final: 0.9006 (m-80) REVERT: A 1184 PHE cc_start: 0.9076 (t80) cc_final: 0.8726 (t80) REVERT: B 283 MET cc_start: 0.9106 (tmm) cc_final: 0.8790 (tmm) REVERT: B 284 LEU cc_start: 0.9784 (mm) cc_final: 0.9401 (mm) REVERT: B 288 TYR cc_start: 0.9463 (m-10) cc_final: 0.9178 (m-10) REVERT: B 334 TYR cc_start: 0.7945 (m-80) cc_final: 0.7524 (m-80) REVERT: B 584 ASN cc_start: 0.9247 (t0) cc_final: 0.8972 (m-40) REVERT: B 667 TYR cc_start: 0.8930 (t80) cc_final: 0.8679 (t80) REVERT: B 691 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9257 (mm-30) REVERT: B 727 TYR cc_start: 0.9386 (t80) cc_final: 0.8852 (t80) REVERT: B 1154 HIS cc_start: 0.9116 (t70) cc_final: 0.8228 (t70) REVERT: B 1158 TYR cc_start: 0.8458 (m-80) cc_final: 0.7898 (m-80) REVERT: C 283 MET cc_start: 0.9571 (tpt) cc_final: 0.9281 (tpp) REVERT: C 334 TYR cc_start: 0.8668 (m-80) cc_final: 0.8446 (m-80) REVERT: C 489 ASN cc_start: 0.9240 (m-40) cc_final: 0.8987 (m-40) REVERT: C 604 ARG cc_start: 0.8583 (ptt-90) cc_final: 0.8317 (ptt-90) REVERT: C 641 GLN cc_start: 0.9417 (tm-30) cc_final: 0.9159 (tm-30) REVERT: C 654 LEU cc_start: 0.9326 (tp) cc_final: 0.9089 (tp) REVERT: C 659 ARG cc_start: 0.8979 (tpp-160) cc_final: 0.8388 (tpp-160) REVERT: C 683 ILE cc_start: 0.9427 (mt) cc_final: 0.9127 (mt) REVERT: C 692 ARG cc_start: 0.9400 (tpp80) cc_final: 0.8787 (ttp80) REVERT: C 715 GLN cc_start: 0.9808 (mp10) cc_final: 0.9576 (mp10) REVERT: C 741 PHE cc_start: 0.9264 (m-80) cc_final: 0.8965 (m-80) REVERT: D 316 MET cc_start: 0.7252 (ptp) cc_final: 0.6915 (ptp) REVERT: D 372 GLU cc_start: 0.9191 (tp30) cc_final: 0.8917 (tp30) REVERT: D 575 GLU cc_start: 0.8809 (tp30) cc_final: 0.8568 (tp30) REVERT: D 658 VAL cc_start: 0.9381 (t) cc_final: 0.9175 (t) REVERT: D 729 LEU cc_start: 0.9427 (tp) cc_final: 0.9121 (tp) REVERT: D 741 PHE cc_start: 0.9312 (m-10) cc_final: 0.8993 (m-10) REVERT: D 1165 LYS cc_start: 0.9348 (ttpt) cc_final: 0.8947 (tptp) REVERT: E 440 ASP cc_start: 0.9670 (p0) cc_final: 0.9469 (p0) REVERT: E 495 TYR cc_start: 0.8781 (m-80) cc_final: 0.8169 (m-80) REVERT: E 564 MET cc_start: 0.9611 (tpp) cc_final: 0.9160 (tmm) REVERT: E 595 PHE cc_start: 0.9433 (m-80) cc_final: 0.9058 (m-80) REVERT: E 641 GLN cc_start: 0.9541 (tm-30) cc_final: 0.9179 (tm-30) REVERT: E 657 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9374 (mm-30) REVERT: E 689 MET cc_start: 0.9682 (mmp) cc_final: 0.9289 (mmm) REVERT: E 691 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9007 (mm-30) REVERT: E 766 LEU cc_start: 0.2582 (tt) cc_final: 0.2134 (tt) REVERT: E 1154 HIS cc_start: 0.9278 (t-90) cc_final: 0.8371 (t-90) REVERT: E 1158 TYR cc_start: 0.9435 (m-10) cc_final: 0.9202 (m-10) REVERT: E 1184 PHE cc_start: 0.9126 (t80) cc_final: 0.8828 (t80) REVERT: F 283 MET cc_start: 0.8963 (tmm) cc_final: 0.8737 (tmm) REVERT: F 466 MET cc_start: 0.8101 (ptt) cc_final: 0.7864 (ppp) REVERT: F 499 TYR cc_start: 0.9270 (p90) cc_final: 0.8690 (p90) REVERT: F 596 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9062 (mm-30) REVERT: F 654 LEU cc_start: 0.9137 (tp) cc_final: 0.8916 (tp) REVERT: F 659 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.8045 (ttp80) REVERT: F 674 TRP cc_start: 0.9353 (t60) cc_final: 0.8726 (t60) REVERT: F 713 HIS cc_start: 0.8438 (m-70) cc_final: 0.7641 (m90) REVERT: F 716 LEU cc_start: 0.9494 (mt) cc_final: 0.9267 (mt) REVERT: F 1154 HIS cc_start: 0.8969 (t70) cc_final: 0.8749 (t-170) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.1962 time to fit residues: 166.7825 Evaluate side-chains 439 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 173 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 295 optimal weight: 9.9990 chunk 307 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.102730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069050 restraints weight = 169169.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071207 restraints weight = 116771.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.072763 restraints weight = 87988.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073922 restraints weight = 71398.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074813 restraints weight = 60778.880| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28404 Z= 0.115 Angle : 0.545 7.023 38466 Z= 0.286 Chirality : 0.040 0.237 4302 Planarity : 0.004 0.067 4950 Dihedral : 4.772 30.371 3762 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 80.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.15), residues: 3438 helix: -0.11 (0.13), residues: 1548 sheet: -1.86 (0.26), residues: 384 loop : -1.62 (0.17), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 591 TYR 0.029 0.001 TYR B 601 PHE 0.015 0.001 PHE D 305 TRP 0.017 0.001 TRP C 674 HIS 0.012 0.001 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00241 (28404) covalent geometry : angle 0.54465 (38466) hydrogen bonds : bond 0.03067 ( 966) hydrogen bonds : angle 5.48142 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 507 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.9118 (mpt180) cc_final: 0.8663 (mmp-170) REVERT: A 370 PHE cc_start: 0.8892 (t80) cc_final: 0.8532 (t80) REVERT: A 373 ILE cc_start: 0.7600 (tt) cc_final: 0.7394 (tt) REVERT: A 399 MET cc_start: 0.5784 (mmt) cc_final: 0.5575 (mmt) REVERT: A 521 MET cc_start: 0.9830 (mtm) cc_final: 0.9593 (mtp) REVERT: A 596 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9020 (mm-30) REVERT: A 598 LEU cc_start: 0.9217 (tp) cc_final: 0.8857 (tp) REVERT: A 689 MET cc_start: 0.9693 (mmp) cc_final: 0.9480 (mmm) REVERT: A 691 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9145 (mm-30) REVERT: A 692 ARG cc_start: 0.9693 (tpp80) cc_final: 0.9475 (mmm-85) REVERT: A 1156 PHE cc_start: 0.9243 (m-10) cc_final: 0.9024 (m-80) REVERT: A 1184 PHE cc_start: 0.9138 (t80) cc_final: 0.8810 (t80) REVERT: B 283 MET cc_start: 0.9139 (tmm) cc_final: 0.8847 (tmm) REVERT: B 284 LEU cc_start: 0.9783 (mm) cc_final: 0.9463 (mm) REVERT: B 288 TYR cc_start: 0.9440 (m-10) cc_final: 0.9161 (m-10) REVERT: B 316 MET cc_start: 0.7896 (mtm) cc_final: 0.7387 (mtm) REVERT: B 334 TYR cc_start: 0.8000 (m-80) cc_final: 0.7587 (m-80) REVERT: B 584 ASN cc_start: 0.9241 (t0) cc_final: 0.8951 (m-40) REVERT: B 667 TYR cc_start: 0.9096 (t80) cc_final: 0.8751 (t80) REVERT: B 691 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9293 (mm-30) REVERT: B 1154 HIS cc_start: 0.9153 (t70) cc_final: 0.8209 (t70) REVERT: B 1158 TYR cc_start: 0.8584 (m-80) cc_final: 0.7882 (m-80) REVERT: C 283 MET cc_start: 0.9577 (tpt) cc_final: 0.9337 (tpp) REVERT: C 334 TYR cc_start: 0.8665 (m-80) cc_final: 0.8365 (m-80) REVERT: C 489 ASN cc_start: 0.9302 (m-40) cc_final: 0.9073 (m-40) REVERT: C 641 GLN cc_start: 0.9367 (tm-30) cc_final: 0.9114 (tm-30) REVERT: C 659 ARG cc_start: 0.9020 (tpp-160) cc_final: 0.8407 (tpp-160) REVERT: C 683 ILE cc_start: 0.9348 (mt) cc_final: 0.9101 (mt) REVERT: C 689 MET cc_start: 0.9664 (mmm) cc_final: 0.9168 (mmm) REVERT: C 692 ARG cc_start: 0.9430 (tpp80) cc_final: 0.8730 (ttp80) REVERT: C 741 PHE cc_start: 0.9256 (m-80) cc_final: 0.8991 (m-80) REVERT: D 316 MET cc_start: 0.8204 (ptp) cc_final: 0.8001 (ptp) REVERT: D 372 GLU cc_start: 0.9185 (tp30) cc_final: 0.8926 (tp30) REVERT: D 623 LEU cc_start: 0.9718 (mp) cc_final: 0.9451 (tt) REVERT: D 729 LEU cc_start: 0.9433 (tp) cc_final: 0.9118 (tp) REVERT: D 741 PHE cc_start: 0.9286 (m-10) cc_final: 0.8957 (m-10) REVERT: D 1165 LYS cc_start: 0.9322 (ttpt) cc_final: 0.8926 (tptp) REVERT: E 495 TYR cc_start: 0.8899 (m-80) cc_final: 0.8281 (m-80) REVERT: E 595 PHE cc_start: 0.9443 (m-80) cc_final: 0.9064 (m-80) REVERT: E 641 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9143 (tm-30) REVERT: E 657 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9236 (mm-30) REVERT: E 689 MET cc_start: 0.9721 (mmp) cc_final: 0.9319 (mmm) REVERT: E 691 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9003 (mm-30) REVERT: E 766 LEU cc_start: 0.2472 (tt) cc_final: 0.2059 (tt) REVERT: E 1137 LEU cc_start: 0.9653 (mm) cc_final: 0.9386 (pp) REVERT: E 1154 HIS cc_start: 0.9228 (t-90) cc_final: 0.8402 (t-90) REVERT: E 1158 TYR cc_start: 0.9439 (m-10) cc_final: 0.9193 (m-10) REVERT: E 1184 PHE cc_start: 0.9175 (t80) cc_final: 0.8885 (t80) REVERT: F 283 MET cc_start: 0.9018 (tmm) cc_final: 0.8776 (tmm) REVERT: F 499 TYR cc_start: 0.9300 (p90) cc_final: 0.8739 (p90) REVERT: F 659 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7957 (ttp80) REVERT: F 674 TRP cc_start: 0.9391 (t60) cc_final: 0.8801 (t60) REVERT: F 689 MET cc_start: 0.9435 (mmm) cc_final: 0.9006 (mmm) REVERT: F 713 HIS cc_start: 0.8487 (m-70) cc_final: 0.7735 (m90) REVERT: F 716 LEU cc_start: 0.9533 (mt) cc_final: 0.9295 (mt) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.1913 time to fit residues: 152.4985 Evaluate side-chains 409 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 86 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 30.0000 chunk 298 optimal weight: 7.9990 chunk 296 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 742 GLN ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS F 328 ASN ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 ASN F 489 ASN ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.097358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.062571 restraints weight = 169989.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064720 restraints weight = 119568.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.066063 restraints weight = 90748.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.067082 restraints weight = 75399.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.067657 restraints weight = 65168.625| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28404 Z= 0.160 Angle : 0.607 7.495 38466 Z= 0.317 Chirality : 0.041 0.201 4302 Planarity : 0.005 0.062 4950 Dihedral : 4.880 30.731 3762 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 91.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3438 helix: -0.49 (0.13), residues: 1554 sheet: -1.94 (0.25), residues: 384 loop : -1.63 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 591 TYR 0.033 0.002 TYR B 601 PHE 0.029 0.002 PHE C1156 TRP 0.026 0.001 TRP B 674 HIS 0.011 0.001 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00321 (28404) covalent geometry : angle 0.60698 (38466) hydrogen bonds : bond 0.03256 ( 966) hydrogen bonds : angle 5.56709 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 482 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.9224 (t70) cc_final: 0.8965 (t-170) REVERT: A 370 PHE cc_start: 0.8919 (t80) cc_final: 0.8528 (t80) REVERT: A 596 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8960 (mm-30) REVERT: A 598 LEU cc_start: 0.9356 (tp) cc_final: 0.9004 (tp) REVERT: A 689 MET cc_start: 0.9697 (mmp) cc_final: 0.9328 (mmm) REVERT: A 691 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9109 (mm-30) REVERT: B 283 MET cc_start: 0.9209 (tmm) cc_final: 0.8892 (tmm) REVERT: B 284 LEU cc_start: 0.9836 (mm) cc_final: 0.9534 (mm) REVERT: B 288 TYR cc_start: 0.9492 (m-10) cc_final: 0.9152 (m-10) REVERT: B 297 MET cc_start: 0.7013 (pmm) cc_final: 0.6770 (pmm) REVERT: B 316 MET cc_start: 0.8225 (mtm) cc_final: 0.7675 (mtm) REVERT: B 334 TYR cc_start: 0.7952 (m-80) cc_final: 0.7592 (m-80) REVERT: B 336 ARG cc_start: 0.7849 (tpt90) cc_final: 0.7610 (tpp-160) REVERT: B 577 MET cc_start: 0.9334 (ttp) cc_final: 0.9047 (ptm) REVERT: B 584 ASN cc_start: 0.9308 (t0) cc_final: 0.9039 (m-40) REVERT: B 667 TYR cc_start: 0.9126 (t80) cc_final: 0.8782 (t80) REVERT: B 691 GLU cc_start: 0.9673 (mm-30) cc_final: 0.9321 (mm-30) REVERT: B 1154 HIS cc_start: 0.9115 (t70) cc_final: 0.8105 (t70) REVERT: B 1158 TYR cc_start: 0.8644 (m-80) cc_final: 0.7791 (m-80) REVERT: C 297 MET cc_start: 0.7966 (ptp) cc_final: 0.7731 (ptp) REVERT: C 334 TYR cc_start: 0.8657 (m-80) cc_final: 0.8380 (m-80) REVERT: C 641 GLN cc_start: 0.9375 (tm-30) cc_final: 0.9145 (tm-30) REVERT: C 683 ILE cc_start: 0.9358 (mt) cc_final: 0.9046 (mt) REVERT: C 692 ARG cc_start: 0.9405 (tpp80) cc_final: 0.9121 (tpt-90) REVERT: C 741 PHE cc_start: 0.9283 (m-80) cc_final: 0.9046 (m-80) REVERT: D 316 MET cc_start: 0.7714 (ptp) cc_final: 0.7089 (ptp) REVERT: D 372 GLU cc_start: 0.9200 (tp30) cc_final: 0.8981 (tp30) REVERT: D 729 LEU cc_start: 0.9442 (tp) cc_final: 0.9076 (tp) REVERT: D 741 PHE cc_start: 0.9164 (m-10) cc_final: 0.8864 (m-10) REVERT: D 1154 HIS cc_start: 0.9326 (t70) cc_final: 0.8799 (t70) REVERT: D 1165 LYS cc_start: 0.9334 (ttpt) cc_final: 0.8881 (tptp) REVERT: E 495 TYR cc_start: 0.9067 (m-80) cc_final: 0.8475 (m-80) REVERT: E 595 PHE cc_start: 0.9466 (m-80) cc_final: 0.9111 (m-80) REVERT: E 641 GLN cc_start: 0.9513 (tm-30) cc_final: 0.9173 (tm-30) REVERT: E 689 MET cc_start: 0.9746 (mmp) cc_final: 0.9452 (mmm) REVERT: E 691 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8982 (mm-30) REVERT: E 766 LEU cc_start: 0.3038 (tt) cc_final: 0.2705 (tt) REVERT: E 1154 HIS cc_start: 0.9238 (t-90) cc_final: 0.8316 (t-90) REVERT: E 1158 TYR cc_start: 0.9456 (m-10) cc_final: 0.9164 (m-10) REVERT: F 283 MET cc_start: 0.9146 (tmm) cc_final: 0.8916 (tmm) REVERT: F 358 GLU cc_start: 0.9474 (mp0) cc_final: 0.9055 (pp20) REVERT: F 466 MET cc_start: 0.8555 (ppp) cc_final: 0.8355 (ppp) REVERT: F 499 TYR cc_start: 0.9270 (p90) cc_final: 0.8751 (p90) REVERT: F 674 TRP cc_start: 0.9407 (t60) cc_final: 0.8837 (t60) REVERT: F 689 MET cc_start: 0.9452 (mmm) cc_final: 0.9093 (mmm) REVERT: F 713 HIS cc_start: 0.8427 (m-70) cc_final: 0.7806 (m-70) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.1899 time to fit residues: 144.3278 Evaluate side-chains 396 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 187 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 134 optimal weight: 0.1980 chunk 88 optimal weight: 0.4980 chunk 22 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 GLN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070338 restraints weight = 166764.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072344 restraints weight = 117658.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073560 restraints weight = 91091.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.074773 restraints weight = 74897.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075666 restraints weight = 64899.057| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28404 Z= 0.102 Angle : 0.537 7.296 38466 Z= 0.282 Chirality : 0.041 0.200 4302 Planarity : 0.004 0.058 4950 Dihedral : 4.706 26.928 3762 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 80.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.15), residues: 3438 helix: -0.14 (0.13), residues: 1518 sheet: -1.94 (0.26), residues: 384 loop : -1.47 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 591 TYR 0.036 0.001 TYR F1158 PHE 0.027 0.001 PHE E1156 TRP 0.047 0.001 TRP D 674 HIS 0.011 0.001 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00221 (28404) covalent geometry : angle 0.53726 (38466) hydrogen bonds : bond 0.03000 ( 966) hydrogen bonds : angle 5.37120 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 492 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.9248 (t70) cc_final: 0.8969 (t70) REVERT: A 318 ARG cc_start: 0.9209 (mmp80) cc_final: 0.8999 (mmm160) REVERT: A 370 PHE cc_start: 0.8925 (t80) cc_final: 0.8557 (t80) REVERT: A 577 MET cc_start: 0.8322 (ppp) cc_final: 0.8013 (ppp) REVERT: A 596 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8875 (mm-30) REVERT: A 689 MET cc_start: 0.9702 (mmp) cc_final: 0.9481 (mmm) REVERT: A 691 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9109 (mm-30) REVERT: A 1184 PHE cc_start: 0.9132 (t80) cc_final: 0.8907 (t80) REVERT: B 283 MET cc_start: 0.9218 (tmm) cc_final: 0.8926 (tmm) REVERT: B 284 LEU cc_start: 0.9822 (mm) cc_final: 0.9542 (mm) REVERT: B 288 TYR cc_start: 0.9542 (m-10) cc_final: 0.9246 (m-10) REVERT: B 297 MET cc_start: 0.7033 (pmm) cc_final: 0.6816 (pmm) REVERT: B 316 MET cc_start: 0.8062 (mtm) cc_final: 0.7434 (mtm) REVERT: B 334 TYR cc_start: 0.7824 (m-80) cc_final: 0.7489 (m-80) REVERT: B 577 MET cc_start: 0.9340 (ttp) cc_final: 0.9090 (ptm) REVERT: B 584 ASN cc_start: 0.9254 (t0) cc_final: 0.8984 (m-40) REVERT: B 667 TYR cc_start: 0.9161 (t80) cc_final: 0.8838 (t80) REVERT: B 691 GLU cc_start: 0.9665 (mm-30) cc_final: 0.9302 (mm-30) REVERT: C 334 TYR cc_start: 0.8596 (m-80) cc_final: 0.8366 (m-80) REVERT: C 489 ASN cc_start: 0.9287 (m110) cc_final: 0.9078 (m-40) REVERT: C 641 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9181 (tm-30) REVERT: C 659 ARG cc_start: 0.9007 (tpp-160) cc_final: 0.8753 (tpp-160) REVERT: C 683 ILE cc_start: 0.9293 (mt) cc_final: 0.9037 (mt) REVERT: C 741 PHE cc_start: 0.9303 (m-80) cc_final: 0.9042 (m-80) REVERT: D 316 MET cc_start: 0.7440 (ptp) cc_final: 0.6939 (ptp) REVERT: D 372 GLU cc_start: 0.9199 (tp30) cc_final: 0.8939 (tp30) REVERT: D 623 LEU cc_start: 0.9730 (mp) cc_final: 0.9425 (tt) REVERT: D 729 LEU cc_start: 0.9446 (tp) cc_final: 0.9139 (tp) REVERT: D 741 PHE cc_start: 0.9163 (m-10) cc_final: 0.8869 (m-10) REVERT: D 1154 HIS cc_start: 0.9419 (t70) cc_final: 0.8617 (t70) REVERT: D 1158 TYR cc_start: 0.9359 (m-80) cc_final: 0.8879 (m-80) REVERT: D 1165 LYS cc_start: 0.9264 (ttpt) cc_final: 0.8869 (tptp) REVERT: E 440 ASP cc_start: 0.9568 (p0) cc_final: 0.9300 (p0) REVERT: E 495 TYR cc_start: 0.9045 (m-80) cc_final: 0.8685 (m-80) REVERT: E 595 PHE cc_start: 0.9465 (m-80) cc_final: 0.9091 (m-80) REVERT: E 641 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9083 (tm-30) REVERT: E 689 MET cc_start: 0.9708 (mmp) cc_final: 0.9315 (mmm) REVERT: E 1137 LEU cc_start: 0.9673 (mm) cc_final: 0.9418 (pp) REVERT: E 1154 HIS cc_start: 0.9224 (t-90) cc_final: 0.8277 (t-90) REVERT: E 1158 TYR cc_start: 0.9479 (m-10) cc_final: 0.9145 (m-10) REVERT: E 1184 PHE cc_start: 0.9146 (t80) cc_final: 0.8917 (t80) REVERT: F 283 MET cc_start: 0.9115 (tmm) cc_final: 0.8872 (tmm) REVERT: F 499 TYR cc_start: 0.9302 (p90) cc_final: 0.8769 (p90) REVERT: F 657 GLU cc_start: 0.9478 (tp30) cc_final: 0.9261 (tp30) REVERT: F 674 TRP cc_start: 0.9400 (t60) cc_final: 0.8839 (t60) REVERT: F 683 ILE cc_start: 0.9375 (mt) cc_final: 0.9157 (mt) REVERT: F 689 MET cc_start: 0.9440 (mmm) cc_final: 0.9006 (mmm) REVERT: F 713 HIS cc_start: 0.8339 (m-70) cc_final: 0.7401 (m90) REVERT: F 716 LEU cc_start: 0.9599 (mt) cc_final: 0.9357 (mt) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.1858 time to fit residues: 145.3074 Evaluate side-chains 406 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 337 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 chunk 335 optimal weight: 0.8980 chunk 106 optimal weight: 0.0070 chunk 129 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 230 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 715 GLN ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.104952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070689 restraints weight = 169212.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072688 restraints weight = 118341.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073970 restraints weight = 90652.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075098 restraints weight = 74716.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.075897 restraints weight = 64619.933| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28404 Z= 0.115 Angle : 0.547 8.591 38466 Z= 0.287 Chirality : 0.041 0.177 4302 Planarity : 0.005 0.121 4950 Dihedral : 4.618 26.565 3762 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 83.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 3438 helix: -0.12 (0.13), residues: 1536 sheet: -1.97 (0.26), residues: 384 loop : -1.42 (0.18), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.000 ARG F 734 TYR 0.033 0.001 TYR C1158 PHE 0.027 0.001 PHE C1156 TRP 0.019 0.001 TRP C 674 HIS 0.011 0.001 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00242 (28404) covalent geometry : angle 0.54697 (38466) hydrogen bonds : bond 0.02977 ( 966) hydrogen bonds : angle 5.34980 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Residue ILE 275 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue ILE 368 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue THR 394 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 410 is missing expected H atoms. Skipping. Residue ILE 411 is missing expected H atoms. Skipping. Residue THR 414 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue ILE 448 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue THR 484 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue ILE 507 is missing expected H atoms. Skipping. Residue THR 511 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue ILE 527 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue ILE 556 is missing expected H atoms. Skipping. Residue THR 559 is missing expected H atoms. Skipping. Residue THR 594 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue ILE 600 is missing expected H atoms. Skipping. Residue ILE 607 is missing expected H atoms. Skipping. Residue THR 616 is missing expected H atoms. Skipping. Residue ILE 622 is missing expected H atoms. Skipping. Residue THR 638 is missing expected H atoms. Skipping. Residue THR 644 is missing expected H atoms. Skipping. Residue ILE 647 is missing expected H atoms. Skipping. Residue THR 649 is missing expected H atoms. Skipping. Residue ILE 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue THR 662 is missing expected H atoms. Skipping. Residue ILE 665 is missing expected H atoms. Skipping. Residue ILE 666 is missing expected H atoms. Skipping. Residue ILE 668 is missing expected H atoms. Skipping. Residue ILE 671 is missing expected H atoms. Skipping. Residue THR 681 is missing expected H atoms. Skipping. Residue ILE 683 is missing expected H atoms. Skipping. Residue THR 684 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue THR 733 is missing expected H atoms. Skipping. Residue ILE 737 is missing expected H atoms. Skipping. Residue ILE 738 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue ILE 748 is missing expected H atoms. Skipping. Residue THR 753 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue THR 1132 is missing expected H atoms. Skipping. Residue ILE 1139 is missing expected H atoms. Skipping. Residue THR 1142 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1146 is missing expected H atoms. Skipping. Residue ILE 1160 is missing expected H atoms. Skipping. Residue ILE 1161 is missing expected H atoms. Skipping. Residue THR 1164 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.9268 (t70) cc_final: 0.8988 (t70) REVERT: A 318 ARG cc_start: 0.9223 (mmp80) cc_final: 0.9007 (mmm160) REVERT: A 370 PHE cc_start: 0.8913 (t80) cc_final: 0.8548 (t80) REVERT: A 399 MET cc_start: 0.6454 (mmt) cc_final: 0.6240 (mmt) REVERT: A 596 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8863 (mm-30) REVERT: A 689 MET cc_start: 0.9715 (mmp) cc_final: 0.9489 (mmm) REVERT: A 691 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9088 (mm-30) REVERT: A 1154 HIS cc_start: 0.9105 (t-90) cc_final: 0.8249 (t-90) REVERT: A 1158 TYR cc_start: 0.8869 (m-80) cc_final: 0.8606 (m-80) REVERT: B 283 MET cc_start: 0.9219 (tmm) cc_final: 0.8920 (tmm) REVERT: B 284 LEU cc_start: 0.9824 (mm) cc_final: 0.9552 (mm) REVERT: B 288 TYR cc_start: 0.9578 (m-10) cc_final: 0.9258 (m-10) REVERT: B 297 MET cc_start: 0.7049 (pmm) cc_final: 0.6821 (pmm) REVERT: B 334 TYR cc_start: 0.7902 (m-80) cc_final: 0.7572 (m-80) REVERT: B 577 MET cc_start: 0.9408 (ttp) cc_final: 0.9170 (ptm) REVERT: B 584 ASN cc_start: 0.9237 (t0) cc_final: 0.8979 (m-40) REVERT: B 667 TYR cc_start: 0.9193 (t80) cc_final: 0.8911 (t80) REVERT: B 691 GLU cc_start: 0.9674 (mm-30) cc_final: 0.9323 (mm-30) REVERT: C 283 MET cc_start: 0.9470 (tpp) cc_final: 0.9260 (tpp) REVERT: C 489 ASN cc_start: 0.9346 (m110) cc_final: 0.9138 (m-40) REVERT: C 641 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9143 (tm-30) REVERT: C 683 ILE cc_start: 0.9393 (mt) cc_final: 0.9069 (mt) REVERT: C 689 MET cc_start: 0.9606 (mmm) cc_final: 0.9316 (mmm) REVERT: C 741 PHE cc_start: 0.9330 (m-80) cc_final: 0.9073 (m-80) REVERT: D 318 ARG cc_start: 0.8860 (mpt180) cc_final: 0.8374 (mmm160) REVERT: D 372 GLU cc_start: 0.9195 (tp30) cc_final: 0.8930 (tp30) REVERT: D 623 LEU cc_start: 0.9707 (mp) cc_final: 0.9412 (tt) REVERT: D 729 LEU cc_start: 0.9433 (tp) cc_final: 0.9126 (tp) REVERT: D 741 PHE cc_start: 0.9186 (m-10) cc_final: 0.8915 (m-10) REVERT: D 1154 HIS cc_start: 0.9372 (t70) cc_final: 0.8604 (t70) REVERT: D 1158 TYR cc_start: 0.9351 (m-80) cc_final: 0.8887 (m-80) REVERT: D 1165 LYS cc_start: 0.9285 (ttpt) cc_final: 0.8884 (tptp) REVERT: E 440 ASP cc_start: 0.9555 (p0) cc_final: 0.9287 (p0) REVERT: E 495 TYR cc_start: 0.9169 (m-80) cc_final: 0.8682 (m-80) REVERT: E 595 PHE cc_start: 0.9463 (m-80) cc_final: 0.9098 (m-80) REVERT: E 641 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9136 (tm-30) REVERT: E 689 MET cc_start: 0.9708 (mmp) cc_final: 0.9293 (mmm) REVERT: E 691 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8960 (mm-30) REVERT: E 1137 LEU cc_start: 0.9670 (mm) cc_final: 0.9407 (pp) REVERT: E 1154 HIS cc_start: 0.9182 (t-90) cc_final: 0.8156 (t-90) REVERT: E 1158 TYR cc_start: 0.9471 (m-10) cc_final: 0.9114 (m-10) REVERT: E 1184 PHE cc_start: 0.9115 (t80) cc_final: 0.8893 (t80) REVERT: F 283 MET cc_start: 0.9045 (tmm) cc_final: 0.8841 (tmm) REVERT: F 466 MET cc_start: 0.8689 (ppp) cc_final: 0.8471 (ppp) REVERT: F 499 TYR cc_start: 0.9260 (p90) cc_final: 0.8744 (p90) REVERT: F 657 GLU cc_start: 0.9511 (tp30) cc_final: 0.9274 (tp30) REVERT: F 674 TRP cc_start: 0.9418 (t60) cc_final: 0.8889 (t60) REVERT: F 683 ILE cc_start: 0.9372 (mt) cc_final: 0.9143 (mt) REVERT: F 689 MET cc_start: 0.9400 (mmm) cc_final: 0.9024 (mmm) REVERT: F 713 HIS cc_start: 0.8467 (m-70) cc_final: 0.7521 (m90) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.1837 time to fit residues: 143.6716 Evaluate side-chains 412 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 9 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 303 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 57 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1136 GLN F 306 HIS ** F 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.101259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.066291 restraints weight = 170176.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068162 restraints weight = 121465.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069299 restraints weight = 94562.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070496 restraints weight = 78620.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071209 restraints weight = 68440.943| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.7016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28404 Z= 0.142 Angle : 0.581 8.741 38466 Z= 0.304 Chirality : 0.041 0.165 4302 Planarity : 0.005 0.088 4950 Dihedral : 4.680 23.251 3762 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 90.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 3438 helix: -0.33 (0.13), residues: 1572 sheet: -2.08 (0.25), residues: 384 loop : -1.47 (0.18), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG F 734 TYR 0.046 0.002 TYR E1158 PHE 0.030 0.002 PHE D 305 TRP 0.029 0.001 TRP E 674 HIS 0.007 0.001 HIS D1154 Details of bonding type rmsd covalent geometry : bond 0.00288 (28404) covalent geometry : angle 0.58094 (38466) hydrogen bonds : bond 0.03118 ( 966) hydrogen bonds : angle 5.46137 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6054.78 seconds wall clock time: 106 minutes 9.75 seconds (6369.75 seconds total)