Starting phenix.real_space_refine on Tue Mar 19 04:08:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/03_2024/6bwd_7297.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/03_2024/6bwd_7297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/03_2024/6bwd_7297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/03_2024/6bwd_7297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/03_2024/6bwd_7297.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/03_2024/6bwd_7297.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 5 5.21 5 S 122 5.16 5 C 15156 2.51 5 N 3822 2.21 5 O 4082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 681": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 681": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 673": "NH1" <-> "NH2" Residue "C ARG 770": "NH1" <-> "NH2" Residue "C ARG 853": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 681": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Residue "D ARG 856": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23187 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5613 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 227} Link IDs: {'CIS': 48, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 887 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 345 Chain: "B" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5618 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 226} Link IDs: {'CIS': 47, 'PTRANS': 27, 'TRANS': 696} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 650 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 5628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5628 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 223} Link IDs: {'CIS': 45, 'PTRANS': 27, 'TRANS': 698} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 640 Unresolved non-hydrogen angles: 867 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 326 Chain: "D" Number of atoms: 5593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5593 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 232} Link IDs: {'CIS': 46, 'PTRANS': 27, 'TRANS': 697} Chain breaks: 15 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 674 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 360 Chain: "A" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 212 Unusual residues: {' MG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 142 Unusual residues: {' MG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 280 Unusual residues: {'Y01': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' MG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 11.65, per 1000 atoms: 0.50 Number of scatterers: 23187 At special positions: 0 Unit cell: (136.53, 136.53, 152.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 Mg 5 11.99 O 4082 8.00 N 3822 7.00 C 15156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 904 " distance=2.02 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 904 " distance=2.02 Simple disulfide: pdb=" SG CYS C 711 " - pdb=" SG CYS C 721 " distance=2.02 Simple disulfide: pdb=" SG CYS D 894 " - pdb=" SG CYS D 904 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 8.53 Conformation dependent library (CDL) restraints added in 3.3 seconds 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 0 sheets defined 71.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.071A pdb=" N UNK A 285 " --> pdb=" O UNK A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.856A pdb=" N GLU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.761A pdb=" N HIS A 417 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 418 " --> pdb=" O HIS A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 418' Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.555A pdb=" N LYS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.971A pdb=" N ILE A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 597 through 604 removed outlier: 3.540A pdb=" N SER A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.581A pdb=" N LEU A 612 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 613 " --> pdb=" O LEU A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 613' Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.891A pdb=" N ILE A 623 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 689 through 714 removed outlier: 4.133A pdb=" N LEU A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 removed outlier: 4.265A pdb=" N VAL A 727 " --> pdb=" O GLN A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 removed outlier: 3.788A pdb=" N TRP A 757 " --> pdb=" O LYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER A 765 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 777 " --> pdb=" O PHE A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 removed outlier: 3.903A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 819 removed outlier: 3.830A pdb=" N ARG A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 814 " --> pdb=" O TRP A 810 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 815 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 832 removed outlier: 4.087A pdb=" N TYR A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 3.550A pdb=" N PHE A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 841 " --> pdb=" O ASN A 837 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 844 " --> pdb=" O TYR A 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 849 " --> pdb=" O MET A 845 " (cutoff:3.500A) Proline residue: A 855 - end of helix removed outlier: 4.002A pdb=" N ILE A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 880 removed outlier: 4.587A pdb=" N HIS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Proline residue: A 878 - end of helix Processing helix chain 'A' and resid 910 through 922 removed outlier: 3.506A pdb=" N ALA A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 920 " --> pdb=" O ALA A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE A 944 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 970 through 974 Processing helix chain 'A' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1031 through 1068 removed outlier: 3.665A pdb=" N ILE A1035 " --> pdb=" O SER A1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 273 through 285 removed outlier: 4.072A pdb=" N UNK B 285 " --> pdb=" O UNK B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.857A pdb=" N GLU B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.760A pdb=" N HIS B 417 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 418 " --> pdb=" O HIS B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 435 through 442 removed outlier: 3.555A pdb=" N LYS B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 470 removed outlier: 3.970A pdb=" N ILE B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU B 491 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN B 538 " --> pdb=" O GLN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 597 through 604 removed outlier: 3.770A pdb=" N SER B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 613 removed outlier: 4.257A pdb=" N MET B 611 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 612 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 613 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.890A pdb=" N ILE B 623 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 Processing helix chain 'B' and resid 689 through 714 removed outlier: 4.133A pdb=" N LEU B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 714 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 743 removed outlier: 4.266A pdb=" N VAL B 727 " --> pdb=" O GLN B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 758 removed outlier: 3.788A pdb=" N TRP B 757 " --> pdb=" O LYS B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER B 765 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 777 " --> pdb=" O PHE B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.902A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 819 removed outlier: 3.831A pdb=" N ARG B 813 " --> pdb=" O PHE B 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 814 " --> pdb=" O TRP B 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 815 " --> pdb=" O TYR B 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 816 " --> pdb=" O VAL B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 832 removed outlier: 4.086A pdb=" N TYR B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 861 removed outlier: 3.549A pdb=" N PHE B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE B 841 " --> pdb=" O ASN B 837 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 844 " --> pdb=" O TYR B 840 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 849 " --> pdb=" O MET B 845 " (cutoff:3.500A) Proline residue: B 855 - end of helix removed outlier: 4.004A pdb=" N ILE B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 880 removed outlier: 4.587A pdb=" N HIS B 877 " --> pdb=" O ASP B 873 " (cutoff:3.500A) Proline residue: B 878 - end of helix Processing helix chain 'B' and resid 910 through 922 removed outlier: 3.507A pdb=" N ALA B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 920 " --> pdb=" O ALA B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE B 944 " --> pdb=" O GLN B 940 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 947 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 970 through 974 Processing helix chain 'B' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1026 No H-bonds generated for 'chain 'B' and resid 1024 through 1026' Processing helix chain 'B' and resid 1031 through 1068 removed outlier: 3.666A pdb=" N ILE B1035 " --> pdb=" O SER B1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 54 through 64 Processing helix chain 'C' and resid 91 through 103 removed outlier: 4.071A pdb=" N UNK C 103 " --> pdb=" O UNK C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.857A pdb=" N GLU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU C 131 " --> pdb=" O PRO C 127 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.761A pdb=" N HIS C 234 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 235 " --> pdb=" O HIS C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.556A pdb=" N LYS C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.971A pdb=" N ILE C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 302 through 320 removed outlier: 4.284A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.809A pdb=" N GLN C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.809A pdb=" N SER C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 430 removed outlier: 4.914A pdb=" N MET C 428 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 429 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 440 removed outlier: 3.891A pdb=" N ILE C 440 " --> pdb=" O MET C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 506 through 531 removed outlier: 4.132A pdb=" N LEU C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 4.266A pdb=" N VAL C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.789A pdb=" N TRP C 574 " --> pdb=" O LYS C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 596 removed outlier: 3.873A pdb=" N SER C 582 " --> pdb=" O TYR C 578 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 593 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 3.903A pdb=" N ILE C 619 " --> pdb=" O ALA C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.831A pdb=" N ARG C 630 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU C 631 " --> pdb=" O TRP C 627 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 632 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 removed outlier: 4.086A pdb=" N TYR C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY C 649 " --> pdb=" O VAL C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 678 removed outlier: 3.550A pdb=" N PHE C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 661 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 666 " --> pdb=" O MET C 662 " (cutoff:3.500A) Proline residue: C 672 - end of helix removed outlier: 4.003A pdb=" N ILE C 676 " --> pdb=" O PRO C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 697 removed outlier: 4.586A pdb=" N HIS C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Proline residue: C 695 - end of helix Processing helix chain 'C' and resid 727 through 739 removed outlier: 3.506A pdb=" N ALA C 733 " --> pdb=" O PRO C 729 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 755 through 770 removed outlier: 4.240A pdb=" N ILE C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 764 " --> pdb=" O ALA C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 791 Processing helix chain 'C' and resid 818 through 840 removed outlier: 3.893A pdb=" N GLU C 834 " --> pdb=" O GLU C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 843 No H-bonds generated for 'chain 'C' and resid 841 through 843' Processing helix chain 'C' and resid 848 through 885 removed outlier: 3.666A pdb=" N ILE C 852 " --> pdb=" O SER C 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 16 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'D' and resid 273 through 285 removed outlier: 4.071A pdb=" N UNK D 285 " --> pdb=" O UNK D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.856A pdb=" N GLU D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.562A pdb=" N MET D 358 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 removed outlier: 3.761A pdb=" N HIS D 417 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 418 " --> pdb=" O HIS D 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 414 through 418' Processing helix chain 'D' and resid 435 through 442 removed outlier: 3.556A pdb=" N LYS D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.971A pdb=" N ILE D 465 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 485 through 503 removed outlier: 4.284A pdb=" N LEU D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 527 through 538 removed outlier: 3.809A pdb=" N GLN D 538 " --> pdb=" O GLN D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 545 Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 574 through 587 Processing helix chain 'D' and resid 597 through 604 removed outlier: 3.802A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 613 removed outlier: 4.256A pdb=" N MET D 611 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 612 " --> pdb=" O ILE D 609 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 613 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.891A pdb=" N ILE D 623 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 687 Processing helix chain 'D' and resid 689 through 714 removed outlier: 4.132A pdb=" N LEU D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 714 " --> pdb=" O PHE D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 743 removed outlier: 4.266A pdb=" N VAL D 727 " --> pdb=" O GLN D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 758 removed outlier: 3.789A pdb=" N TRP D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 779 removed outlier: 3.873A pdb=" N SER D 765 " --> pdb=" O TYR D 761 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 773 " --> pdb=" O ALA D 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 805 removed outlier: 3.902A pdb=" N ILE D 802 " --> pdb=" O ALA D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.829A pdb=" N ARG D 813 " --> pdb=" O PHE D 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 814 " --> pdb=" O TRP D 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 815 " --> pdb=" O TYR D 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 816 " --> pdb=" O VAL D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 832 removed outlier: 4.086A pdb=" N TYR D 827 " --> pdb=" O GLN D 823 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY D 832 " --> pdb=" O VAL D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 861 removed outlier: 3.550A pdb=" N PHE D 839 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 841 " --> pdb=" O ASN D 837 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE D 844 " --> pdb=" O TYR D 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 849 " --> pdb=" O MET D 845 " (cutoff:3.500A) Proline residue: D 855 - end of helix removed outlier: 4.003A pdb=" N ILE D 859 " --> pdb=" O PRO D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 880 removed outlier: 4.586A pdb=" N HIS D 877 " --> pdb=" O ASP D 873 " (cutoff:3.500A) Proline residue: D 878 - end of helix Processing helix chain 'D' and resid 910 through 922 removed outlier: 3.506A pdb=" N ALA D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE D 920 " --> pdb=" O ALA D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 938 through 953 removed outlier: 4.240A pdb=" N ILE D 944 " --> pdb=" O GLN D 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 953 through 958 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 1001 through 1023 removed outlier: 3.893A pdb=" N GLU D1017 " --> pdb=" O GLU D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1026 No H-bonds generated for 'chain 'D' and resid 1024 through 1026' Processing helix chain 'D' and resid 1031 through 1068 removed outlier: 3.665A pdb=" N ILE D1035 " --> pdb=" O SER D1031 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2856 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: 6.23 Time building geometry restraints manager: 9.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3939 1.32 - 1.44: 6177 1.44 - 1.57: 13281 1.57 - 1.69: 36 1.69 - 1.81: 212 Bond restraints: 23645 Sorted by residual: bond pdb=" CAV Y01 C1303 " pdb=" CAZ Y01 C1303 " ideal model delta sigma weight residual 1.507 1.362 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CAV Y01 C1306 " pdb=" CAZ Y01 C1306 " ideal model delta sigma weight residual 1.507 1.378 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" CAZ Y01 B1204 " pdb=" CBH Y01 B1204 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAZ Y01 A1203 " pdb=" CBH Y01 A1203 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAV Y01 D1203 " pdb=" CAZ Y01 D1203 " ideal model delta sigma weight residual 1.507 1.390 0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 23640 not shown) Histogram of bond angle deviations from ideal: 93.74 - 103.15: 265 103.15 - 112.56: 12260 112.56 - 121.97: 15124 121.97 - 131.38: 4421 131.38 - 140.79: 159 Bond angle restraints: 32229 Sorted by residual: angle pdb=" C ILE C 167 " pdb=" N GLY C 168 " pdb=" CA GLY C 168 " ideal model delta sigma weight residual 121.41 140.79 -19.38 1.96e+00 2.60e-01 9.78e+01 angle pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta sigma weight residual 122.82 134.84 -12.02 1.42e+00 4.96e-01 7.16e+01 angle pdb=" C TRP B 480 " pdb=" N GLN B 481 " pdb=" CA GLN B 481 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta sigma weight residual 122.82 134.82 -12.00 1.42e+00 4.96e-01 7.14e+01 ... (remaining 32224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 14400 26.92 - 53.84: 460 53.84 - 80.76: 38 80.76 - 107.68: 17 107.68 - 134.60: 8 Dihedral angle restraints: 14923 sinusoidal: 5811 harmonic: 9112 Sorted by residual: dihedral pdb=" CA TRP A 480 " pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta harmonic sigma weight residual 180.00 45.40 134.60 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA TRP D 480 " pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta harmonic sigma weight residual 180.00 45.45 134.55 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA TRP C 297 " pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta harmonic sigma weight residual 180.00 45.47 134.53 0 5.00e+00 4.00e-02 7.24e+02 ... (remaining 14920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3292 0.106 - 0.212: 334 0.212 - 0.318: 81 0.318 - 0.425: 43 0.425 - 0.531: 25 Chirality restraints: 3775 Sorted by residual: chirality pdb=" CBF Y01 A1206 " pdb=" CAS Y01 A1206 " pdb=" CBD Y01 A1206 " pdb=" CBH Y01 A1206 " both_signs ideal model delta sigma weight residual False -2.45 -2.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CBG Y01 C1303 " pdb=" CAQ Y01 C1303 " pdb=" CBD Y01 C1303 " pdb=" CBI Y01 C1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CBG Y01 B1205 " pdb=" CAQ Y01 B1205 " pdb=" CBD Y01 B1205 " pdb=" CBI Y01 B1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 3772 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 167 " -0.033 2.00e-02 2.50e+03 6.63e-02 4.39e+01 pdb=" C ILE C 167 " 0.115 2.00e-02 2.50e+03 pdb=" O ILE C 167 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY C 168 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 605 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO D 606 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO D 606 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 606 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 353 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C VAL A 353 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL A 353 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A 354 " 0.023 2.00e-02 2.50e+03 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 1 1.98 - 2.71: 1268 2.71 - 3.44: 32255 3.44 - 4.17: 51645 4.17 - 4.90: 88268 Nonbonded interactions: 173437 Sorted by model distance: nonbonded pdb="MG MG D1201 " pdb=" O HOH D1307 " model vdw 1.254 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH B1301 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH A1304 " model vdw 2.047 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH C1404 " model vdw 2.073 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH D1303 " model vdw 2.079 2.170 ... (remaining 173432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 346 or (resid 347 through 348 and (name N or nam \ e CA or name C or name O or name CB )) or resid 349 through 351 or (resid 352 an \ d (name N or name CA or name C or name O or name CB )) or resid 353 through 362 \ or (resid 363 through 365 and (name N or name CA or name C or name O or name CB \ )) or resid 366 through 432 or (resid 433 through 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 443 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 455 through 484 or (resi \ d 485 and (name N or name CA or name C or name O or name CB )) or resid 486 thro \ ugh 514 or (resid 515 through 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 538 or (resid 539 through 540 and (name N or nam \ e CA or name C or name O or name CB )) or resid 541 through 550 or (resid 551 an \ d (name N or name CA or name C or name O or name CB )) or resid 552 through 1068 \ or resid 1203)) selection = (chain 'B' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 346 or (resid 347 through 348 an \ d (name N or name CA or name C or name O or name CB )) or resid 349 through 353 \ or (resid 354 through 355 and (name N or name CA or name C or name O or name CB \ )) or resid 356 through 362 or (resid 363 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 439 or (resid 440 and (name \ N or name CA or name C or name O or name CB )) or resid 441 through 443 or (resi \ d 454 and (name N or name CA or name C or name O or name CB )) or resid 455 thro \ ugh 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) o \ r resid 486 through 514 or (resid 515 through 516 and (name N or name CA or name \ C or name O or name CB )) or resid 517 through 522 or (resid 523 and (name N or \ name CA or name C or name O or name CB )) or resid 524 through 538 or (resid 53 \ 9 through 540 and (name N or name CA or name C or name O or name CB )) or resid \ 541 through 1068 or resid 1203)) selection = (chain 'C' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 163 or (resid 164 through 165 an \ d (name N or name CA or name C or name O or name CB )) or resid 166 through 170 \ or (resid 171 through 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 179 or (resid 180 through 182 and (name N or name CA or \ name C or name O or name CB )) or resid 183 through 232 or (resid 233 through 23 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 235 through \ 249 or (resid 250 through 251 and (name N or name CA or name C or name O or name \ CB )) or resid 252 through 256 or (resid 257 and (name N or name CA or name C o \ r name O or name CB )) or resid 258 through 300 or (resid 301 through 302 and (n \ ame N or name CA or name C or name O or name CB )) or resid 303 through 331 or ( \ resid 332 through 333 and (name N or name CA or name C or name O or name CB )) o \ r resid 334 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 355 or (resid 356 through 357 and (name N or \ name CA or name C or name O or name CB )) or resid 358 through 885 or resid 130 \ 3)) selection = (chain 'D' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 353 or (resid 354 through 355 an \ d (name N or name CA or name C or name O or name CB )) or resid 356 through 433 \ or (resid 434 and (name N or name CA or name C or name O or name CB )) or resid \ 435 through 439 or (resid 440 and (name N or name CA or name C or name O or name \ CB )) or resid 441 through 443 or (resid 454 and (name N or name CA or name C o \ r name O or name CB )) or resid 455 through 550 or (resid 551 and (name N or nam \ e CA or name C or name O or name CB )) or resid 552 through 605 or (resid 606 an \ d (name N or name CA or name C or name O or name CB )) or resid 607 through 1068 \ or resid 1203)) } 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: 0.780 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: 0.020 Extract box with map and model: 4.750 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 55.480 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.011 0.145 23645 Z= 0.718 Angle : 1.676 19.383 32229 Z= 0.897 Chirality : 0.092 0.531 3775 Planarity : 0.009 0.135 3968 Dihedral : 13.875 134.605 8951 Min Nonbonded Distance : 1.254 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % Rotamer: Outliers : 0.57 % Allowed : 5.51 % Favored : 93.92 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.33 % Twisted Proline : 3.70 % Twisted General : 3.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.12), residues: 2528 helix: -3.51 (0.09), residues: 1578 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 868 HIS 0.009 0.002 HIS D 415 PHE 0.041 0.003 PHE D 999 TYR 0.035 0.003 TYR A 708 ARG 0.011 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 628 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ILE cc_start: 0.7732 (mt) cc_final: 0.7529 (mt) REVERT: A 429 MET cc_start: 0.5428 (ppp) cc_final: 0.5004 (ppp) REVERT: A 513 THR cc_start: 0.7569 (p) cc_final: 0.7087 (t) REVERT: A 586 MET cc_start: 0.8072 (mtt) cc_final: 0.7793 (mtm) REVERT: A 753 LYS cc_start: 0.6326 (mttt) cc_final: 0.6071 (mttm) REVERT: A 818 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8793 (tp) REVERT: A 1006 LYS cc_start: 0.8394 (mttt) cc_final: 0.7619 (mttt) REVERT: A 1010 ASP cc_start: 0.7502 (m-30) cc_final: 0.7288 (m-30) REVERT: A 1045 MET cc_start: 0.8244 (tmm) cc_final: 0.7629 (tmm) REVERT: B 374 ILE cc_start: 0.7987 (mt) cc_final: 0.7615 (tp) REVERT: B 429 MET cc_start: 0.6810 (ppp) cc_final: 0.6566 (ppp) REVERT: B 518 LYS cc_start: 0.8585 (tttt) cc_final: 0.8330 (ttpp) REVERT: B 561 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8030 (ptpt) REVERT: B 583 ASP cc_start: 0.8034 (m-30) cc_final: 0.7758 (m-30) REVERT: B 1010 ASP cc_start: 0.7845 (m-30) cc_final: 0.7591 (m-30) REVERT: C 162 ILE cc_start: 0.8565 (mt) cc_final: 0.8313 (mt) REVERT: C 408 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5782 (mmm) REVERT: C 533 MET cc_start: 0.7612 (mmm) cc_final: 0.7356 (mmm) REVERT: C 623 ASN cc_start: 0.8543 (t0) cc_final: 0.8191 (t0) REVERT: C 689 LYS cc_start: 0.7215 (mttt) cc_final: 0.6845 (tptp) REVERT: C 745 ASN cc_start: 0.8763 (t160) cc_final: 0.8445 (m-40) REVERT: C 823 LYS cc_start: 0.8383 (mttt) cc_final: 0.7842 (mttt) REVERT: C 827 ASP cc_start: 0.7339 (m-30) cc_final: 0.7066 (m-30) REVERT: C 853 ARG cc_start: 0.8303 (tmm-80) cc_final: 0.8032 (ttp-170) REVERT: C 862 MET cc_start: 0.8409 (tmm) cc_final: 0.8166 (tmm) REVERT: D 354 ILE cc_start: 0.7951 (mp) cc_final: 0.7546 (mp) REVERT: D 429 MET cc_start: 0.6572 (ppp) cc_final: 0.6299 (ppp) REVERT: D 470 MET cc_start: 0.8256 (mmm) cc_final: 0.7651 (mmm) REVERT: D 487 MET cc_start: 0.9020 (tmt) cc_final: 0.8784 (tmm) REVERT: D 598 LYS cc_start: 0.8139 (mttt) cc_final: 0.7821 (ptmm) REVERT: D 767 THR cc_start: 0.8173 (p) cc_final: 0.7929 (p) REVERT: D 1039 PHE cc_start: 0.8402 (t80) cc_final: 0.8171 (t80) outliers start: 11 outliers final: 2 residues processed: 637 average time/residue: 0.3309 time to fit residues: 326.5267 Evaluate side-chains 431 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 427 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 576 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 146 optimal weight: 0.0970 chunk 179 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 578 GLN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A1005 GLN A1048 GLN B 395 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 553 ASN B 578 GLN B 590 ASN B 806 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 395 GLN C 540 GLN C 580 ASN C 745 ASN C 865 GLN D 395 GLN D 522 ASN D 538 GLN D 553 ASN D 578 GLN D 590 ASN D 763 ASN ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN D1014 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23645 Z= 0.262 Angle : 0.996 14.633 32229 Z= 0.501 Chirality : 0.050 0.291 3775 Planarity : 0.005 0.085 3968 Dihedral : 10.960 98.145 4675 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.94 % Favored : 90.15 % Rotamer: Outliers : 4.73 % Allowed : 11.59 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.15 % Twisted Proline : 3.70 % Twisted General : 1.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.15), residues: 2528 helix: -1.96 (0.11), residues: 1682 sheet: None (None), residues: 0 loop : -3.95 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 949 HIS 0.004 0.001 HIS C 232 PHE 0.024 0.002 PHE D 478 TYR 0.024 0.002 TYR D 960 ARG 0.007 0.001 ARG D1034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 483 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: A 353 VAL cc_start: 0.8197 (t) cc_final: 0.7952 (p) REVERT: A 591 MET cc_start: 0.4887 (ptp) cc_final: 0.4128 (ptp) REVERT: A 818 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8919 (tp) REVERT: A 958 MET cc_start: 0.8682 (mmm) cc_final: 0.8402 (mmm) REVERT: A 1006 LYS cc_start: 0.8386 (mttt) cc_final: 0.7806 (ttpt) REVERT: A 1007 LYS cc_start: 0.8404 (mttt) cc_final: 0.8079 (tmtt) REVERT: B 307 LEU cc_start: 0.8452 (tp) cc_final: 0.8204 (tt) REVERT: B 314 GLU cc_start: 0.7958 (tp30) cc_final: 0.7707 (tp30) REVERT: B 429 MET cc_start: 0.6941 (ppp) cc_final: 0.6661 (ppp) REVERT: B 561 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7844 (mttm) REVERT: B 1006 LYS cc_start: 0.8459 (mttt) cc_final: 0.8062 (mttt) REVERT: C 246 MET cc_start: 0.6572 (ppp) cc_final: 0.6019 (ppp) REVERT: C 257 ARG cc_start: 0.7468 (mtp180) cc_final: 0.7220 (mtm-85) REVERT: C 358 THR cc_start: 0.8900 (p) cc_final: 0.8699 (p) REVERT: C 378 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7664 (mttp) REVERT: C 408 MET cc_start: 0.6351 (mmm) cc_final: 0.6080 (mmm) REVERT: C 651 MET cc_start: 0.8689 (ttm) cc_final: 0.8415 (mtt) REVERT: C 745 ASN cc_start: 0.8731 (t0) cc_final: 0.8493 (m-40) REVERT: C 780 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7257 (mmmt) REVERT: C 823 LYS cc_start: 0.8507 (mttt) cc_final: 0.7559 (tppt) REVERT: C 824 LYS cc_start: 0.8528 (mttt) cc_final: 0.7942 (tmtt) REVERT: C 835 MET cc_start: 0.8424 (ttm) cc_final: 0.8224 (ttm) REVERT: C 860 GLU cc_start: 0.6415 (mm-30) cc_final: 0.6030 (mm-30) REVERT: D 429 MET cc_start: 0.7143 (ppp) cc_final: 0.6494 (ppp) REVERT: D 533 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 538 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7612 (pp30) REVERT: D 561 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7597 (mttm) REVERT: D 598 LYS cc_start: 0.8025 (mttt) cc_final: 0.7617 (ptmm) REVERT: D 818 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8893 (tp) REVERT: D 1006 LYS cc_start: 0.8333 (mttt) cc_final: 0.7822 (ttpt) REVERT: D 1043 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5225 (mm-30) outliers start: 91 outliers final: 42 residues processed: 542 average time/residue: 0.3222 time to fit residues: 277.2890 Evaluate side-chains 445 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 400 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1012 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 865 GLN Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 538 GLN Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 0.0040 chunk 302 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 277 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 522 ASN B 538 GLN B 896 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 GLN D 590 ASN D 763 ASN ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23645 Z= 0.324 Angle : 0.998 14.815 32229 Z= 0.497 Chirality : 0.051 0.313 3775 Planarity : 0.005 0.068 3968 Dihedral : 10.449 96.742 4668 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.36 % Favored : 88.77 % Rotamer: Outliers : 5.93 % Allowed : 13.93 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.23 % Twisted Proline : 3.70 % Twisted General : 1.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.16), residues: 2528 helix: -1.27 (0.12), residues: 1666 sheet: None (None), residues: 0 loop : -3.82 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 480 HIS 0.005 0.001 HIS A 415 PHE 0.024 0.002 PHE A 777 TYR 0.030 0.002 TYR C 525 ARG 0.005 0.001 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 449 time to evaluate : 2.337 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.5785 (ppp) cc_final: 0.4917 (ppp) REVERT: A 470 MET cc_start: 0.8848 (mmm) cc_final: 0.8499 (mmm) REVERT: A 591 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.4743 (ptp) REVERT: A 710 PHE cc_start: 0.9122 (t80) cc_final: 0.8889 (t80) REVERT: A 872 LYS cc_start: 0.7206 (mttt) cc_final: 0.6122 (mptt) REVERT: A 882 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7492 (pt) REVERT: A 1003 GLU cc_start: 0.7394 (pm20) cc_final: 0.7128 (pm20) REVERT: B 353 VAL cc_start: 0.7461 (p) cc_final: 0.7025 (t) REVERT: B 429 MET cc_start: 0.7149 (ppp) cc_final: 0.6531 (ppp) REVERT: B 561 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8111 (mttm) REVERT: B 707 LEU cc_start: 0.8757 (mt) cc_final: 0.8469 (mt) REVERT: B 882 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7605 (pt) REVERT: B 1044 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8064 (mm-40) REVERT: C 246 MET cc_start: 0.6619 (ppp) cc_final: 0.6005 (ppp) REVERT: C 257 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7455 (mtm-85) REVERT: C 378 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7817 (mttm) REVERT: C 745 ASN cc_start: 0.8719 (t0) cc_final: 0.8479 (m-40) REVERT: C 823 LYS cc_start: 0.8527 (mttt) cc_final: 0.8004 (tppt) REVERT: C 824 LYS cc_start: 0.8574 (mttt) cc_final: 0.8271 (tmtt) REVERT: C 860 GLU cc_start: 0.5765 (mm-30) cc_final: 0.5352 (mm-30) REVERT: D 375 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6539 (t80) REVERT: D 429 MET cc_start: 0.7498 (ppp) cc_final: 0.7124 (ppp) REVERT: D 533 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7513 (tm-30) REVERT: D 561 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7837 (mttm) REVERT: D 818 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8960 (tp) REVERT: D 1043 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5774 (mm-30) outliers start: 114 outliers final: 66 residues processed: 518 average time/residue: 0.3033 time to fit residues: 252.9543 Evaluate side-chains 460 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 389 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 807 ILE Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1008 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1049 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 145 optimal weight: 0.0050 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 0.0970 chunk 281 optimal weight: 5.9990 chunk 297 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 266 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 763 ASN A 806 ASN A 837 ASN B 461 ASN B 481 GLN B 877 HIS ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN C 355 GLN C 580 ASN C 753 ASN C 831 GLN D 395 GLN D 473 GLN D 482 HIS ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 ASN ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23645 Z= 0.198 Angle : 0.900 13.890 32229 Z= 0.452 Chirality : 0.047 0.273 3775 Planarity : 0.004 0.057 3968 Dihedral : 9.671 87.046 4668 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.06 % Favored : 90.19 % Rotamer: Outliers : 4.73 % Allowed : 17.15 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.31 % Twisted Proline : 0.93 % Twisted General : 0.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.16), residues: 2528 helix: -0.76 (0.13), residues: 1668 sheet: None (None), residues: 0 loop : -3.81 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 480 HIS 0.003 0.001 HIS A 482 PHE 0.023 0.002 PHE A1039 TYR 0.020 0.001 TYR D 708 ARG 0.006 0.000 ARG B1034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 435 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.5770 (ppp) cc_final: 0.5032 (ppp) REVERT: A 470 MET cc_start: 0.8767 (mmm) cc_final: 0.8465 (mmm) REVERT: A 561 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7705 (mttp) REVERT: A 567 ARG cc_start: 0.6887 (ttp-110) cc_final: 0.6625 (ptp90) REVERT: A 731 ILE cc_start: 0.8962 (mt) cc_final: 0.8628 (mt) REVERT: A 882 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7251 (pt) REVERT: A 1003 GLU cc_start: 0.7358 (pm20) cc_final: 0.7122 (pm20) REVERT: B 429 MET cc_start: 0.7020 (ppp) cc_final: 0.6356 (ppp) REVERT: B 561 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7916 (mttp) REVERT: B 723 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: B 872 LYS cc_start: 0.7332 (mttt) cc_final: 0.6743 (tptp) REVERT: B 882 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7240 (pt) REVERT: B 1044 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8069 (mm-40) REVERT: C 246 MET cc_start: 0.6699 (ppp) cc_final: 0.6110 (ppp) REVERT: C 257 ARG cc_start: 0.7500 (mtp180) cc_final: 0.7269 (mtm-85) REVERT: C 355 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7670 (pp30) REVERT: C 378 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7845 (mttp) REVERT: C 635 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8906 (tp) REVERT: C 651 MET cc_start: 0.8545 (ttm) cc_final: 0.8260 (mtt) REVERT: C 699 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7152 (pt) REVERT: C 728 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9236 (m) REVERT: C 745 ASN cc_start: 0.8933 (t0) cc_final: 0.8681 (m-40) REVERT: C 823 LYS cc_start: 0.8265 (mttt) cc_final: 0.7904 (tppt) REVERT: C 824 LYS cc_start: 0.8578 (mttt) cc_final: 0.8248 (tmtt) REVERT: D 375 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6435 (t80) REVERT: D 429 MET cc_start: 0.7372 (ppp) cc_final: 0.7002 (ppp) REVERT: D 470 MET cc_start: 0.8657 (mmm) cc_final: 0.8222 (mmp) REVERT: D 533 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7341 (tm-30) REVERT: D 561 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7934 (mttm) REVERT: D 758 PHE cc_start: 0.8322 (m-80) cc_final: 0.8031 (m-80) REVERT: D 773 PHE cc_start: 0.8583 (t80) cc_final: 0.8346 (t80) REVERT: D 818 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8931 (tp) REVERT: D 834 MET cc_start: 0.8494 (ttm) cc_final: 0.8214 (mtt) REVERT: D 882 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7270 (pt) REVERT: D 911 THR cc_start: 0.9515 (OUTLIER) cc_final: 0.9156 (m) REVERT: D 1006 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7195 (tppt) REVERT: D 1036 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.8230 (ttp80) REVERT: D 1043 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5631 (mm-30) outliers start: 91 outliers final: 63 residues processed: 492 average time/residue: 0.3218 time to fit residues: 250.7921 Evaluate side-chains 463 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 389 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 723 GLN Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1042 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.0370 chunk 267 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 763 ASN A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1044 GLN B1048 GLN C 580 ASN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1057 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23645 Z= 0.215 Angle : 0.892 13.519 32229 Z= 0.448 Chirality : 0.048 0.272 3775 Planarity : 0.004 0.058 3968 Dihedral : 9.402 83.312 4668 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.01 % Favored : 89.32 % Rotamer: Outliers : 4.83 % Allowed : 20.22 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.31 % Twisted Proline : 0.93 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2528 helix: -0.43 (0.13), residues: 1640 sheet: None (None), residues: 0 loop : -3.77 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 297 HIS 0.004 0.001 HIS A 482 PHE 0.029 0.002 PHE C 295 TYR 0.015 0.001 TYR D 960 ARG 0.005 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 418 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5695 (ppp) cc_final: 0.4939 (ppp) REVERT: A 470 MET cc_start: 0.8840 (mmm) cc_final: 0.8531 (mmm) REVERT: A 561 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7817 (mttp) REVERT: A 591 MET cc_start: 0.4401 (ptp) cc_final: 0.3239 (tpp) REVERT: A 882 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7176 (pt) REVERT: A 1003 GLU cc_start: 0.7356 (pm20) cc_final: 0.6849 (pm20) REVERT: A 1004 ASP cc_start: 0.6765 (m-30) cc_final: 0.5959 (m-30) REVERT: B 353 VAL cc_start: 0.7197 (p) cc_final: 0.6974 (t) REVERT: B 429 MET cc_start: 0.7117 (ppp) cc_final: 0.6400 (ppp) REVERT: B 561 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8066 (mttp) REVERT: B 872 LYS cc_start: 0.7149 (mttt) cc_final: 0.6675 (tptp) REVERT: B 882 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7107 (pt) REVERT: B 1005 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8374 (mt0) REVERT: B 1044 GLN cc_start: 0.8465 (tm130) cc_final: 0.7993 (mm-40) REVERT: C 246 MET cc_start: 0.6806 (ppp) cc_final: 0.6174 (ppp) REVERT: C 378 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8053 (mttm) REVERT: C 635 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8865 (tp) REVERT: C 651 MET cc_start: 0.8548 (ttm) cc_final: 0.8249 (mtt) REVERT: C 699 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7148 (pt) REVERT: C 728 THR cc_start: 0.9571 (OUTLIER) cc_final: 0.9255 (m) REVERT: C 823 LYS cc_start: 0.8469 (mttt) cc_final: 0.8096 (tppt) REVERT: C 824 LYS cc_start: 0.8629 (mttt) cc_final: 0.8297 (tmtt) REVERT: D 314 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8205 (tp30) REVERT: D 375 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6577 (t80) REVERT: D 429 MET cc_start: 0.7305 (ppp) cc_final: 0.6631 (ppp) REVERT: D 470 MET cc_start: 0.8706 (mmm) cc_final: 0.8281 (mmp) REVERT: D 533 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7440 (tm-30) REVERT: D 545 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7645 (mmtm) REVERT: D 561 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8091 (mttm) REVERT: D 568 LEU cc_start: 0.0411 (OUTLIER) cc_final: 0.0032 (pt) REVERT: D 758 PHE cc_start: 0.8433 (m-80) cc_final: 0.8141 (m-80) REVERT: D 773 PHE cc_start: 0.8713 (t80) cc_final: 0.8468 (t80) REVERT: D 818 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8877 (tp) REVERT: D 834 MET cc_start: 0.8465 (ttm) cc_final: 0.8231 (mtt) REVERT: D 882 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7191 (pt) REVERT: D 911 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9191 (m) REVERT: D 933 PHE cc_start: 0.8405 (t80) cc_final: 0.8201 (t80) REVERT: D 966 LEU cc_start: 0.7581 (mt) cc_final: 0.7376 (mp) REVERT: D 1006 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7248 (tppt) REVERT: D 1007 LYS cc_start: 0.8394 (mttt) cc_final: 0.8109 (tmtt) REVERT: D 1043 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5606 (mm-30) outliers start: 93 outliers final: 65 residues processed: 478 average time/residue: 0.3219 time to fit residues: 244.7092 Evaluate side-chains 472 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 394 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1048 GLN Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1049 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 2.9990 chunk 268 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 156 optimal weight: 9.9990 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 461 ASN A 763 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN B1048 GLN C 580 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN D 522 ASN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 ASN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23645 Z= 0.210 Angle : 0.883 13.133 32229 Z= 0.441 Chirality : 0.047 0.263 3775 Planarity : 0.004 0.054 3968 Dihedral : 9.067 69.946 4668 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.45 % Favored : 89.75 % Rotamer: Outliers : 5.15 % Allowed : 21.62 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.43 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2528 helix: -0.30 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -3.76 (0.18), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 480 HIS 0.004 0.001 HIS D 482 PHE 0.029 0.002 PHE A 777 TYR 0.014 0.001 TYR D 960 ARG 0.005 0.000 ARG D1036 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 414 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5700 (ppp) cc_final: 0.4880 (ppp) REVERT: A 470 MET cc_start: 0.8770 (mmm) cc_final: 0.8456 (mmm) REVERT: A 845 MET cc_start: 0.8399 (ttm) cc_final: 0.8123 (ttm) REVERT: A 882 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7085 (pt) REVERT: A 922 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8297 (tp40) REVERT: A 1003 GLU cc_start: 0.7266 (pm20) cc_final: 0.6906 (pm20) REVERT: A 1004 ASP cc_start: 0.6632 (m-30) cc_final: 0.5904 (m-30) REVERT: B 429 MET cc_start: 0.7011 (ppp) cc_final: 0.6291 (ppp) REVERT: B 561 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8045 (mttp) REVERT: B 872 LYS cc_start: 0.7078 (mttt) cc_final: 0.6589 (tptt) REVERT: B 882 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7224 (pt) REVERT: B 1005 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: C 246 MET cc_start: 0.6678 (ppp) cc_final: 0.6057 (ppp) REVERT: C 378 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8114 (mttm) REVERT: C 385 LEU cc_start: 0.0628 (OUTLIER) cc_final: 0.0355 (pt) REVERT: C 635 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8850 (tp) REVERT: C 651 MET cc_start: 0.8505 (ttm) cc_final: 0.8242 (mtt) REVERT: C 699 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7100 (pt) REVERT: C 728 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9229 (m) REVERT: C 783 LEU cc_start: 0.7655 (mt) cc_final: 0.7425 (mp) REVERT: C 823 LYS cc_start: 0.8435 (mttt) cc_final: 0.8093 (tppt) REVERT: C 824 LYS cc_start: 0.8642 (mttt) cc_final: 0.8306 (tmtt) REVERT: C 861 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8213 (tm-30) REVERT: D 314 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8289 (tp30) REVERT: D 375 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6494 (t80) REVERT: D 429 MET cc_start: 0.7282 (ppp) cc_final: 0.6635 (ppp) REVERT: D 470 MET cc_start: 0.8630 (mmm) cc_final: 0.8234 (mmp) REVERT: D 533 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7506 (tm-30) REVERT: D 545 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7530 (mmtm) REVERT: D 568 LEU cc_start: 0.0586 (OUTLIER) cc_final: 0.0328 (pt) REVERT: D 818 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8852 (tp) REVERT: D 834 MET cc_start: 0.8410 (ttm) cc_final: 0.8189 (mtt) REVERT: D 882 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7297 (pt) REVERT: D 911 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9204 (m) REVERT: D 1006 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7213 (tppt) REVERT: D 1007 LYS cc_start: 0.8410 (mttt) cc_final: 0.8101 (tmtt) REVERT: D 1018 MET cc_start: 0.7992 (ttm) cc_final: 0.7635 (ttm) REVERT: D 1043 GLU cc_start: 0.5903 (mm-30) cc_final: 0.5660 (mm-30) REVERT: D 1044 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8335 (mm-40) outliers start: 99 outliers final: 71 residues processed: 479 average time/residue: 0.3209 time to fit residues: 245.0575 Evaluate side-chains 477 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 392 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 936 ASN Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 936 ASN Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1049 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 250 optimal weight: 0.0770 chunk 166 optimal weight: 0.1980 chunk 296 optimal weight: 0.0570 chunk 185 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 763 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 538 GLN B 922 GLN B 936 ASN B1014 GLN C 580 ASN C 753 ASN D 481 GLN D 538 GLN ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 ASN D1014 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23645 Z= 0.197 Angle : 0.869 12.671 32229 Z= 0.435 Chirality : 0.046 0.265 3775 Planarity : 0.004 0.056 3968 Dihedral : 8.645 67.385 4666 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.75 % Allowed : 10.13 % Favored : 89.12 % Rotamer: Outliers : 5.25 % Allowed : 22.45 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.56 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2528 helix: -0.10 (0.14), residues: 1653 sheet: None (None), residues: 0 loop : -3.59 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 480 HIS 0.003 0.001 HIS A 482 PHE 0.026 0.001 PHE A 777 TYR 0.013 0.001 TYR D 960 ARG 0.006 0.000 ARG D1036 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 413 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5926 (ppp) cc_final: 0.5140 (ppp) REVERT: A 470 MET cc_start: 0.8764 (mmm) cc_final: 0.8477 (mmm) REVERT: A 538 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7871 (pp30) REVERT: A 591 MET cc_start: 0.4539 (tpt) cc_final: 0.3713 (mtp) REVERT: A 882 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7037 (pt) REVERT: A 1006 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7306 (tppt) REVERT: A 1025 ASP cc_start: 0.7035 (t70) cc_final: 0.6813 (t70) REVERT: B 429 MET cc_start: 0.6729 (ppp) cc_final: 0.6064 (ppp) REVERT: B 470 MET cc_start: 0.8797 (mmm) cc_final: 0.8515 (mmp) REVERT: B 561 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8005 (mttp) REVERT: B 568 LEU cc_start: 0.0223 (OUTLIER) cc_final: -0.0152 (pt) REVERT: B 740 ARG cc_start: 0.7697 (tmm-80) cc_final: 0.5640 (mmp80) REVERT: B 882 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.6974 (pt) REVERT: B 1005 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: C 246 MET cc_start: 0.6608 (ppp) cc_final: 0.5978 (ppp) REVERT: C 257 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7312 (mtm-85) REVERT: C 385 LEU cc_start: 0.1558 (OUTLIER) cc_final: 0.1337 (pt) REVERT: C 408 MET cc_start: 0.5208 (mmm) cc_final: 0.4599 (mmp) REVERT: C 699 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7148 (pt) REVERT: C 728 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9250 (m) REVERT: C 823 LYS cc_start: 0.8328 (mttt) cc_final: 0.8107 (tppt) REVERT: C 824 LYS cc_start: 0.8657 (mttt) cc_final: 0.8336 (tmtt) REVERT: C 861 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8184 (tm-30) REVERT: D 314 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: D 375 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6527 (t80) REVERT: D 429 MET cc_start: 0.7264 (ppp) cc_final: 0.6734 (ppp) REVERT: D 470 MET cc_start: 0.8642 (mmm) cc_final: 0.8234 (mmp) REVERT: D 533 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7380 (tm-30) REVERT: D 568 LEU cc_start: 0.1275 (OUTLIER) cc_final: 0.1049 (pt) REVERT: D 773 PHE cc_start: 0.8609 (t80) cc_final: 0.8370 (t80) REVERT: D 882 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7259 (pt) REVERT: D 911 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9202 (m) REVERT: D 1006 LYS cc_start: 0.8048 (ttmt) cc_final: 0.7296 (tppt) REVERT: D 1007 LYS cc_start: 0.8386 (mttt) cc_final: 0.8127 (tmtt) outliers start: 101 outliers final: 69 residues processed: 480 average time/residue: 0.3153 time to fit residues: 239.9460 Evaluate side-chains 465 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 383 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 936 ASN Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 937 VAL Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1014 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN A 763 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 936 ASN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23645 Z= 0.256 Angle : 0.904 13.856 32229 Z= 0.451 Chirality : 0.048 0.272 3775 Planarity : 0.004 0.054 3968 Dihedral : 8.673 67.876 4666 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.01 % Favored : 89.12 % Rotamer: Outliers : 5.35 % Allowed : 22.66 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.56 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.17), residues: 2528 helix: -0.10 (0.13), residues: 1651 sheet: None (None), residues: 0 loop : -3.52 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 480 HIS 0.004 0.001 HIS A 482 PHE 0.030 0.002 PHE A 777 TYR 0.015 0.001 TYR A 840 ARG 0.006 0.000 ARG C 851 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 407 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.6063 (ppp) cc_final: 0.5247 (ppp) REVERT: A 470 MET cc_start: 0.8782 (mmm) cc_final: 0.8470 (mmm) REVERT: A 524 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 568 LEU cc_start: 0.1199 (OUTLIER) cc_final: 0.0896 (pt) REVERT: A 586 MET cc_start: 0.8238 (tpp) cc_final: 0.7842 (mmt) REVERT: A 840 TYR cc_start: 0.8748 (m-80) cc_final: 0.8378 (m-80) REVERT: A 882 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7235 (pt) REVERT: B 429 MET cc_start: 0.6926 (ppp) cc_final: 0.6256 (ppp) REVERT: B 470 MET cc_start: 0.8819 (mmm) cc_final: 0.8562 (mmp) REVERT: B 561 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8050 (mttp) REVERT: B 568 LEU cc_start: 0.0373 (OUTLIER) cc_final: -0.0040 (pt) REVERT: B 591 MET cc_start: 0.4152 (mmp) cc_final: 0.3085 (tpp) REVERT: B 740 ARG cc_start: 0.7784 (tmm-80) cc_final: 0.5775 (mmt-90) REVERT: B 882 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7158 (pt) REVERT: B 1005 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: C 246 MET cc_start: 0.6513 (ppp) cc_final: 0.5940 (ppp) REVERT: C 257 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7330 (mtm-85) REVERT: C 350 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 385 LEU cc_start: 0.1330 (OUTLIER) cc_final: 0.1125 (pt) REVERT: C 408 MET cc_start: 0.5048 (mmm) cc_final: 0.4525 (mmp) REVERT: C 699 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7076 (pt) REVERT: C 728 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9182 (m) REVERT: C 823 LYS cc_start: 0.8363 (mttt) cc_final: 0.8091 (tppt) REVERT: C 824 LYS cc_start: 0.8686 (mttt) cc_final: 0.8332 (tmtt) REVERT: D 375 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6645 (t80) REVERT: D 429 MET cc_start: 0.7267 (ppp) cc_final: 0.6685 (ppp) REVERT: D 470 MET cc_start: 0.8694 (mmm) cc_final: 0.8303 (mmp) REVERT: D 533 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7658 (tm-30) REVERT: D 568 LEU cc_start: 0.1336 (OUTLIER) cc_final: 0.1074 (pt) REVERT: D 882 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7164 (pt) REVERT: D 911 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9166 (m) REVERT: D 1006 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7313 (tppt) REVERT: D 1007 LYS cc_start: 0.8446 (mttt) cc_final: 0.8165 (tmtt) REVERT: D 1018 MET cc_start: 0.7987 (ttm) cc_final: 0.7729 (ttm) REVERT: D 1041 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7844 (ttm110) outliers start: 103 outliers final: 76 residues processed: 474 average time/residue: 0.3302 time to fit residues: 250.9347 Evaluate side-chains 483 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 394 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 936 ASN Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 937 VAL Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1048 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 166 optimal weight: 0.0270 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 275 optimal weight: 0.2980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 ASN A 806 ASN A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 461 ASN B 538 GLN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN C 580 ASN C 753 ASN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 ASN D1005 GLN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23645 Z= 0.204 Angle : 0.876 12.978 32229 Z= 0.439 Chirality : 0.047 0.278 3775 Planarity : 0.004 0.054 3968 Dihedral : 8.476 65.565 4666 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.85 % Favored : 89.32 % Rotamer: Outliers : 4.78 % Allowed : 24.38 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.56 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2528 helix: -0.03 (0.13), residues: 1678 sheet: None (None), residues: 0 loop : -3.55 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 480 HIS 0.003 0.001 HIS A 482 PHE 0.032 0.002 PHE A 478 TYR 0.016 0.001 TYR B 840 ARG 0.006 0.000 ARG D1036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 416 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5880 (ppp) cc_final: 0.5169 (ppp) REVERT: A 470 MET cc_start: 0.8749 (mmm) cc_final: 0.8469 (mmm) REVERT: A 586 MET cc_start: 0.8176 (tpp) cc_final: 0.7881 (mmt) REVERT: A 840 TYR cc_start: 0.8731 (m-80) cc_final: 0.8457 (m-80) REVERT: A 882 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6975 (pt) REVERT: A 1006 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7326 (tppt) REVERT: B 429 MET cc_start: 0.6836 (ppp) cc_final: 0.6144 (ppp) REVERT: B 470 MET cc_start: 0.8779 (mmm) cc_final: 0.8530 (mmp) REVERT: B 561 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8044 (mttp) REVERT: B 568 LEU cc_start: 0.0537 (OUTLIER) cc_final: 0.0219 (pt) REVERT: B 591 MET cc_start: 0.3915 (mmp) cc_final: 0.2945 (tpp) REVERT: B 882 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7076 (pt) REVERT: B 1005 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: B 1044 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7926 (mp10) REVERT: C 246 MET cc_start: 0.6756 (ppp) cc_final: 0.6087 (ppp) REVERT: C 257 ARG cc_start: 0.7556 (mtm180) cc_final: 0.7309 (mtm-85) REVERT: C 385 LEU cc_start: 0.1048 (OUTLIER) cc_final: 0.0820 (pt) REVERT: C 699 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7127 (pt) REVERT: C 728 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9224 (m) REVERT: C 824 LYS cc_start: 0.8644 (mttt) cc_final: 0.8347 (tmtt) REVERT: D 375 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6678 (t80) REVERT: D 429 MET cc_start: 0.7270 (ppp) cc_final: 0.6739 (ppp) REVERT: D 470 MET cc_start: 0.8616 (mmm) cc_final: 0.8217 (mmp) REVERT: D 533 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7570 (tm-30) REVERT: D 568 LEU cc_start: 0.1193 (OUTLIER) cc_final: 0.0928 (pt) REVERT: D 760 ASP cc_start: 0.8289 (t0) cc_final: 0.7871 (t0) REVERT: D 882 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7211 (pt) REVERT: D 911 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9199 (m) REVERT: D 1006 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7332 (tppt) REVERT: D 1007 LYS cc_start: 0.8473 (mttt) cc_final: 0.8164 (tmtt) REVERT: D 1041 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7920 (ttm110) outliers start: 92 outliers final: 73 residues processed: 478 average time/residue: 0.3140 time to fit residues: 239.0799 Evaluate side-chains 477 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 393 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 936 ASN Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 936 ASN Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.9990 chunk 292 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 306 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 763 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 538 GLN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN C 278 ASN C 355 GLN C 580 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 ASN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23645 Z= 0.263 Angle : 0.911 14.160 32229 Z= 0.455 Chirality : 0.049 0.283 3775 Planarity : 0.005 0.055 3968 Dihedral : 8.562 66.546 4666 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.93 % Favored : 89.16 % Rotamer: Outliers : 5.09 % Allowed : 24.17 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.56 % Twisted Proline : 0.93 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2528 helix: -0.03 (0.13), residues: 1675 sheet: None (None), residues: 0 loop : -3.42 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 297 HIS 0.004 0.001 HIS A 482 PHE 0.034 0.002 PHE C 295 TYR 0.019 0.001 TYR B 840 ARG 0.006 0.000 ARG D1036 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 407 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.6114 (ppp) cc_final: 0.5353 (ppp) REVERT: A 470 MET cc_start: 0.8778 (mmm) cc_final: 0.8476 (mmm) REVERT: A 586 MET cc_start: 0.8261 (tpp) cc_final: 0.7916 (mmt) REVERT: A 840 TYR cc_start: 0.8804 (m-80) cc_final: 0.8534 (m-80) REVERT: A 882 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7122 (pt) REVERT: A 1006 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7504 (tppt) REVERT: B 429 MET cc_start: 0.6890 (ppp) cc_final: 0.6144 (ppp) REVERT: B 470 MET cc_start: 0.8826 (mmm) cc_final: 0.8583 (mmp) REVERT: B 524 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.6998 (t80) REVERT: B 568 LEU cc_start: 0.1204 (OUTLIER) cc_final: 0.0892 (pt) REVERT: B 591 MET cc_start: 0.3731 (mmp) cc_final: 0.2866 (tpp) REVERT: B 740 ARG cc_start: 0.7796 (tmm-80) cc_final: 0.5699 (mmt-90) REVERT: B 882 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7133 (pt) REVERT: B 1005 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: C 246 MET cc_start: 0.6538 (ppp) cc_final: 0.5950 (ppp) REVERT: C 350 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 355 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: C 385 LEU cc_start: 0.2052 (OUTLIER) cc_final: 0.1828 (pt) REVERT: C 408 MET cc_start: 0.3795 (mmp) cc_final: 0.2855 (tpp) REVERT: C 699 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7041 (pt) REVERT: C 728 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9195 (m) REVERT: C 823 LYS cc_start: 0.8369 (tppt) cc_final: 0.7971 (ttpt) REVERT: C 824 LYS cc_start: 0.8685 (mttt) cc_final: 0.8352 (tmtt) REVERT: D 314 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: D 375 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6750 (t80) REVERT: D 429 MET cc_start: 0.7341 (ppp) cc_final: 0.6812 (ppp) REVERT: D 470 MET cc_start: 0.8678 (mmm) cc_final: 0.8299 (mmp) REVERT: D 533 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7634 (tm-30) REVERT: D 568 LEU cc_start: 0.2004 (OUTLIER) cc_final: 0.1784 (pt) REVERT: D 760 ASP cc_start: 0.8359 (t0) cc_final: 0.8012 (t0) REVERT: D 882 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7298 (pt) REVERT: D 911 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9184 (m) REVERT: D 923 TYR cc_start: 0.7482 (t80) cc_final: 0.7187 (m-80) REVERT: D 1006 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7375 (tppt) REVERT: D 1007 LYS cc_start: 0.8500 (mttt) cc_final: 0.8182 (tmtt) REVERT: D 1018 MET cc_start: 0.8059 (ttm) cc_final: 0.7811 (ttm) REVERT: D 1041 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7954 (ttm110) outliers start: 98 outliers final: 78 residues processed: 473 average time/residue: 0.3193 time to fit residues: 240.7528 Evaluate side-chains 490 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 398 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 936 ASN Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 816 PHE Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 471 LYS Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.9990 chunk 260 optimal weight: 0.0020 chunk 74 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 896 ASN D 936 ASN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.165182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134024 restraints weight = 33616.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136552 restraints weight = 19854.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137763 restraints weight = 13760.567| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 23645 Z= 0.319 Angle : 1.138 59.199 32229 Z= 0.624 Chirality : 0.049 0.475 3775 Planarity : 0.006 0.171 3968 Dihedral : 8.557 66.572 4666 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.01 % Favored : 89.08 % Rotamer: Outliers : 4.99 % Allowed : 24.53 % Favored : 70.48 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.56 % Twisted Proline : 0.93 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2528 helix: -0.02 (0.13), residues: 1675 sheet: None (None), residues: 0 loop : -3.42 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 297 HIS 0.004 0.001 HIS A 482 PHE 0.026 0.002 PHE A 777 TYR 0.018 0.001 TYR B 840 ARG 0.005 0.000 ARG D1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.67 seconds wall clock time: 89 minutes 15.47 seconds (5355.47 seconds total)