Starting phenix.real_space_refine on Sat Mar 7 05:10:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p60_13213/03_2026/7p60_13213.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p60_13213/03_2026/7p60_13213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p60_13213/03_2026/7p60_13213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p60_13213/03_2026/7p60_13213.map" model { file = "/net/cci-nas-00/data/ceres_data/7p60_13213/03_2026/7p60_13213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p60_13213/03_2026/7p60_13213.cif" } resolution = 3.8 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: 4 Type Number sf(0) Gaussians S 159 5.16 5 C 24939 2.51 5 N 6450 2.21 5 O 6858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38406 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "E" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "F" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "G" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 8.38, per 1000 atoms: 0.22 Number of scatterers: 38406 At special positions: 0 Unit cell: (156.24, 153.636, 192.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 159 16.00 O 6858 8.00 N 6450 7.00 C 24939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9006 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 29 sheets defined 49.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.679A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 4.925A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.652A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.665A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.526A pdb=" N GLY A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.815A pdb=" N THR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.395A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.786A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.753A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 removed outlier: 4.098A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.561A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.695A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.676A pdb=" N GLU A 808 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.041A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.940A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.020A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.068A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 removed outlier: 4.144A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 287 removed outlier: 4.624A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 344 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.120A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.615A pdb=" N PHE B 443 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 444 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.818A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.613A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.528A pdb=" N ILE B 610 " --> pdb=" O PRO B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.729A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 removed outlier: 3.640A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.700A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.750A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.655A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.686A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.613A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.583A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.829A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.882A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.661A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.824A pdb=" N THR C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 344 Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.332A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.568A pdb=" N VAL C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.816A pdb=" N ILE C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 4.128A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.981A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.501A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 removed outlier: 3.777A pdb=" N ILE C 658 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.598A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.564A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.592A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 removed outlier: 3.679A pdb=" N GLU C 808 " --> pdb=" O ARG C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.704A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 4.957A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.154A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.099A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.124A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 287 removed outlier: 4.440A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 344 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.066A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 411 Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.721A pdb=" N LEU D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 495 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.940A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 543 removed outlier: 3.500A pdb=" N ASP D 538 " --> pdb=" O ILE D 535 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 608 through 613 removed outlier: 3.652A pdb=" N SER D 612 " --> pdb=" O HIS D 608 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 613 " --> pdb=" O SER D 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 608 through 613' Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.829A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 660 removed outlier: 3.522A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.770A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.757A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 776 removed outlier: 3.618A pdb=" N CYS D 776 " --> pdb=" O LEU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.572A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.511A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.820A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.840A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.678A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.525A pdb=" N GLY E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.787A pdb=" N THR E 303 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 344 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.622A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.439A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 419 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.562A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.563A pdb=" N GLU E 493 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 515 removed outlier: 3.942A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.024A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 607 through 613 removed outlier: 3.853A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 637 Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.802A pdb=" N ILE E 658 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 701 through 707 Processing helix chain 'E' and resid 724 through 730 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.702A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.800A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 792 Processing helix chain 'E' and resid 795 through 808 removed outlier: 3.663A pdb=" N GLU E 808 " --> pdb=" O ARG E 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.855A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 4.955A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.348A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 removed outlier: 4.119A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 256 removed outlier: 4.195A pdb=" N GLU F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 287 removed outlier: 4.584A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 343 Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.191A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 411 Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.799A pdb=" N LEU F 445 " --> pdb=" O VAL F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 495 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.775A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 543 removed outlier: 3.874A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'F' and resid 631 through 636 removed outlier: 3.719A pdb=" N GLN F 636 " --> pdb=" O ILE F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 660 removed outlier: 3.501A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.590A pdb=" N LEU F 681 " --> pdb=" O PRO F 678 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 removed outlier: 3.621A pdb=" N LEU F 707 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 Processing helix chain 'F' and resid 747 through 753 removed outlier: 3.803A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 776 removed outlier: 3.579A pdb=" N CYS F 776 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 808 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.613A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.827A pdb=" N GLU H 111 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR H 112 " --> pdb=" O TYR H 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 108 through 112' Processing sheet with id=AA1, first strand: chain 'A' and resid 292 through 296 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.411A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 474 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LYS A 501 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 498 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR A 524 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 500 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN A 575 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 551 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.389A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.824A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 645 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 668 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.139A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN C 575 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU C 551 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 668 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 691 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 760 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.325A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AB3, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.467A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 551 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 691 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 460 through 461 Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.542A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN E 575 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU E 551 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 668 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 760 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 459 through 461 removed outlier: 6.278A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.283A pdb=" N LEU F 428 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU F 430 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU F 454 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 432 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU F 474 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS F 501 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 476 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 691 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 460 through 461 Processing sheet with id=AC2, first strand: chain 'F' and resid 759 through 760 removed outlier: 6.278A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.884A pdb=" N GLY G 10 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER G 124 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL G 12 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP G 36 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.653A pdb=" N TYR G 114 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.981A pdb=" N GLY I 10 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER I 124 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL I 12 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.652A pdb=" N TYR I 114 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 13 removed outlier: 8.278A pdb=" N GLU H 32 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA H 52 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.707A pdb=" N TYR H 114 " --> pdb=" O ALA H 98 " (cutoff:3.500A) 1756 hydrogen bonds defined for protein. 4434 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: 7.54 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12145 1.34 - 1.46: 8946 1.46 - 1.58: 17966 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 39273 Sorted by residual: bond pdb=" CA TYR I 109 " pdb=" C TYR I 109 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.80e-02 3.09e+03 1.62e+00 bond pdb=" CA TYR G 109 " pdb=" C TYR G 109 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.80e-02 3.09e+03 1.55e+00 bond pdb=" N LEU F 700 " pdb=" CA LEU F 700 " ideal model delta sigma weight residual 1.463 1.448 0.015 1.22e-02 6.72e+03 1.44e+00 bond pdb=" CA ILE E 438 " pdb=" CB ILE E 438 " ideal model delta sigma weight residual 1.537 1.524 0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CA ILE A 438 " pdb=" CB ILE A 438 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.04e+00 ... (remaining 39268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 52813 2.27 - 4.54: 398 4.54 - 6.81: 30 6.81 - 9.08: 2 9.08 - 11.35: 1 Bond angle restraints: 53244 Sorted by residual: angle pdb=" N PHE E 372 " pdb=" CA PHE E 372 " pdb=" C PHE E 372 " ideal model delta sigma weight residual 114.04 107.81 6.23 1.24e+00 6.50e-01 2.52e+01 angle pdb=" N VAL D 397 " pdb=" CA VAL D 397 " pdb=" C VAL D 397 " ideal model delta sigma weight residual 111.90 107.91 3.99 8.10e-01 1.52e+00 2.43e+01 angle pdb=" N ILE E 535 " pdb=" CA ILE E 535 " pdb=" C ILE E 535 " ideal model delta sigma weight residual 112.96 108.71 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" N ILE C 535 " pdb=" CA ILE C 535 " pdb=" C ILE C 535 " ideal model delta sigma weight residual 112.96 108.77 4.19 1.00e+00 1.00e+00 1.76e+01 angle pdb=" CA LEU F 584 " pdb=" CB LEU F 584 " pdb=" CG LEU F 584 " ideal model delta sigma weight residual 116.30 127.65 -11.35 3.50e+00 8.16e-02 1.05e+01 ... (remaining 53239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 21644 17.46 - 34.92: 1626 34.92 - 52.38: 342 52.38 - 69.84: 66 69.84 - 87.30: 19 Dihedral angle restraints: 23697 sinusoidal: 9813 harmonic: 13884 Sorted by residual: dihedral pdb=" CB CYS F 57 " pdb=" SG CYS F 57 " pdb=" SG CYS F 65 " pdb=" CB CYS F 65 " ideal model delta sinusoidal sigma weight residual -86.00 -43.03 -42.97 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual -86.00 -44.81 -41.19 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual -86.00 -47.04 -38.96 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 23694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3191 0.027 - 0.053: 1851 0.053 - 0.080: 709 0.080 - 0.106: 234 0.106 - 0.133: 111 Chirality restraints: 6096 Sorted by residual: chirality pdb=" CA ILE B 677 " pdb=" N ILE B 677 " pdb=" C ILE B 677 " pdb=" CB ILE B 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE C 677 " pdb=" N ILE C 677 " pdb=" C ILE C 677 " pdb=" CB ILE C 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE E 677 " pdb=" N ILE E 677 " pdb=" C ILE E 677 " pdb=" CB ILE E 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 6093 not shown) Planarity restraints: 6615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 724 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO C 725 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 725 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 725 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 724 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO E 725 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 725 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 725 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 395 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.36e+00 pdb=" C SER D 395 " 0.020 2.00e-02 2.50e+03 pdb=" O SER D 395 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 396 " -0.007 2.00e-02 2.50e+03 ... (remaining 6612 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 939 2.68 - 3.24: 40166 3.24 - 3.79: 64404 3.79 - 4.35: 84709 4.35 - 4.90: 136453 Nonbonded interactions: 326671 Sorted by model distance: nonbonded pdb=" OE1 GLN G 39 " pdb=" OH TYR G 95 " model vdw 2.130 3.040 nonbonded pdb=" OD2 ASP E 102 " pdb=" OH TYR F 106 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASN C 554 " pdb=" OG1 THR C 579 " model vdw 2.164 3.040 nonbonded pdb=" OD2 ASP A 102 " pdb=" OH TYR B 106 " model vdw 2.167 3.040 ... (remaining 326666 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.390 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.440 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 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 : 0.004 0.030 39294 Z= 0.185 Angle : 0.553 11.352 53286 Z= 0.307 Chirality : 0.040 0.133 6096 Planarity : 0.003 0.041 6615 Dihedral : 13.063 87.299 14628 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.44 % Allowed : 10.01 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.13), residues: 4638 helix: 0.12 (0.12), residues: 2034 sheet: -0.93 (0.19), residues: 768 loop : -0.26 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 731 TYR 0.017 0.001 TYR A 281 PHE 0.010 0.001 PHE D 324 TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00388 (39273) covalent geometry : angle 0.55261 (53244) SS BOND : bond 0.00237 ( 21) SS BOND : angle 0.57708 ( 42) hydrogen bonds : bond 0.17229 ( 1734) hydrogen bonds : angle 6.54783 ( 4434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 623 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7960 (mtm) cc_final: 0.7585 (mtp) REVERT: A 274 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7135 (mmtt) REVERT: A 278 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6993 (mt) REVERT: A 590 MET cc_start: 0.6499 (mpp) cc_final: 0.5798 (mmp) REVERT: A 598 LEU cc_start: 0.6151 (mt) cc_final: 0.5921 (mm) REVERT: A 663 ASN cc_start: 0.5374 (m110) cc_final: 0.4553 (t0) REVERT: B 17 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5043 (m-80) REVERT: B 36 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7793 (tp) REVERT: B 104 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.8508 (t70) REVERT: B 165 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.5903 (p0) REVERT: B 265 MET cc_start: 0.6938 (mmm) cc_final: 0.6734 (mmm) REVERT: B 343 MET cc_start: 0.8332 (ttm) cc_final: 0.7712 (ttm) REVERT: B 375 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7113 (ttm) REVERT: B 434 MET cc_start: 0.7632 (mtp) cc_final: 0.7123 (ptm) REVERT: B 592 ASN cc_start: 0.8048 (m-40) cc_final: 0.7581 (t0) REVERT: B 623 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6294 (t0) REVERT: B 650 HIS cc_start: 0.6857 (m90) cc_final: 0.6274 (t70) REVERT: B 668 TYR cc_start: 0.5959 (m-80) cc_final: 0.4499 (m-10) REVERT: B 699 PHE cc_start: 0.4843 (p90) cc_final: 0.4487 (p90) REVERT: B 738 LEU cc_start: 0.8279 (mt) cc_final: 0.8006 (mt) REVERT: B 791 PHE cc_start: 0.1603 (t80) cc_final: 0.0945 (t80) REVERT: C 35 MET cc_start: 0.7819 (mtm) cc_final: 0.7505 (mtp) REVERT: C 103 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6936 (tmm-80) REVERT: C 154 GLU cc_start: 0.7677 (pt0) cc_final: 0.7384 (tp30) REVERT: C 294 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: C 323 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7540 (m) REVERT: C 332 TYR cc_start: 0.7930 (t80) cc_final: 0.7704 (t80) REVERT: C 340 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7998 (tp) REVERT: C 374 PHE cc_start: 0.7926 (t80) cc_final: 0.7677 (t80) REVERT: C 513 TYR cc_start: 0.4062 (m-80) cc_final: 0.3838 (m-10) REVERT: C 590 MET cc_start: 0.5662 (mpp) cc_final: 0.5437 (mmt) REVERT: C 720 ILE cc_start: 0.4853 (mp) cc_final: 0.4194 (tt) REVERT: C 749 ARG cc_start: 0.4435 (mtp180) cc_final: 0.3802 (mtm180) REVERT: D 17 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5238 (m-80) REVERT: D 36 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8089 (tp) REVERT: D 155 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5956 (m170) REVERT: D 157 VAL cc_start: 0.8073 (t) cc_final: 0.7830 (p) REVERT: D 236 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: D 275 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6716 (t80) REVERT: D 338 TYR cc_start: 0.7162 (t80) cc_final: 0.6838 (t80) REVERT: D 343 MET cc_start: 0.8425 (ttm) cc_final: 0.7968 (mtp) REVERT: D 350 LYS cc_start: 0.6117 (tppt) cc_final: 0.5175 (mmtm) REVERT: D 353 PHE cc_start: 0.5065 (OUTLIER) cc_final: 0.3204 (t80) REVERT: D 401 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7375 (mtpp) REVERT: D 520 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: D 542 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: D 629 ILE cc_start: 0.5301 (pt) cc_final: 0.4960 (mm) REVERT: D 648 TYR cc_start: 0.4788 (m-80) cc_final: 0.3503 (m-80) REVERT: D 650 HIS cc_start: 0.6427 (m-70) cc_final: 0.6023 (t-170) REVERT: D 699 PHE cc_start: 0.3801 (p90) cc_final: 0.3260 (p90) REVERT: D 726 GLU cc_start: 0.7283 (tt0) cc_final: 0.6721 (tp30) REVERT: D 743 LEU cc_start: 0.3425 (OUTLIER) cc_final: 0.3174 (mp) REVERT: D 765 ARG cc_start: 0.4818 (OUTLIER) cc_final: 0.3708 (mpp-170) REVERT: E 35 MET cc_start: 0.8033 (mtm) cc_final: 0.7652 (mtp) REVERT: E 104 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8451 (t70) REVERT: E 274 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6998 (tppt) REVERT: E 340 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8128 (tp) REVERT: E 341 TRP cc_start: 0.5581 (t60) cc_final: 0.4770 (t60) REVERT: E 358 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.5850 (tt0) REVERT: E 445 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.4107 (mp) REVERT: E 451 LEU cc_start: 0.6327 (tp) cc_final: 0.6038 (tp) REVERT: E 637 HIS cc_start: 0.6536 (m170) cc_final: 0.6105 (m90) REVERT: E 676 LYS cc_start: 0.3918 (tppt) cc_final: 0.3394 (mttp) REVERT: E 692 LEU cc_start: 0.7271 (mt) cc_final: 0.7009 (mt) REVERT: E 720 ILE cc_start: 0.4939 (mm) cc_final: 0.4246 (mm) REVERT: E 728 PHE cc_start: 0.2461 (m-80) cc_final: 0.1642 (m-80) REVERT: F 17 TYR cc_start: 0.6091 (OUTLIER) cc_final: 0.5085 (m-80) REVERT: F 36 LEU cc_start: 0.8417 (mt) cc_final: 0.8068 (tp) REVERT: F 234 LYS cc_start: 0.6392 (mmtt) cc_final: 0.6068 (ptpp) REVERT: F 388 LYS cc_start: 0.7678 (tptt) cc_final: 0.7319 (ttmt) REVERT: F 434 MET cc_start: 0.7948 (mtp) cc_final: 0.7538 (ptm) REVERT: F 483 ILE cc_start: 0.6556 (tt) cc_final: 0.6150 (tt) REVERT: F 527 LEU cc_start: 0.6157 (pp) cc_final: 0.5831 (tp) REVERT: F 554 ASN cc_start: 0.6229 (m110) cc_final: 0.5668 (m-40) REVERT: F 568 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.5444 (p-80) REVERT: F 570 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5950 (pp30) REVERT: F 596 LEU cc_start: 0.7084 (tp) cc_final: 0.6355 (pp) REVERT: F 603 LEU cc_start: 0.7141 (mm) cc_final: 0.6837 (mm) REVERT: F 616 LEU cc_start: 0.6041 (tp) cc_final: 0.5619 (tp) REVERT: F 629 ILE cc_start: 0.5867 (pt) cc_final: 0.5509 (mm) REVERT: F 648 TYR cc_start: 0.4806 (m-80) cc_final: 0.4455 (m-80) REVERT: F 699 PHE cc_start: 0.3622 (p90) cc_final: 0.3391 (p90) REVERT: G 20 LEU cc_start: 0.4968 (mt) cc_final: 0.4748 (tp) REVERT: I 38 ARG cc_start: 0.6564 (ptt180) cc_final: 0.6263 (ptp-170) REVERT: I 83 MET cc_start: 0.2892 (OUTLIER) cc_final: 0.2638 (mpp) REVERT: I 90 ASP cc_start: 0.1713 (OUTLIER) cc_final: 0.1462 (m-30) REVERT: H 20 LEU cc_start: 0.4600 (mt) cc_final: 0.4279 (tp) REVERT: H 25 SER cc_start: 0.5498 (p) cc_final: 0.4850 (m) REVERT: H 32 GLU cc_start: 0.6722 (tp30) cc_final: 0.5470 (tt0) REVERT: H 81 LEU cc_start: 0.6823 (tp) cc_final: 0.6367 (tp) REVERT: H 83 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.3613 (mpp) outliers start: 233 outliers final: 59 residues processed: 825 average time/residue: 0.2427 time to fit residues: 318.9025 Evaluate side-chains 369 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 276 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.0670 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN A 637 HIS A 709 ASN A 737 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 637 HIS C 708 GLN C 709 ASN D 66 ASN D 478 HIS D 576 ASN D 637 HIS E 105 GLN E 288 ASN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN E 672 ASN E 709 ASN E 729 GLN F 467 GLN F 592 ASN F 650 HIS G 30 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 82 GLN H 84 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.118273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.098020 restraints weight = 117112.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.097449 restraints weight = 134453.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.098028 restraints weight = 104004.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.098188 restraints weight = 74679.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.098276 restraints weight = 69921.403| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39294 Z= 0.157 Angle : 0.618 13.921 53286 Z= 0.319 Chirality : 0.043 0.196 6096 Planarity : 0.004 0.102 6615 Dihedral : 6.820 74.904 5300 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.11 % Allowed : 14.19 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.12), residues: 4638 helix: -0.03 (0.11), residues: 2121 sheet: -0.78 (0.19), residues: 765 loop : -0.46 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 550 TYR 0.017 0.001 TYR E 281 PHE 0.020 0.001 PHE E 699 TRP 0.025 0.002 TRP D 143 HIS 0.019 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00342 (39273) covalent geometry : angle 0.61823 (53244) SS BOND : bond 0.00415 ( 21) SS BOND : angle 0.73534 ( 42) hydrogen bonds : bond 0.04382 ( 1734) hydrogen bonds : angle 5.16127 ( 4434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 333 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7321 (mmtt) REVERT: A 278 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7766 (mt) REVERT: A 340 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8257 (tp) REVERT: A 358 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5736 (pp20) REVERT: A 598 LEU cc_start: 0.6974 (mt) cc_final: 0.6724 (mm) REVERT: B 17 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.4461 (m-80) REVERT: B 36 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7659 (tp) REVERT: B 104 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8508 (t70) REVERT: B 353 PHE cc_start: 0.5764 (OUTLIER) cc_final: 0.3433 (t80) REVERT: B 588 LYS cc_start: 0.6707 (ptpt) cc_final: 0.6365 (mmmm) REVERT: B 743 LEU cc_start: 0.2487 (OUTLIER) cc_final: 0.2031 (mm) REVERT: C 294 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: C 332 TYR cc_start: 0.8260 (t80) cc_final: 0.7995 (t80) REVERT: C 340 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8447 (tp) REVERT: C 590 MET cc_start: 0.6151 (mpp) cc_final: 0.5737 (mmt) REVERT: C 686 LYS cc_start: 0.5702 (tppt) cc_final: 0.5173 (mtmt) REVERT: D 17 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.4909 (m-80) REVERT: D 36 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7870 (tp) REVERT: D 353 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.3397 (t80) REVERT: D 390 PHE cc_start: 0.6933 (t80) cc_final: 0.6636 (t80) REVERT: D 401 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: D 441 THR cc_start: 0.5797 (OUTLIER) cc_final: 0.5595 (m) REVERT: D 756 LEU cc_start: 0.4907 (tp) cc_final: 0.4696 (mt) REVERT: D 765 ARG cc_start: 0.4855 (OUTLIER) cc_final: 0.3840 (mpp-170) REVERT: E 35 MET cc_start: 0.7876 (mtm) cc_final: 0.7658 (mtp) REVERT: E 274 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7157 (mmtt) REVERT: E 292 ASP cc_start: 0.8544 (p0) cc_final: 0.7998 (p0) REVERT: E 340 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8348 (tp) REVERT: E 358 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5596 (pt0) REVERT: E 402 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5142 (mp) REVERT: E 551 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7360 (pt) REVERT: E 676 LYS cc_start: 0.3011 (tppt) cc_final: 0.2630 (mttp) REVERT: E 720 ILE cc_start: 0.4400 (mm) cc_final: 0.4020 (mm) REVERT: F 17 TYR cc_start: 0.5711 (OUTLIER) cc_final: 0.4771 (m-80) REVERT: F 234 LYS cc_start: 0.6019 (mmtt) cc_final: 0.5810 (ptpp) REVERT: F 350 LYS cc_start: 0.6592 (tptt) cc_final: 0.5999 (mmtm) REVERT: F 353 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.2569 (t80) REVERT: F 568 HIS cc_start: 0.5896 (OUTLIER) cc_final: 0.5269 (p-80) REVERT: F 764 ASN cc_start: 0.4104 (m-40) cc_final: 0.3668 (p0) REVERT: F 767 GLU cc_start: 0.5065 (mp0) cc_final: 0.4840 (pm20) REVERT: H 25 SER cc_start: 0.5235 (p) cc_final: 0.4880 (m) outliers start: 176 outliers final: 82 residues processed: 477 average time/residue: 0.2305 time to fit residues: 180.4375 Evaluate side-chains 343 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 236 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 HIS Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 161 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 592 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN B 637 HIS B 650 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 729 GLN D 478 HIS D 576 ASN D 592 ASN D 637 HIS E 467 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 592 ASN E 625 ASN F 614 HIS I 84 ASN H 30 GLN H 120 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.116884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.098058 restraints weight = 116264.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.098900 restraints weight = 168034.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.099349 restraints weight = 143186.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.099405 restraints weight = 111387.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.099671 restraints weight = 97266.664| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 39294 Z= 0.164 Angle : 0.590 11.555 53286 Z= 0.304 Chirality : 0.043 0.181 6096 Planarity : 0.004 0.074 6615 Dihedral : 6.243 76.012 5235 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.46 % Allowed : 15.20 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4638 helix: -0.12 (0.11), residues: 2124 sheet: -0.65 (0.19), residues: 759 loop : -0.53 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 345 TYR 0.017 0.001 TYR D 338 PHE 0.016 0.002 PHE E 156 TRP 0.030 0.002 TRP B 143 HIS 0.010 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00368 (39273) covalent geometry : angle 0.59041 (53244) SS BOND : bond 0.00479 ( 21) SS BOND : angle 0.61844 ( 42) hydrogen bonds : bond 0.03786 ( 1734) hydrogen bonds : angle 4.87074 ( 4434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 276 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7174 (mmtt) REVERT: A 340 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 344 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7097 (tp) REVERT: A 358 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5395 (pp20) REVERT: A 402 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4838 (mp) REVERT: B 17 TYR cc_start: 0.5577 (OUTLIER) cc_final: 0.4469 (m-80) REVERT: B 104 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8299 (t70) REVERT: B 353 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.3180 (t80) REVERT: B 536 VAL cc_start: 0.6498 (OUTLIER) cc_final: 0.6279 (t) REVERT: C 35 MET cc_start: 0.7805 (mtp) cc_final: 0.7522 (mtp) REVERT: C 103 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6464 (tmm-80) REVERT: C 294 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: C 301 SER cc_start: 0.7941 (p) cc_final: 0.7312 (t) REVERT: C 332 TYR cc_start: 0.8152 (t80) cc_final: 0.7937 (t80) REVERT: C 340 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8373 (tp) REVERT: C 358 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5502 (pp20) REVERT: C 590 MET cc_start: 0.6512 (mpp) cc_final: 0.6087 (mmt) REVERT: D 17 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.5042 (m-80) REVERT: D 36 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7933 (tp) REVERT: D 343 MET cc_start: 0.7580 (mtp) cc_final: 0.7248 (mtp) REVERT: D 353 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.3758 (t80) REVERT: D 401 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8087 (mtpp) REVERT: D 542 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6106 (mp0) REVERT: D 765 ARG cc_start: 0.4500 (OUTLIER) cc_final: 0.3604 (mpp-170) REVERT: E 274 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7296 (mmtt) REVERT: E 292 ASP cc_start: 0.8324 (p0) cc_final: 0.7790 (p0) REVERT: E 358 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5526 (pt0) REVERT: E 402 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5318 (mp) REVERT: E 551 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7414 (pt) REVERT: E 676 LYS cc_start: 0.2731 (tppt) cc_final: 0.2352 (mttp) REVERT: E 720 ILE cc_start: 0.4438 (mm) cc_final: 0.4167 (mm) REVERT: F 17 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.4832 (m-80) REVERT: F 350 LYS cc_start: 0.6550 (tptt) cc_final: 0.5931 (mmtm) REVERT: F 353 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.2305 (t80) REVERT: F 568 HIS cc_start: 0.5919 (OUTLIER) cc_final: 0.5391 (p-80) REVERT: H 25 SER cc_start: 0.5203 (p) cc_final: 0.4831 (m) REVERT: H 30 GLN cc_start: 0.4499 (OUTLIER) cc_final: 0.4198 (pp30) REVERT: H 74 ASN cc_start: 0.5561 (p0) cc_final: 0.5303 (t0) outliers start: 191 outliers final: 109 residues processed: 444 average time/residue: 0.2113 time to fit residues: 157.5147 Evaluate side-chains 367 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 231 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 HIS Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 263 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 361 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 413 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 406 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS C 650 HIS D 637 HIS D 649 ASN D 650 HIS D 663 ASN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 663 ASN G 30 GLN H 30 GLN H 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.115240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.096562 restraints weight = 115445.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097445 restraints weight = 188059.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097820 restraints weight = 149953.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097868 restraints weight = 112235.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.098457 restraints weight = 91546.111| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 39294 Z= 0.200 Angle : 0.624 10.900 53286 Z= 0.322 Chirality : 0.044 0.179 6096 Planarity : 0.004 0.056 6615 Dihedral : 6.319 75.778 5225 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.49 % Allowed : 16.29 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.12), residues: 4638 helix: -0.26 (0.11), residues: 2103 sheet: -0.64 (0.19), residues: 759 loop : -0.69 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 309 TYR 0.016 0.002 TYR B 332 PHE 0.020 0.002 PHE D 244 TRP 0.027 0.002 TRP D 143 HIS 0.021 0.002 HIS D 637 Details of bonding type rmsd covalent geometry : bond 0.00454 (39273) covalent geometry : angle 0.62371 (53244) SS BOND : bond 0.00979 ( 21) SS BOND : angle 0.70620 ( 42) hydrogen bonds : bond 0.03807 ( 1734) hydrogen bonds : angle 4.79414 ( 4434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 256 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6978 (mmtt) REVERT: A 340 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8333 (tp) REVERT: A 344 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7175 (tp) REVERT: A 356 ILE cc_start: 0.2519 (OUTLIER) cc_final: 0.2213 (mp) REVERT: A 358 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5720 (pp20) REVERT: A 402 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5231 (mp) REVERT: A 590 MET cc_start: 0.5428 (mmp) cc_final: 0.4668 (mmp) REVERT: A 598 LEU cc_start: 0.7040 (mm) cc_final: 0.6468 (mm) REVERT: A 720 ILE cc_start: 0.4165 (OUTLIER) cc_final: 0.3772 (tt) REVERT: B 17 TYR cc_start: 0.5767 (OUTLIER) cc_final: 0.4743 (m-80) REVERT: B 104 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8256 (t70) REVERT: B 353 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.3291 (t80) REVERT: B 536 VAL cc_start: 0.6400 (OUTLIER) cc_final: 0.6162 (t) REVERT: B 791 PHE cc_start: 0.1444 (t80) cc_final: 0.1187 (t80) REVERT: C 35 MET cc_start: 0.7769 (mtp) cc_final: 0.7478 (mtp) REVERT: C 103 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6473 (tmm-80) REVERT: C 301 SER cc_start: 0.8090 (p) cc_final: 0.7593 (t) REVERT: C 340 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8322 (tp) REVERT: C 358 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5658 (pp20) REVERT: C 376 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7466 (mm) REVERT: C 478 HIS cc_start: 0.6560 (m-70) cc_final: 0.6229 (m90) REVERT: C 590 MET cc_start: 0.6919 (mpp) cc_final: 0.6524 (mmt) REVERT: C 720 ILE cc_start: 0.4618 (OUTLIER) cc_final: 0.4384 (tp) REVERT: C 775 GLU cc_start: 0.3978 (OUTLIER) cc_final: 0.3560 (mp0) REVERT: D 17 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5520 (m-80) REVERT: D 36 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8094 (tp) REVERT: D 173 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7372 (mm) REVERT: D 353 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.3277 (t80) REVERT: D 401 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7947 (mtpp) REVERT: D 542 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: D 765 ARG cc_start: 0.4628 (OUTLIER) cc_final: 0.3623 (mpp-170) REVERT: E 292 ASP cc_start: 0.8261 (p0) cc_final: 0.7624 (p0) REVERT: E 358 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5912 (tt0) REVERT: E 516 LYS cc_start: 0.4130 (tptt) cc_final: 0.3721 (mttm) REVERT: E 653 TYR cc_start: 0.3658 (p90) cc_final: 0.3288 (p90) REVERT: E 720 ILE cc_start: 0.4643 (mm) cc_final: 0.4386 (mm) REVERT: F 17 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.4981 (m-80) REVERT: F 350 LYS cc_start: 0.6607 (tptt) cc_final: 0.5701 (mmtm) REVERT: F 353 PHE cc_start: 0.4917 (OUTLIER) cc_final: 0.2036 (t80) REVERT: F 568 HIS cc_start: 0.6023 (OUTLIER) cc_final: 0.5339 (p-80) REVERT: F 580 LYS cc_start: 0.7207 (mttm) cc_final: 0.6045 (tptm) REVERT: F 767 GLU cc_start: 0.5324 (pm20) cc_final: 0.4658 (mp0) REVERT: H 74 ASN cc_start: 0.5620 (p0) cc_final: 0.5234 (t0) outliers start: 235 outliers final: 149 residues processed: 466 average time/residue: 0.2100 time to fit residues: 164.7719 Evaluate side-chains 395 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 218 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 HIS Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 115 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 442 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 409 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN D 637 HIS D 650 HIS D 708 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.115426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.095060 restraints weight = 114701.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.094141 restraints weight = 140446.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.094815 restraints weight = 105003.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.094970 restraints weight = 77406.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.095048 restraints weight = 72427.946| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39294 Z= 0.150 Angle : 0.570 10.295 53286 Z= 0.294 Chirality : 0.042 0.197 6096 Planarity : 0.004 0.049 6615 Dihedral : 6.110 73.822 5217 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.86 % Allowed : 18.18 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4638 helix: -0.22 (0.11), residues: 2124 sheet: -0.63 (0.20), residues: 762 loop : -0.69 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 419 TYR 0.020 0.001 TYR A 689 PHE 0.016 0.001 PHE D 611 TRP 0.025 0.002 TRP D 143 HIS 0.013 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00339 (39273) covalent geometry : angle 0.56992 (53244) SS BOND : bond 0.00221 ( 21) SS BOND : angle 0.63036 ( 42) hydrogen bonds : bond 0.03522 ( 1734) hydrogen bonds : angle 4.65429 ( 4434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 236 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7142 (mmtt) REVERT: A 323 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8146 (m) REVERT: A 340 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8199 (tp) REVERT: A 344 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7214 (tp) REVERT: A 358 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5822 (pp20) REVERT: A 598 LEU cc_start: 0.7046 (mm) cc_final: 0.6588 (mp) REVERT: A 720 ILE cc_start: 0.4193 (OUTLIER) cc_final: 0.3958 (tp) REVERT: A 756 LEU cc_start: 0.3478 (OUTLIER) cc_final: 0.2282 (tp) REVERT: B 17 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.4554 (m-80) REVERT: B 104 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8045 (t70) REVERT: B 353 PHE cc_start: 0.5780 (OUTLIER) cc_final: 0.3213 (t80) REVERT: B 764 ASN cc_start: 0.4546 (m-40) cc_final: 0.3502 (p0) REVERT: B 791 PHE cc_start: 0.1728 (t80) cc_final: 0.1517 (t80) REVERT: C 35 MET cc_start: 0.7760 (mtp) cc_final: 0.7533 (mtp) REVERT: C 301 SER cc_start: 0.8015 (p) cc_final: 0.7457 (t) REVERT: C 340 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8434 (tp) REVERT: C 358 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5688 (pp20) REVERT: C 478 HIS cc_start: 0.6722 (m-70) cc_final: 0.6426 (m-70) REVERT: C 516 LYS cc_start: 0.3885 (tptt) cc_final: 0.2970 (mttm) REVERT: C 590 MET cc_start: 0.6898 (mpp) cc_final: 0.6539 (mmt) REVERT: C 720 ILE cc_start: 0.4911 (OUTLIER) cc_final: 0.4398 (tt) REVERT: C 775 GLU cc_start: 0.3986 (OUTLIER) cc_final: 0.3590 (mp0) REVERT: D 17 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5569 (m-80) REVERT: D 173 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7423 (mm) REVERT: D 353 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.3364 (t80) REVERT: D 401 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7915 (mtpp) REVERT: D 542 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: D 765 ARG cc_start: 0.4536 (OUTLIER) cc_final: 0.3587 (mpp-170) REVERT: E 292 ASP cc_start: 0.8142 (p0) cc_final: 0.7548 (p0) REVERT: E 358 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5980 (tt0) REVERT: E 516 LYS cc_start: 0.4311 (tptt) cc_final: 0.3739 (mttm) REVERT: E 653 TYR cc_start: 0.3932 (p90) cc_final: 0.3421 (p90) REVERT: E 720 ILE cc_start: 0.4807 (mm) cc_final: 0.4515 (mm) REVERT: F 17 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.4734 (m-80) REVERT: F 350 LYS cc_start: 0.6749 (tptt) cc_final: 0.5725 (mmtt) REVERT: F 353 PHE cc_start: 0.4941 (OUTLIER) cc_final: 0.1967 (t80) REVERT: F 568 HIS cc_start: 0.6144 (OUTLIER) cc_final: 0.5398 (p-80) REVERT: F 580 LYS cc_start: 0.7300 (mttm) cc_final: 0.6079 (tptm) REVERT: F 736 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6448 (pp) REVERT: F 767 GLU cc_start: 0.5692 (pm20) cc_final: 0.4845 (mp0) REVERT: H 19 ARG cc_start: 0.4129 (mmm160) cc_final: 0.3750 (mmm160) REVERT: H 74 ASN cc_start: 0.5658 (p0) cc_final: 0.5380 (t0) outliers start: 208 outliers final: 139 residues processed: 419 average time/residue: 0.2067 time to fit residues: 147.0467 Evaluate side-chains 381 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 217 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 451 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 322 optimal weight: 10.0000 chunk 239 optimal weight: 0.8980 chunk 198 optimal weight: 0.0030 chunk 305 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN D 650 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN F 575 ASN H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.116419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.097945 restraints weight = 115528.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.099020 restraints weight = 165664.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.099048 restraints weight = 131628.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.099113 restraints weight = 95812.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.099282 restraints weight = 81160.273| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 39294 Z= 0.113 Angle : 0.541 10.757 53286 Z= 0.276 Chirality : 0.041 0.209 6096 Planarity : 0.003 0.043 6615 Dihedral : 5.805 72.685 5211 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.48 % Allowed : 18.65 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.13), residues: 4638 helix: -0.08 (0.11), residues: 2127 sheet: -0.57 (0.20), residues: 762 loop : -0.59 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 685 TYR 0.021 0.001 TYR A 689 PHE 0.015 0.001 PHE E 699 TRP 0.019 0.002 TRP D 143 HIS 0.012 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00248 (39273) covalent geometry : angle 0.54090 (53244) SS BOND : bond 0.00250 ( 21) SS BOND : angle 0.60699 ( 42) hydrogen bonds : bond 0.03313 ( 1734) hydrogen bonds : angle 4.48638 ( 4434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 239 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7114 (mmtt) REVERT: A 340 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8185 (tp) REVERT: A 344 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7535 (tp) REVERT: A 358 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5636 (pp20) REVERT: A 590 MET cc_start: 0.5431 (mmp) cc_final: 0.5090 (mmt) REVERT: A 720 ILE cc_start: 0.4147 (OUTLIER) cc_final: 0.3902 (tp) REVERT: A 756 LEU cc_start: 0.3212 (OUTLIER) cc_final: 0.1923 (tp) REVERT: B 17 TYR cc_start: 0.5368 (OUTLIER) cc_final: 0.4137 (m-80) REVERT: B 353 PHE cc_start: 0.6016 (OUTLIER) cc_final: 0.3555 (t80) REVERT: B 764 ASN cc_start: 0.4081 (m-40) cc_final: 0.3283 (p0) REVERT: C 35 MET cc_start: 0.7772 (mtp) cc_final: 0.7428 (mtp) REVERT: C 294 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: C 301 SER cc_start: 0.8008 (p) cc_final: 0.7358 (t) REVERT: C 340 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8390 (tp) REVERT: C 358 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5603 (pp20) REVERT: C 478 HIS cc_start: 0.6461 (m-70) cc_final: 0.6192 (m-70) REVERT: C 590 MET cc_start: 0.7059 (mpp) cc_final: 0.6815 (mmt) REVERT: C 720 ILE cc_start: 0.4469 (OUTLIER) cc_final: 0.4103 (tt) REVERT: C 775 GLU cc_start: 0.4108 (OUTLIER) cc_final: 0.3662 (mp0) REVERT: D 17 TYR cc_start: 0.5818 (OUTLIER) cc_final: 0.5276 (m-80) REVERT: D 173 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7486 (mm) REVERT: D 353 PHE cc_start: 0.6037 (OUTLIER) cc_final: 0.3709 (t80) REVERT: D 401 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7931 (mtpp) REVERT: D 542 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: D 765 ARG cc_start: 0.4461 (OUTLIER) cc_final: 0.3522 (mpp-170) REVERT: E 292 ASP cc_start: 0.7925 (p0) cc_final: 0.7511 (p0) REVERT: E 309 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7508 (mmm-85) REVERT: E 343 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6615 (ttm) REVERT: E 358 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: E 653 TYR cc_start: 0.3795 (p90) cc_final: 0.3308 (p90) REVERT: F 17 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.4526 (m-80) REVERT: F 353 PHE cc_start: 0.5032 (OUTLIER) cc_final: 0.1994 (t80) REVERT: F 580 LYS cc_start: 0.6990 (mttm) cc_final: 0.5923 (tptm) REVERT: F 692 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6945 (mp) REVERT: F 723 LEU cc_start: 0.5118 (tp) cc_final: 0.4634 (mp) REVERT: F 767 GLU cc_start: 0.5403 (pm20) cc_final: 0.4548 (mp0) REVERT: H 19 ARG cc_start: 0.4490 (mmm160) cc_final: 0.4074 (mmm160) REVERT: H 25 SER cc_start: 0.5709 (p) cc_final: 0.5416 (m) outliers start: 192 outliers final: 117 residues processed: 403 average time/residue: 0.2052 time to fit residues: 141.8451 Evaluate side-chains 359 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 217 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 699 PHE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 380 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 233 optimal weight: 0.3980 chunk 354 optimal weight: 3.9990 chunk 434 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 406 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS B 663 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 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 = 0.4181 r_free = 0.4181 target = 0.113941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.093658 restraints weight = 115592.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.092638 restraints weight = 139429.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.093493 restraints weight = 115248.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.093325 restraints weight = 83815.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.093837 restraints weight = 73679.350| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 39294 Z= 0.194 Angle : 0.627 12.836 53286 Z= 0.320 Chirality : 0.044 0.290 6096 Planarity : 0.004 0.049 6615 Dihedral : 6.051 75.886 5196 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.51 % Allowed : 18.84 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.12), residues: 4638 helix: -0.27 (0.11), residues: 2106 sheet: -0.70 (0.20), residues: 732 loop : -0.70 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 419 TYR 0.023 0.002 TYR A 689 PHE 0.025 0.002 PHE D 611 TRP 0.023 0.002 TRP D 143 HIS 0.016 0.001 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.00448 (39273) covalent geometry : angle 0.62653 (53244) SS BOND : bond 0.00318 ( 21) SS BOND : angle 0.76330 ( 42) hydrogen bonds : bond 0.03719 ( 1734) hydrogen bonds : angle 4.62717 ( 4434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 224 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7200 (mmtt) REVERT: A 340 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 344 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7492 (tp) REVERT: A 358 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5930 (pp20) REVERT: A 720 ILE cc_start: 0.4426 (OUTLIER) cc_final: 0.3997 (tt) REVERT: B 17 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4589 (m-80) REVERT: B 104 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.8217 (t70) REVERT: B 353 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.3163 (t80) REVERT: B 622 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4767 (mmtm) REVERT: B 764 ASN cc_start: 0.4603 (m-40) cc_final: 0.3851 (p0) REVERT: C 35 MET cc_start: 0.7861 (mtp) cc_final: 0.7583 (mtp) REVERT: C 301 SER cc_start: 0.8158 (p) cc_final: 0.7636 (t) REVERT: C 340 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8363 (tp) REVERT: C 358 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.5853 (pp20) REVERT: C 516 LYS cc_start: 0.3971 (tptt) cc_final: 0.3619 (mttm) REVERT: C 590 MET cc_start: 0.7437 (mpp) cc_final: 0.7116 (mmt) REVERT: C 699 PHE cc_start: 0.4796 (OUTLIER) cc_final: 0.4474 (t80) REVERT: C 720 ILE cc_start: 0.4781 (OUTLIER) cc_final: 0.4346 (tt) REVERT: C 775 GLU cc_start: 0.3720 (OUTLIER) cc_final: 0.3329 (mp0) REVERT: D 173 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7726 (mm) REVERT: D 353 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.3403 (t80) REVERT: D 401 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7881 (mtpp) REVERT: D 542 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: D 765 ARG cc_start: 0.4315 (mmp80) cc_final: 0.3469 (mpp-170) REVERT: E 292 ASP cc_start: 0.8082 (p0) cc_final: 0.7172 (p0) REVERT: E 309 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7411 (tmt-80) REVERT: E 343 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6850 (ttm) REVERT: E 358 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5789 (pt0) REVERT: E 647 TRP cc_start: 0.5699 (p90) cc_final: 0.4851 (p90) REVERT: E 653 TYR cc_start: 0.4009 (p90) cc_final: 0.3505 (p90) REVERT: F 17 TYR cc_start: 0.5904 (OUTLIER) cc_final: 0.4700 (m-80) REVERT: F 350 LYS cc_start: 0.6765 (tptt) cc_final: 0.5668 (mmtt) REVERT: F 353 PHE cc_start: 0.4579 (OUTLIER) cc_final: 0.1518 (t80) REVERT: F 580 LYS cc_start: 0.7202 (mttm) cc_final: 0.6124 (tmtt) REVERT: F 767 GLU cc_start: 0.6158 (pm20) cc_final: 0.4996 (mp0) outliers start: 193 outliers final: 142 residues processed: 395 average time/residue: 0.2055 time to fit residues: 138.3639 Evaluate side-chains 367 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 202 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 361 SER Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 82 optimal weight: 0.8980 chunk 403 optimal weight: 0.9980 chunk 406 optimal weight: 10.0000 chunk 365 optimal weight: 0.6980 chunk 434 optimal weight: 7.9990 chunk 420 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 345 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 211 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS D 660 ASN ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 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 = 0.4210 r_free = 0.4210 target = 0.115661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.096959 restraints weight = 113937.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.097042 restraints weight = 184285.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097696 restraints weight = 148239.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.097885 restraints weight = 103048.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.098113 restraints weight = 94266.069| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39294 Z= 0.116 Angle : 0.547 13.704 53286 Z= 0.279 Chirality : 0.041 0.243 6096 Planarity : 0.003 0.046 6615 Dihedral : 5.684 74.126 5192 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.87 % Allowed : 19.84 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.13), residues: 4638 helix: -0.08 (0.11), residues: 2100 sheet: -0.57 (0.20), residues: 753 loop : -0.57 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 685 TYR 0.015 0.001 TYR A 689 PHE 0.018 0.001 PHE D 699 TRP 0.029 0.002 TRP D 143 HIS 0.013 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00254 (39273) covalent geometry : angle 0.54678 (53244) SS BOND : bond 0.00155 ( 21) SS BOND : angle 0.60887 ( 42) hydrogen bonds : bond 0.03305 ( 1734) hydrogen bonds : angle 4.41968 ( 4434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 225 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7160 (mmtt) REVERT: A 340 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 358 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5843 (pp20) REVERT: B 17 TYR cc_start: 0.5650 (OUTLIER) cc_final: 0.4454 (m-80) REVERT: B 104 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8109 (t70) REVERT: B 353 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.3494 (t80) REVERT: B 764 ASN cc_start: 0.3978 (m-40) cc_final: 0.3329 (p0) REVERT: C 301 SER cc_start: 0.8066 (p) cc_final: 0.7436 (t) REVERT: C 340 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8386 (tp) REVERT: C 358 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5930 (pp20) REVERT: C 478 HIS cc_start: 0.6388 (m-70) cc_final: 0.6102 (m90) REVERT: C 590 MET cc_start: 0.7228 (mpp) cc_final: 0.7024 (mmt) REVERT: C 699 PHE cc_start: 0.4689 (OUTLIER) cc_final: 0.4155 (t80) REVERT: C 720 ILE cc_start: 0.4475 (OUTLIER) cc_final: 0.4142 (tt) REVERT: C 775 GLU cc_start: 0.3784 (OUTLIER) cc_final: 0.3343 (mp0) REVERT: D 17 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.5063 (m-80) REVERT: D 353 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.3674 (t80) REVERT: D 401 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7895 (mtpp) REVERT: D 542 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: D 765 ARG cc_start: 0.4265 (mmp80) cc_final: 0.3450 (mpp-170) REVERT: D 767 GLU cc_start: 0.5386 (mp0) cc_final: 0.4760 (mp0) REVERT: E 292 ASP cc_start: 0.7885 (p0) cc_final: 0.7491 (p0) REVERT: E 309 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7515 (mmm-85) REVERT: E 343 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6802 (ttm) REVERT: E 358 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: E 647 TRP cc_start: 0.5909 (p90) cc_final: 0.4916 (p90) REVERT: E 653 TYR cc_start: 0.3837 (p90) cc_final: 0.3387 (p90) REVERT: F 17 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: F 353 PHE cc_start: 0.4906 (OUTLIER) cc_final: 0.1665 (t80) REVERT: F 580 LYS cc_start: 0.7003 (mttm) cc_final: 0.5995 (tmtt) REVERT: F 692 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6902 (mp) REVERT: F 767 GLU cc_start: 0.5891 (pm20) cc_final: 0.4777 (mp0) REVERT: G 74 ASN cc_start: 0.5611 (OUTLIER) cc_final: 0.5377 (t0) outliers start: 166 outliers final: 117 residues processed: 370 average time/residue: 0.2109 time to fit residues: 133.9968 Evaluate side-chains 345 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 206 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 699 PHE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 361 SER Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 177 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 279 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 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 = 0.4212 r_free = 0.4212 target = 0.115809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.096937 restraints weight = 115165.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.097735 restraints weight = 184008.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.098266 restraints weight = 144234.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.098375 restraints weight = 102919.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.098888 restraints weight = 87643.043| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39294 Z= 0.115 Angle : 0.542 10.341 53286 Z= 0.276 Chirality : 0.041 0.212 6096 Planarity : 0.003 0.048 6615 Dihedral : 5.520 74.596 5187 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.76 % Allowed : 20.31 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.13), residues: 4638 helix: -0.04 (0.11), residues: 2103 sheet: -0.51 (0.20), residues: 723 loop : -0.61 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 419 TYR 0.017 0.001 TYR H 60 PHE 0.027 0.001 PHE A 374 TRP 0.024 0.001 TRP D 143 HIS 0.012 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00255 (39273) covalent geometry : angle 0.54163 (53244) SS BOND : bond 0.00173 ( 21) SS BOND : angle 0.56674 ( 42) hydrogen bonds : bond 0.03251 ( 1734) hydrogen bonds : angle 4.35234 ( 4434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 222 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7148 (mmtt) REVERT: A 358 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5647 (pp20) REVERT: A 590 MET cc_start: 0.5700 (mmp) cc_final: 0.5362 (mmt) REVERT: B 17 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.4348 (m-80) REVERT: B 104 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8130 (t70) REVERT: B 353 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.3355 (t80) REVERT: B 764 ASN cc_start: 0.4039 (m-40) cc_final: 0.3320 (p0) REVERT: C 294 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: C 301 SER cc_start: 0.8099 (p) cc_final: 0.7455 (t) REVERT: C 340 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8402 (tp) REVERT: C 358 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5691 (pp20) REVERT: C 478 HIS cc_start: 0.6611 (m-70) cc_final: 0.6331 (m90) REVERT: C 699 PHE cc_start: 0.4757 (OUTLIER) cc_final: 0.4149 (t80) REVERT: C 720 ILE cc_start: 0.4400 (OUTLIER) cc_final: 0.4087 (tt) REVERT: C 775 GLU cc_start: 0.3640 (OUTLIER) cc_final: 0.3228 (mp0) REVERT: D 17 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: D 353 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.3974 (t80) REVERT: D 401 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7921 (mtpp) REVERT: D 542 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: D 729 GLN cc_start: 0.3833 (tp40) cc_final: 0.3628 (tp-100) REVERT: D 765 ARG cc_start: 0.4379 (mmp80) cc_final: 0.3488 (mpp-170) REVERT: E 292 ASP cc_start: 0.7739 (p0) cc_final: 0.7278 (p0) REVERT: E 309 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7514 (mmm-85) REVERT: E 343 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6812 (ttm) REVERT: E 358 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5870 (tt0) REVERT: E 647 TRP cc_start: 0.5929 (p90) cc_final: 0.4929 (p90) REVERT: E 653 TYR cc_start: 0.3883 (p90) cc_final: 0.3590 (p90) REVERT: F 17 TYR cc_start: 0.5842 (OUTLIER) cc_final: 0.4409 (m-80) REVERT: F 353 PHE cc_start: 0.4854 (OUTLIER) cc_final: 0.1645 (t80) REVERT: F 580 LYS cc_start: 0.7053 (mttm) cc_final: 0.6057 (tmtt) REVERT: F 692 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6973 (mp) REVERT: F 736 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6397 (pp) REVERT: F 767 GLU cc_start: 0.5912 (pm20) cc_final: 0.4815 (mp0) outliers start: 161 outliers final: 126 residues processed: 360 average time/residue: 0.2098 time to fit residues: 129.2828 Evaluate side-chains 355 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 207 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 699 PHE Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 429 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 262 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** 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 = 0.4205 r_free = 0.4205 target = 0.115418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.096931 restraints weight = 114689.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.098635 restraints weight = 192963.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.098815 restraints weight = 141661.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.098962 restraints weight = 108863.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.099429 restraints weight = 87755.476| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39294 Z= 0.132 Angle : 0.557 11.604 53286 Z= 0.284 Chirality : 0.042 0.275 6096 Planarity : 0.004 0.048 6615 Dihedral : 5.530 74.215 5185 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.59 % Allowed : 20.66 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.12), residues: 4638 helix: -0.10 (0.11), residues: 2106 sheet: -0.51 (0.20), residues: 717 loop : -0.66 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 685 TYR 0.012 0.001 TYR C 281 PHE 0.020 0.001 PHE C 331 TRP 0.050 0.002 TRP B 143 HIS 0.012 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00297 (39273) covalent geometry : angle 0.55740 (53244) SS BOND : bond 0.00198 ( 21) SS BOND : angle 0.58924 ( 42) hydrogen bonds : bond 0.03297 ( 1734) hydrogen bonds : angle 4.34657 ( 4434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 220 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7117 (mmtt) REVERT: A 358 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.5650 (pp20) REVERT: A 590 MET cc_start: 0.5580 (mmp) cc_final: 0.5175 (mmt) REVERT: B 17 TYR cc_start: 0.5697 (OUTLIER) cc_final: 0.4470 (m-80) REVERT: B 104 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8191 (t70) REVERT: B 353 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.3510 (t80) REVERT: C 294 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: C 301 SER cc_start: 0.8156 (p) cc_final: 0.7516 (t) REVERT: C 340 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8429 (tp) REVERT: C 358 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5697 (pp20) REVERT: C 478 HIS cc_start: 0.6578 (m-70) cc_final: 0.6300 (m90) REVERT: C 699 PHE cc_start: 0.4638 (OUTLIER) cc_final: 0.4132 (t80) REVERT: C 720 ILE cc_start: 0.4501 (OUTLIER) cc_final: 0.4192 (tt) REVERT: C 775 GLU cc_start: 0.3762 (OUTLIER) cc_final: 0.3339 (mp0) REVERT: D 17 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.4899 (m-80) REVERT: D 353 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.3998 (t80) REVERT: D 375 MET cc_start: 0.7370 (ttp) cc_final: 0.7165 (ttp) REVERT: D 401 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7910 (mtpp) REVERT: D 542 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: D 622 LYS cc_start: 0.5533 (OUTLIER) cc_final: 0.4467 (tptt) REVERT: D 765 ARG cc_start: 0.4510 (mmp80) cc_final: 0.3523 (mpp-170) REVERT: E 292 ASP cc_start: 0.7758 (p0) cc_final: 0.7296 (p0) REVERT: E 309 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7549 (mmm-85) REVERT: E 343 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6801 (ttm) REVERT: E 358 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6055 (pt0) REVERT: E 374 PHE cc_start: 0.5704 (t80) cc_final: 0.4985 (t80) REVERT: E 647 TRP cc_start: 0.5945 (p90) cc_final: 0.5040 (p90) REVERT: E 653 TYR cc_start: 0.4052 (p90) cc_final: 0.3739 (p90) REVERT: F 17 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.4520 (m-80) REVERT: F 353 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.1631 (t80) REVERT: F 580 LYS cc_start: 0.7028 (mttm) cc_final: 0.6051 (tmtt) REVERT: F 692 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7042 (mp) REVERT: F 736 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6400 (pp) REVERT: F 767 GLU cc_start: 0.5923 (pm20) cc_final: 0.4847 (mp0) outliers start: 154 outliers final: 123 residues processed: 355 average time/residue: 0.2057 time to fit residues: 125.5506 Evaluate side-chains 351 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 205 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 699 PHE Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 361 SER Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 127 optimal weight: 0.0980 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 328 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 300 optimal weight: 0.0980 chunk 442 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS B 764 ASN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS D 708 GLN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN ** I 30 GLN ** 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 = 0.4214 r_free = 0.4214 target = 0.115952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.095867 restraints weight = 115091.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.095029 restraints weight = 134109.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.095569 restraints weight = 105903.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.095788 restraints weight = 73635.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.095896 restraints weight = 69676.469| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 39294 Z= 0.108 Angle : 0.548 11.762 53286 Z= 0.277 Chirality : 0.041 0.294 6096 Planarity : 0.003 0.048 6615 Dihedral : 5.415 73.107 5185 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.27 % Allowed : 20.96 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.13), residues: 4638 helix: -0.04 (0.11), residues: 2109 sheet: -0.48 (0.20), residues: 723 loop : -0.59 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 266 TYR 0.013 0.001 TYR D 264 PHE 0.029 0.001 PHE A 374 TRP 0.043 0.002 TRP B 143 HIS 0.011 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00236 (39273) covalent geometry : angle 0.54826 (53244) SS BOND : bond 0.00179 ( 21) SS BOND : angle 0.56490 ( 42) hydrogen bonds : bond 0.03214 ( 1734) hydrogen bonds : angle 4.27833 ( 4434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5353.92 seconds wall clock time: 94 minutes 12.87 seconds (5652.87 seconds total)