Starting phenix.real_space_refine on Sat Aug 8 04:48:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2026/8hwa_35051.cif" } resolution = 3.7 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= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 144 5.16 5 C 16283 2.51 5 N 4370 2.21 5 O 4916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "B" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "D" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "E" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "F" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1876 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.98, per 1000 atoms: 0.23 Number of scatterers: 25740 At special positions: 0 Unit cell: (125.925, 128.115, 173.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 23 15.00 Mg 4 11.99 O 4916 8.00 N 4370 7.00 C 16283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS E 385 " distance=2.03 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: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 42 sheets defined 42.3% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.689A pdb=" N ARG A 24 " --> pdb=" O PRO A 20 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 25' Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.533A pdb=" N GLU A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.580A pdb=" N ILE A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.799A pdb=" N ASN A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.714A pdb=" N ARG A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 6.152A pdb=" N ALA A 172 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 174 " --> pdb=" O THR A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.805A pdb=" N ASP A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.716A pdb=" N LEU A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.601A pdb=" N ALA A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.515A pdb=" N SER A 381 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 384 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.184A pdb=" N LYS A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.918A pdb=" N ILE A 531 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.734A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.075A pdb=" N ARG A 619 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.061A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.706A pdb=" N PHE A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.695A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 398 Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.547A pdb=" N ASP B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.560A pdb=" N LYS B 450 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.767A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.601A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.784A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 660 removed outlier: 3.963A pdb=" N GLY B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.507A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 701 removed outlier: 3.868A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.962A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 398 removed outlier: 3.516A pdb=" N ASP C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.539A pdb=" N ASP C 432 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.808A pdb=" N ILE C 531 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.541A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.222A pdb=" N GLY C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 692 removed outlier: 3.779A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 693 through 699 removed outlier: 3.819A pdb=" N TYR C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.675A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.941A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 398 removed outlier: 3.501A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 435 removed outlier: 4.312A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.859A pdb=" N THR D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 529 through 534' Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 576 Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.572A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.059A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 removed outlier: 4.037A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 693 through 699 removed outlier: 3.809A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.618A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 4.285A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 398 removed outlier: 3.558A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 435 removed outlier: 4.075A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.531A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 475 through 488 removed outlier: 3.569A pdb=" N ARG E 479 " --> pdb=" O ASN E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.637A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.621A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 removed outlier: 4.016A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 642 Processing helix chain 'E' and resid 654 through 661 removed outlier: 3.744A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 removed outlier: 3.549A pdb=" N PHE E 668 " --> pdb=" O TYR E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 692 removed outlier: 4.035A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 689 through 692' Processing helix chain 'E' and resid 693 through 698 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.757A pdb=" N GLN F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 78 through 104 removed outlier: 3.977A pdb=" N GLN F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP F 88 " --> pdb=" O THR F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 119 removed outlier: 4.376A pdb=" N ASN F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.503A pdb=" N LYS F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 203 through 207 removed outlier: 3.538A pdb=" N TYR F 207 " --> pdb=" O ILE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 242 through 254 removed outlier: 3.511A pdb=" N ILE F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 264 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.866A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 383 removed outlier: 4.869A pdb=" N SER F 381 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 398 removed outlier: 3.520A pdb=" N ASP F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 435 removed outlier: 4.208A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 475 through 488 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.777A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 3.557A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.725A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.538A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 removed outlier: 3.523A pdb=" N ASN F 641 " --> pdb=" O GLU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 659 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 Processing helix chain 'F' and resid 693 through 699 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 20 through 27 Processing helix chain 'K' and resid 36 through 47 removed outlier: 3.550A pdb=" N GLU K 41 " --> pdb=" O CYS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 104 Processing helix chain 'K' and resid 108 through 119 removed outlier: 3.643A pdb=" N VAL K 112 " --> pdb=" O ILE K 108 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN K 119 " --> pdb=" O SER K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 159 removed outlier: 4.710A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 203 through 207 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.568A pdb=" N GLU A 33 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 13 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 12 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 73 removed outlier: 6.927A pdb=" N THR A 140 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N MET A 69 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N LEU A 138 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N VAL A 71 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ILE A 136 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LEU A 73 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N HIS A 134 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N SER A 132 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 125 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS A 134 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 73 removed outlier: 6.927A pdb=" N THR A 140 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N MET A 69 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N LEU A 138 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N VAL A 71 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ILE A 136 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LEU A 73 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N HIS A 134 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 219 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.567A pdb=" N TYR A 306 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.567A pdb=" N TYR A 306 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.592A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.856A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 553 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 581 through 582 removed outlier: 3.893A pdb=" N ASN A 594 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 630 removed outlier: 6.839A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 339 through 341 removed outlier: 3.577A pdb=" N LEU B 340 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.673A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.910A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 503 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB6, first strand: chain 'B' and resid 629 through 631 Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AB8, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.910A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 419 " --> pdb=" O TYR C 428 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.204A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 631 removed outlier: 6.883A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 340 through 341 removed outlier: 3.518A pdb=" N ILE D 351 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.920A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 419 " --> pdb=" O TYR D 428 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 525 through 526 removed outlier: 6.991A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER D 556 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC7, first strand: chain 'D' and resid 629 through 631 Processing sheet with id=AC8, first strand: chain 'E' and resid 340 through 341 Processing sheet with id=AC9, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.776A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.714A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 502 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 629 through 631 Processing sheet with id=AD3, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AD4, first strand: chain 'F' and resid 32 through 35 removed outlier: 3.625A pdb=" N GLU F 33 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE F 12 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 64 through 73 removed outlier: 11.008A pdb=" N VAL F 65 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ASP F 139 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 67 " --> pdb=" O PHE F 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AD7, first strand: chain 'F' and resid 294 through 299 removed outlier: 3.704A pdb=" N LYS F 317 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 340 through 341 Processing sheet with id=AD9, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.678A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 525 through 527 removed outlier: 6.022A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 628 through 631 removed outlier: 6.396A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 7 through 8 Processing sheet with id=AE4, first strand: chain 'K' and resid 33 through 35 removed outlier: 3.520A pdb=" N GLU K 33 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE K 12 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 64 through 73 removed outlier: 6.911A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 12.129A pdb=" N MET K 69 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N LEU K 138 " --> pdb=" O MET K 69 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N VAL K 71 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N ILE K 136 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 12.810A pdb=" N LEU K 73 " --> pdb=" O HIS K 134 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N HIS K 134 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 124 through 125 840 hydrogen bonds defined for protein. 2358 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: 5.52 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6095 1.33 - 1.45: 5196 1.45 - 1.57: 14744 1.57 - 1.70: 39 1.70 - 1.82: 207 Bond restraints: 26281 Sorted by residual: bond pdb=" C1' DT S 4 " pdb=" N1 DT S 4 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.18e+00 bond pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " ideal model delta sigma weight residual 1.435 1.470 -0.035 1.30e-02 5.92e+03 7.38e+00 bond pdb=" C1' DT S 3 " pdb=" N1 DT S 3 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.09e+00 bond pdb=" N ASP F 431 " pdb=" CA ASP F 431 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.88e+00 bond pdb=" C3' DT S 2 " pdb=" C2' DT S 2 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.57e+00 ... (remaining 26276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 35269 2.51 - 5.03: 287 5.03 - 7.54: 32 7.54 - 10.06: 3 10.06 - 12.57: 2 Bond angle restraints: 35593 Sorted by residual: angle pdb=" N LEU B 700 " pdb=" CA LEU B 700 " pdb=" C LEU B 700 " ideal model delta sigma weight residual 113.50 107.98 5.52 1.23e+00 6.61e-01 2.01e+01 angle pdb=" N LEU C 700 " pdb=" CA LEU C 700 " pdb=" C LEU C 700 " ideal model delta sigma weight residual 114.39 108.05 6.34 1.45e+00 4.76e-01 1.91e+01 angle pdb=" CB MET F 116 " pdb=" CG MET F 116 " pdb=" SD MET F 116 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N3 DT S 2 " pdb=" C4 DT S 2 " pdb=" O4 DT S 2 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT S 5 " pdb=" C4 DT S 5 " pdb=" O4 DT S 5 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 35588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 15428 31.32 - 62.64: 656 62.64 - 93.95: 46 93.95 - 125.27: 0 125.27 - 156.59: 2 Dihedral angle restraints: 16132 sinusoidal: 6841 harmonic: 9291 Sorted by residual: dihedral pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " pdb=" SG CYS E 385 " pdb=" CB CYS E 385 " ideal model delta sinusoidal sigma weight residual -86.00 -23.24 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 63.41 156.59 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 67.24 152.76 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 16129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2713 0.036 - 0.073: 907 0.073 - 0.109: 307 0.109 - 0.145: 53 0.145 - 0.182: 4 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA LEU B 700 " pdb=" N LEU B 700 " pdb=" C LEU B 700 " pdb=" CB LEU B 700 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB ILE F 681 " pdb=" CA ILE F 681 " pdb=" CG1 ILE F 681 " pdb=" CG2 ILE F 681 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA LEU E 700 " pdb=" N LEU E 700 " pdb=" C LEU E 700 " pdb=" CB LEU E 700 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 3981 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 236 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.46e+01 pdb=" C TRP A 236 " -0.066 2.00e-02 2.50e+03 pdb=" O TRP A 236 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 237 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 361 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 362 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 375 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO F 376 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 376 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 376 " 0.030 5.00e-02 4.00e+02 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 180 2.55 - 3.13: 19464 3.13 - 3.72: 38400 3.72 - 4.31: 51885 4.31 - 4.90: 87277 Nonbonded interactions: 197206 Sorted by model distance: nonbonded pdb=" O3A ATP D1001 " pdb="MG MG D1002 " model vdw 1.956 2.170 nonbonded pdb=" O2B ATP C1001 " pdb="MG MG C1002 " model vdw 2.005 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.023 2.170 nonbonded pdb=" O1A ATP D1001 " pdb="MG MG D1002 " model vdw 2.031 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A1002 " model vdw 2.044 2.170 ... (remaining 197201 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 700) selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 323 through 701) selection = (chain 'C' and resid 323 through 701) selection = (chain 'D' and resid 323 through 701) selection = (chain 'E' and resid 323 through 701) } 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: 3.040 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.310 Find NCS groups from input model: 0.590 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 : 0.003 0.051 26282 Z= 0.141 Angle : 0.588 12.570 35595 Z= 0.339 Chirality : 0.041 0.182 3984 Planarity : 0.004 0.058 4537 Dihedral : 16.332 156.590 10087 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 0.35 % Allowed : 15.50 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -1.15 (0.15), residues: 3133 helix: 0.54 (0.16), residues: 1073 sheet: -1.39 (0.25), residues: 454 loop : -1.48 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.020 0.001 TYR D 664 PHE 0.018 0.001 PHE D 698 TRP 0.008 0.001 TRP A 350 HIS 0.003 0.000 HIS B 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (26281) covalent geometry : angle 0.58650 / 0.34 (35593) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 4.99716 / 2.76 ( 2) hydrogen bonds : bond 0.21464 / 14.27 ( 836) hydrogen bonds : angle 6.86020 / 4.74 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 684 MET cc_start: 0.8370 (tmm) cc_final: 0.7876 (tmm) REVERT: F 138 LEU cc_start: 0.7020 (mp) cc_final: 0.6584 (pt) REVERT: F 322 ASP cc_start: 0.7504 (t70) cc_final: 0.7051 (t70) REVERT: F 684 MET cc_start: 0.7655 (tpp) cc_final: 0.6494 (tpp) outliers start: 10 outliers final: 1 residues processed: 231 average time/residue: 0.1694 time to fit residues: 61.7370 Evaluate side-chains 203 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.0050 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN E 529 GLN F 294 HIS F 352 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 548 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** 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 = 0.3548 r_free = 0.3548 target = 0.109854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.082115 restraints weight = 57170.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085228 restraints weight = 31404.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.086259 restraints weight = 19079.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086585 restraints weight = 16427.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086716 restraints weight = 14943.052| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26282 Z= 0.157 Angle : 0.552 8.548 35595 Z= 0.288 Chirality : 0.043 0.309 3984 Planarity : 0.004 0.062 4537 Dihedral : 9.964 155.483 3668 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 2.36 % Allowed : 14.22 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -1.15 (0.15), residues: 3133 helix: 0.46 (0.16), residues: 1119 sheet: -1.33 (0.24), residues: 477 loop : -1.49 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 612 TYR 0.019 0.001 TYR C 482 PHE 0.017 0.001 PHE A 243 TRP 0.012 0.001 TRP A 350 HIS 0.004 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (26281) covalent geometry : angle 0.55187 / 0.29 (35593) SS BOND : bond 0.00205 / 0.11 ( 1) SS BOND : angle 2.46539 / 1.35 ( 2) hydrogen bonds : bond 0.04192 / 2.85 ( 836) hydrogen bonds : angle 5.01618 / 3.48 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 225 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7271 (ttp80) REVERT: A 534 ASP cc_start: 0.8156 (t0) cc_final: 0.7834 (t70) REVERT: B 534 ASP cc_start: 0.8505 (t0) cc_final: 0.8294 (t0) REVERT: C 471 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9272 (pp) REVERT: D 522 ASP cc_start: 0.8575 (t70) cc_final: 0.8314 (t0) REVERT: E 382 GLU cc_start: 0.7561 (mp0) cc_final: 0.7221 (mp0) REVERT: E 529 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (pp30) REVERT: E 660 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8356 (mp10) REVERT: F 194 ILE cc_start: 0.8909 (pt) cc_final: 0.8513 (mm) REVERT: F 322 ASP cc_start: 0.7591 (t70) cc_final: 0.7179 (t70) REVERT: F 547 MET cc_start: 0.8577 (ttm) cc_final: 0.8295 (ttm) REVERT: F 684 MET cc_start: 0.8330 (tpp) cc_final: 0.7724 (tpp) REVERT: K 40 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8385 (tt) outliers start: 68 outliers final: 43 residues processed: 276 average time/residue: 0.1472 time to fit residues: 65.3855 Evaluate side-chains 247 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 256 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN D 529 GLN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN F 198 GLN F 548 HIS F 661 ASN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083792 restraints weight = 56890.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087008 restraints weight = 30448.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088104 restraints weight = 18378.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088384 restraints weight = 15535.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088482 restraints weight = 14570.726| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26282 Z= 0.099 Angle : 0.501 10.228 35595 Z= 0.259 Chirality : 0.042 0.311 3984 Planarity : 0.004 0.058 4537 Dihedral : 9.702 155.069 3667 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 2.15 % Allowed : 14.64 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -0.98 (0.15), residues: 3133 helix: 0.56 (0.16), residues: 1136 sheet: -1.18 (0.24), residues: 476 loop : -1.39 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 612 TYR 0.014 0.001 TYR A 482 PHE 0.013 0.001 PHE D 698 TRP 0.009 0.001 TRP A 350 HIS 0.014 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (26281) covalent geometry : angle 0.50067 / 0.26 (35593) SS BOND : bond 0.00310 / 0.16 ( 1) SS BOND : angle 1.81663 / 0.99 ( 2) hydrogen bonds : bond 0.03439 / 2.34 ( 836) hydrogen bonds : angle 4.61220 / 3.20 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3242 (ttt) cc_final: 0.3011 (ttm) REVERT: A 99 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7177 (ttp80) REVERT: A 534 ASP cc_start: 0.8183 (t0) cc_final: 0.7818 (t70) REVERT: B 534 ASP cc_start: 0.8472 (t0) cc_final: 0.8245 (t0) REVERT: C 471 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9243 (pp) REVERT: C 579 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7516 (mt-10) REVERT: D 522 ASP cc_start: 0.8566 (t70) cc_final: 0.8304 (t0) REVERT: E 382 GLU cc_start: 0.7554 (mp0) cc_final: 0.7143 (mp0) REVERT: E 426 MET cc_start: 0.7139 (mmm) cc_final: 0.6925 (mmm) REVERT: E 660 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: F 180 LEU cc_start: 0.8098 (tt) cc_final: 0.7700 (mt) REVERT: F 194 ILE cc_start: 0.8922 (pt) cc_final: 0.8566 (mm) REVERT: F 322 ASP cc_start: 0.7521 (t70) cc_final: 0.7122 (t70) REVERT: F 332 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8247 (ttm-80) REVERT: F 547 MET cc_start: 0.8583 (ttm) cc_final: 0.8270 (ttm) outliers start: 62 outliers final: 35 residues processed: 275 average time/residue: 0.1480 time to fit residues: 65.3393 Evaluate side-chains 237 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 279 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 ASN F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.080784 restraints weight = 56682.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083702 restraints weight = 31242.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.084937 restraints weight = 19480.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085112 restraints weight = 16765.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085279 restraints weight = 15218.446| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26282 Z= 0.182 Angle : 0.559 10.338 35595 Z= 0.288 Chirality : 0.043 0.313 3984 Planarity : 0.004 0.059 4537 Dihedral : 9.639 156.307 3667 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 3.30 % Allowed : 14.50 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -1.03 (0.15), residues: 3133 helix: 0.58 (0.16), residues: 1126 sheet: -1.26 (0.24), residues: 477 loop : -1.43 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 612 TYR 0.023 0.001 TYR C 482 PHE 0.015 0.001 PHE A 554 TRP 0.011 0.001 TRP A 350 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (26281) covalent geometry : angle 0.55862 / 0.29 (35593) SS BOND : bond 0.00847 / 0.45 ( 1) SS BOND : angle 1.93238 / 1.11 ( 2) hydrogen bonds : bond 0.03856 / 2.63 ( 836) hydrogen bonds : angle 4.61609 / 3.20 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 210 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7257 (ttp80) REVERT: A 534 ASP cc_start: 0.8207 (t70) cc_final: 0.7837 (t70) REVERT: B 534 ASP cc_start: 0.8496 (t0) cc_final: 0.8273 (t0) REVERT: C 471 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9279 (pp) REVERT: D 522 ASP cc_start: 0.8568 (t70) cc_final: 0.8244 (t0) REVERT: D 660 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: E 382 GLU cc_start: 0.7535 (mp0) cc_final: 0.7060 (mp0) REVERT: E 426 MET cc_start: 0.7208 (mmm) cc_final: 0.6982 (mmm) REVERT: E 660 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: F 194 ILE cc_start: 0.8965 (pt) cc_final: 0.8707 (mt) REVERT: F 322 ASP cc_start: 0.7667 (t70) cc_final: 0.7258 (t70) REVERT: F 684 MET cc_start: 0.7993 (tpp) cc_final: 0.7261 (tpp) REVERT: K 40 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8391 (tt) outliers start: 95 outliers final: 59 residues processed: 287 average time/residue: 0.1500 time to fit residues: 69.4977 Evaluate side-chains 253 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 36 optimal weight: 0.0470 chunk 45 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 147 optimal weight: 0.0070 chunk 175 optimal weight: 8.9990 chunk 228 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 ASN F 109 HIS F 548 HIS F 629 HIS K 25 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083883 restraints weight = 56222.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086965 restraints weight = 30766.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088011 restraints weight = 18803.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088316 restraints weight = 16128.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088523 restraints weight = 14619.934| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26282 Z= 0.090 Angle : 0.502 11.209 35595 Z= 0.257 Chirality : 0.041 0.319 3984 Planarity : 0.003 0.056 4537 Dihedral : 9.222 155.047 3667 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 2.15 % Allowed : 15.85 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -0.83 (0.15), residues: 3133 helix: 0.65 (0.16), residues: 1144 sheet: -1.09 (0.25), residues: 475 loop : -1.29 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 612 TYR 0.014 0.001 TYR B 482 PHE 0.009 0.001 PHE A 89 TRP 0.009 0.001 TRP A 350 HIS 0.016 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (26281) covalent geometry : angle 0.50218 / 0.26 (35593) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.83223 / 0.45 ( 2) hydrogen bonds : bond 0.02935 / 2.01 ( 836) hydrogen bonds : angle 4.29300 / 2.97 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.8003 (t70) cc_final: 0.7633 (t70) REVERT: C 471 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9254 (pp) REVERT: D 522 ASP cc_start: 0.8478 (t70) cc_final: 0.8133 (t0) REVERT: D 660 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: E 382 GLU cc_start: 0.7560 (mp0) cc_final: 0.7087 (mp0) REVERT: E 426 MET cc_start: 0.7173 (mmm) cc_final: 0.6946 (mmm) REVERT: E 660 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: F 1 MET cc_start: 0.2479 (ttt) cc_final: 0.2210 (ttt) REVERT: F 180 LEU cc_start: 0.8053 (tt) cc_final: 0.7628 (mt) REVERT: F 194 ILE cc_start: 0.8897 (pt) cc_final: 0.8507 (mm) REVERT: F 332 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8150 (ttm-80) REVERT: F 547 MET cc_start: 0.8471 (ttm) cc_final: 0.8220 (ttm) REVERT: F 684 MET cc_start: 0.8098 (tpp) cc_final: 0.7679 (tpp) REVERT: K 40 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8364 (tt) outliers start: 62 outliers final: 40 residues processed: 268 average time/residue: 0.1533 time to fit residues: 66.0077 Evaluate side-chains 244 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 229 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 312 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 ASN E 328 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** K 109 HIS ** 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 = 0.3501 r_free = 0.3501 target = 0.106841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079271 restraints weight = 57383.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.082270 restraints weight = 31426.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083237 restraints weight = 19386.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083555 restraints weight = 16742.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083713 restraints weight = 15356.125| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26282 Z= 0.247 Angle : 0.613 10.606 35595 Z= 0.316 Chirality : 0.045 0.316 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.464 157.503 3667 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 3.16 % Allowed : 16.16 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -1.05 (0.15), residues: 3133 helix: 0.50 (0.16), residues: 1134 sheet: -1.27 (0.24), residues: 491 loop : -1.41 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 99 TYR 0.028 0.002 TYR C 482 PHE 0.017 0.002 PHE D 626 TRP 0.013 0.001 TRP A 350 HIS 0.010 0.001 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (26281) covalent geometry : angle 0.61323 / 0.32 (35593) SS BOND : bond 0.00510 / 0.27 ( 1) SS BOND : angle 0.85828 / 0.50 ( 2) hydrogen bonds : bond 0.04310 / 2.94 ( 836) hydrogen bonds : angle 4.67447 / 3.25 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 197 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5348 (OUTLIER) cc_final: 0.4925 (p0) REVERT: A 99 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7175 (ttp80) REVERT: A 150 MET cc_start: 0.9150 (ttm) cc_final: 0.8911 (ttt) REVERT: A 447 ASP cc_start: 0.7909 (t0) cc_final: 0.7695 (t0) REVERT: A 534 ASP cc_start: 0.8093 (t70) cc_final: 0.7720 (t70) REVERT: B 572 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: C 471 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9303 (pp) REVERT: D 522 ASP cc_start: 0.8515 (t70) cc_final: 0.8172 (t0) REVERT: D 660 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: E 382 GLU cc_start: 0.7481 (mp0) cc_final: 0.7010 (mp0) REVERT: E 426 MET cc_start: 0.7299 (mmm) cc_final: 0.7054 (mmm) REVERT: E 660 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: F 180 LEU cc_start: 0.8024 (tt) cc_final: 0.7508 (mt) REVERT: F 322 ASP cc_start: 0.7793 (t70) cc_final: 0.7424 (t70) REVERT: F 383 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9290 (mp) REVERT: K 40 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8438 (tt) outliers start: 91 outliers final: 62 residues processed: 275 average time/residue: 0.1452 time to fit residues: 65.4041 Evaluate side-chains 251 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 193 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 281 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.082487 restraints weight = 56444.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.085520 restraints weight = 30497.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086532 restraints weight = 18772.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.086863 restraints weight = 16196.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.087080 restraints weight = 14920.367| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26282 Z= 0.103 Angle : 0.519 12.135 35595 Z= 0.265 Chirality : 0.042 0.329 3984 Planarity : 0.003 0.056 4537 Dihedral : 9.120 155.580 3667 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 2.25 % Allowed : 17.10 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -0.77 (0.15), residues: 3133 helix: 0.74 (0.16), residues: 1135 sheet: -1.09 (0.24), residues: 481 loop : -1.26 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.015 0.001 TYR B 482 PHE 0.009 0.001 PHE A 243 TRP 0.010 0.001 TRP A 350 HIS 0.004 0.001 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (26281) covalent geometry : angle 0.51890 / 0.27 (35593) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 0.59482 / 0.33 ( 2) hydrogen bonds : bond 0.03017 / 2.06 ( 836) hydrogen bonds : angle 4.24292 / 2.94 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7200 (ttp80) REVERT: A 534 ASP cc_start: 0.8020 (t70) cc_final: 0.7634 (t70) REVERT: B 572 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: C 471 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9280 (pp) REVERT: D 522 ASP cc_start: 0.8460 (t70) cc_final: 0.8095 (t0) REVERT: D 575 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8486 (mtpp) REVERT: D 660 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: E 382 GLU cc_start: 0.7536 (mp0) cc_final: 0.7047 (mp0) REVERT: E 426 MET cc_start: 0.7254 (mmm) cc_final: 0.7015 (mmm) REVERT: E 660 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8395 (mp10) REVERT: F 288 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8567 (mmm160) REVERT: F 332 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8080 (ttm-80) outliers start: 65 outliers final: 46 residues processed: 258 average time/residue: 0.1551 time to fit residues: 63.9984 Evaluate side-chains 241 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 257 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 284 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080170 restraints weight = 56904.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083439 restraints weight = 30807.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084358 restraints weight = 18763.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.084529 restraints weight = 15880.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.084681 restraints weight = 15551.556| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26282 Z= 0.203 Angle : 0.591 12.543 35595 Z= 0.300 Chirality : 0.044 0.325 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.250 157.348 3667 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 2.84 % Allowed : 17.17 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -0.88 (0.15), residues: 3133 helix: 0.66 (0.16), residues: 1135 sheet: -1.26 (0.24), residues: 495 loop : -1.29 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.024 0.001 TYR C 482 PHE 0.015 0.001 PHE D 626 TRP 0.011 0.001 TRP A 350 HIS 0.007 0.001 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (26281) covalent geometry : angle 0.59129 / 0.30 (35593) SS BOND : bond 0.00396 / 0.21 ( 1) SS BOND : angle 0.76983 / 0.45 ( 2) hydrogen bonds : bond 0.03787 / 2.58 ( 836) hydrogen bonds : angle 4.43537 / 3.09 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 188 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7221 (ttp80) REVERT: A 534 ASP cc_start: 0.8056 (t70) cc_final: 0.7688 (t70) REVERT: B 572 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: C 471 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9286 (pp) REVERT: D 522 ASP cc_start: 0.8495 (t70) cc_final: 0.8153 (t0) REVERT: D 660 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: E 382 GLU cc_start: 0.7475 (mp0) cc_final: 0.6986 (mp0) REVERT: E 426 MET cc_start: 0.7324 (mmm) cc_final: 0.7063 (mmm) REVERT: E 560 ASP cc_start: 0.7243 (t70) cc_final: 0.6857 (m-30) REVERT: E 660 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: F 288 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8567 (tpt90) outliers start: 82 outliers final: 64 residues processed: 253 average time/residue: 0.1621 time to fit residues: 65.6792 Evaluate side-chains 251 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 259 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 200 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 291 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 ASN F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083054 restraints weight = 56875.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086204 restraints weight = 30663.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087139 restraints weight = 18831.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.087528 restraints weight = 16477.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087723 restraints weight = 14976.389| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26282 Z= 0.098 Angle : 0.531 13.183 35595 Z= 0.268 Chirality : 0.042 0.332 3984 Planarity : 0.004 0.057 4537 Dihedral : 8.953 155.795 3667 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 2.19 % Allowed : 17.66 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -0.68 (0.15), residues: 3133 helix: 0.74 (0.16), residues: 1152 sheet: -1.06 (0.24), residues: 481 loop : -1.14 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 152 TYR 0.015 0.001 TYR B 482 PHE 0.009 0.001 PHE A 243 TRP 0.009 0.001 TRP A 350 HIS 0.004 0.000 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (26281) covalent geometry : angle 0.53051 / 0.27 (35593) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 0.63984 / 0.35 ( 2) hydrogen bonds : bond 0.02830 / 1.92 ( 836) hydrogen bonds : angle 4.13005 / 2.87 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7927 (mp0) cc_final: 0.7687 (mp0) REVERT: A 99 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7635 (ttp80) REVERT: A 534 ASP cc_start: 0.8021 (t70) cc_final: 0.7636 (t70) REVERT: B 612 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6927 (mtt180) REVERT: C 382 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7751 (mm-30) REVERT: C 471 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9281 (pp) REVERT: D 522 ASP cc_start: 0.8436 (t70) cc_final: 0.8050 (t0) REVERT: D 660 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: E 382 GLU cc_start: 0.7534 (mp0) cc_final: 0.7032 (mp0) REVERT: E 426 MET cc_start: 0.7244 (mmm) cc_final: 0.7002 (mmm) REVERT: E 660 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: E 684 MET cc_start: 0.8441 (tmm) cc_final: 0.7989 (tmm) REVERT: F 180 LEU cc_start: 0.7937 (tt) cc_final: 0.7373 (mt) REVERT: F 288 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8584 (mmm160) REVERT: F 332 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8181 (ttm-80) REVERT: K 40 LEU cc_start: 0.8690 (mt) cc_final: 0.8432 (mt) outliers start: 63 outliers final: 53 residues processed: 263 average time/residue: 0.1514 time to fit residues: 63.5822 Evaluate side-chains 260 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 128 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 274 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082156 restraints weight = 56521.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084767 restraints weight = 30638.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.086472 restraints weight = 20872.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087571 restraints weight = 16372.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.088241 restraints weight = 14023.322| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26282 Z= 0.109 Angle : 0.551 13.283 35595 Z= 0.276 Chirality : 0.042 0.328 3984 Planarity : 0.004 0.056 4537 Dihedral : 8.839 156.609 3667 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.12 % Allowed : 18.07 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -0.57 (0.15), residues: 3133 helix: 0.85 (0.16), residues: 1136 sheet: -1.04 (0.24), residues: 483 loop : -1.06 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 152 TYR 0.015 0.001 TYR B 482 PHE 0.011 0.001 PHE A 243 TRP 0.010 0.001 TRP A 350 HIS 0.004 0.001 HIS F 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (26281) covalent geometry : angle 0.55142 / 0.28 (35593) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.47920 / 0.27 ( 2) hydrogen bonds : bond 0.02960 / 2.02 ( 836) hydrogen bonds : angle 4.11434 / 2.87 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7204 (ttp80) REVERT: A 534 ASP cc_start: 0.7991 (t70) cc_final: 0.7661 (t70) REVERT: B 572 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8250 (m-30) REVERT: B 684 MET cc_start: 0.7851 (tmm) cc_final: 0.7610 (ttp) REVERT: C 382 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7755 (mm-30) REVERT: C 471 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9284 (pp) REVERT: D 522 ASP cc_start: 0.8423 (t70) cc_final: 0.8062 (t0) REVERT: D 660 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: E 382 GLU cc_start: 0.7544 (mp0) cc_final: 0.7009 (mp0) REVERT: E 426 MET cc_start: 0.7256 (mmm) cc_final: 0.7012 (mmm) REVERT: E 660 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8360 (mp10) REVERT: F 180 LEU cc_start: 0.7943 (tt) cc_final: 0.7361 (mt) REVERT: F 288 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8567 (mmm160) REVERT: F 332 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8161 (ttm-80) outliers start: 61 outliers final: 53 residues processed: 259 average time/residue: 0.1542 time to fit residues: 63.9122 Evaluate side-chains 259 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 160 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 chunk 170 optimal weight: 0.0370 chunk 55 optimal weight: 0.6980 chunk 278 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083716 restraints weight = 56106.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.086817 restraints weight = 29636.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087752 restraints weight = 18439.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088090 restraints weight = 15862.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088321 restraints weight = 14563.046| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26282 Z= 0.097 Angle : 0.542 13.032 35595 Z= 0.271 Chirality : 0.042 0.329 3984 Planarity : 0.003 0.056 4537 Dihedral : 8.658 156.400 3667 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.01 % Allowed : 18.31 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % 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: -0.54 (0.15), residues: 3133 helix: 0.82 (0.16), residues: 1155 sheet: -1.02 (0.24), residues: 485 loop : -1.02 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 152 TYR 0.014 0.001 TYR B 482 PHE 0.025 0.001 PHE A 120 TRP 0.009 0.001 TRP A 350 HIS 0.003 0.000 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (26281) covalent geometry : angle 0.54194 / 0.27 (35593) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.51662 / 0.29 ( 2) hydrogen bonds : bond 0.02818 / 1.93 ( 836) hydrogen bonds : angle 4.04685 / 2.82 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3312.39 seconds wall clock time: 58 minutes 37.80 seconds (3517.80 seconds total)