Starting phenix.real_space_refine on Fri Sep 19 05:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bwd_7297/09_2025/6bwd_7297.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bwd_7297/09_2025/6bwd_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 { model { file = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2025/6bwd_7297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2025/6bwd_7297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2025/6bwd_7297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bwd_7297/09_2025/6bwd_7297.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 8, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 5, 'ASP:plan': 4, 'TRP:plan': 2} 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: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 8, 'GLU:plan': 8, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 5, 'ASP:plan': 3, 'TRP:plan': 2} 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: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 8, 'GLU:plan': 6, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 5, 'ASP:plan': 3, 'TRP:plan': 2} 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: {'UNK:plan-1': 121, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 11, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 5, 'ASP:plan': 5, 'TRP:plan': 2} 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: 5.18, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 876.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.73 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: 3.88 Time building geometry restraints manager: 2.32 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: 0.00 - 3.88: 31018 3.88 - 7.75: 996 7.75 - 11.63: 159 11.63 - 15.51: 46 15.51 - 19.38: 10 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 Time spend for trying shortcut: 0.00 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: 0.870 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.190 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- 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 23649 Z= 0.545 Angle : 1.676 19.383 32237 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 : 13.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG A 477 TYR 0.035 0.003 TYR A 708 PHE 0.041 0.003 PHE D 999 TRP 0.032 0.004 TRP B 868 HIS 0.009 0.002 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.01139 (23645) covalent geometry : angle 1.67584 (32229) SS BOND : bond 0.00844 ( 4) SS BOND : angle 1.26265 ( 8) hydrogen bonds : bond 0.18906 ( 994) hydrogen bonds : angle 10.87707 ( 2856) *********************** 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 to be fit. rotamer outliers: 11 poor density : 628 time to evaluate : 0.862 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: 0.1601 time to fit residues: 159.4753 Evaluate side-chains 431 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 427 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 553 ASN A 578 GLN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 935 ASN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1048 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN B 578 GLN B 590 ASN B 806 ASN C 370 ASN C 395 GLN C 540 GLN C 745 ASN C 752 ASN ** C 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 GLN D 522 ASN D 553 ASN D 578 GLN D 590 ASN D1005 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.173592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144635 restraints weight = 33598.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.146974 restraints weight = 19652.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148020 restraints weight = 13054.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148511 restraints weight = 10636.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148559 restraints weight = 9743.466| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23649 Z= 0.181 Angle : 0.988 14.751 32237 Z= 0.497 Chirality : 0.050 0.282 3775 Planarity : 0.005 0.082 3968 Dihedral : 10.802 95.794 4675 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.70 % Favored : 90.39 % Rotamer: Outliers : 4.31 % Allowed : 11.33 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.19 % Twisted Proline : 2.78 % Twisted General : 1.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.95 (0.15), residues: 2528 helix: -1.93 (0.11), residues: 1676 sheet: None (None), residues: 0 loop : -3.87 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1034 TYR 0.025 0.002 TYR D 960 PHE 0.023 0.002 PHE B 418 TRP 0.023 0.002 TRP B 949 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00379 (23645) covalent geometry : angle 0.98792 (32229) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.78184 ( 8) hydrogen bonds : bond 0.04167 ( 994) hydrogen bonds : angle 5.13864 ( 2856) *********************** 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 589 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 506 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.6009 (ptp) cc_final: 0.4964 (ptp) REVERT: A 816 ASP cc_start: 0.8330 (t0) cc_final: 0.7941 (t0) REVERT: A 1006 LYS cc_start: 0.8378 (mttt) cc_final: 0.7857 (ttpt) REVERT: B 307 LEU cc_start: 0.8501 (tp) cc_final: 0.8245 (tt) REVERT: B 429 MET cc_start: 0.6669 (ppp) cc_final: 0.6469 (ppp) REVERT: B 561 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7834 (mttm) REVERT: B 755 LYS cc_start: 0.7022 (pttm) cc_final: 0.6798 (tppt) REVERT: B 891 ILE cc_start: 0.8447 (mt) cc_final: 0.8229 (mt) REVERT: B 1006 LYS cc_start: 0.8448 (mttt) cc_final: 0.8102 (mttt) REVERT: C 246 MET cc_start: 0.6380 (ppp) cc_final: 0.5871 (ppp) REVERT: C 257 ARG cc_start: 0.7341 (mtp180) cc_final: 0.7105 (mtm-85) REVERT: C 378 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7621 (mttp) REVERT: C 408 MET cc_start: 0.7007 (mmm) cc_final: 0.6777 (mmm) REVERT: C 651 MET cc_start: 0.8615 (ttm) cc_final: 0.8377 (mtt) REVERT: C 745 ASN cc_start: 0.8948 (t0) cc_final: 0.8466 (m-40) REVERT: C 780 LYS cc_start: 0.7610 (mmmt) cc_final: 0.7391 (mmmt) REVERT: C 823 LYS cc_start: 0.8486 (mttt) cc_final: 0.7605 (tppt) REVERT: C 824 LYS cc_start: 0.8607 (mttt) cc_final: 0.8018 (tmtt) REVERT: C 835 MET cc_start: 0.8438 (ttm) cc_final: 0.8227 (ttm) REVERT: C 853 ARG cc_start: 0.8296 (tmm-80) cc_final: 0.7999 (ttp-170) REVERT: C 860 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6251 (mm-30) REVERT: D 561 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7664 (mttm) REVERT: D 591 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5023 (ttm) REVERT: D 598 LYS cc_start: 0.7974 (mttt) cc_final: 0.7630 (ptmm) REVERT: D 818 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8932 (tp) REVERT: D 834 MET cc_start: 0.8475 (ttm) cc_final: 0.8238 (mtt) REVERT: D 1006 LYS cc_start: 0.8313 (mttt) cc_final: 0.7801 (ttmt) REVERT: D 1017 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7525 (tm-30) REVERT: D 1021 ASP cc_start: 0.8128 (m-30) cc_final: 0.7922 (m-30) REVERT: D 1043 GLU cc_start: 0.5974 (mm-30) cc_final: 0.5180 (mm-30) outliers start: 83 outliers final: 41 residues processed: 558 average time/residue: 0.1509 time to fit residues: 133.9327 Evaluate side-chains 459 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 416 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 385 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 D residue 308 THR Chi-restraints excluded: chain D residue 518 LYS 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 591 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 807 ILE 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 123 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 260 optimal weight: 0.0370 chunk 246 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 481 GLN B 896 ASN C 298 GLN C 861 GLN C 865 GLN D 395 GLN D 936 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141897 restraints weight = 33600.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144243 restraints weight = 21451.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145849 restraints weight = 13513.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146421 restraints weight = 10623.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146918 restraints weight = 10248.251| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23649 Z= 0.168 Angle : 0.932 13.723 32237 Z= 0.468 Chirality : 0.049 0.281 3775 Planarity : 0.005 0.062 3968 Dihedral : 10.011 93.999 4668 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.02 % Favored : 90.15 % Rotamer: Outliers : 4.73 % Allowed : 15.02 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.35 % Twisted Proline : 0.00 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.16), residues: 2528 helix: -1.20 (0.12), residues: 1667 sheet: None (None), residues: 0 loop : -3.61 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1034 TYR 0.020 0.001 TYR C 525 PHE 0.018 0.002 PHE A 777 TRP 0.025 0.002 TRP A 480 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00354 (23645) covalent geometry : angle 0.93187 (32229) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.64867 ( 8) hydrogen bonds : bond 0.03844 ( 994) hydrogen bonds : angle 4.53702 ( 2856) *********************** 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 538 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 447 time to evaluate : 0.685 Fit side-chains REVERT: A 429 MET cc_start: 0.5136 (ppp) cc_final: 0.4213 (ppp) REVERT: A 470 MET cc_start: 0.8782 (mmm) cc_final: 0.8403 (mmm) REVERT: A 487 MET cc_start: 0.8749 (tmm) cc_final: 0.8463 (ttt) REVERT: A 710 PHE cc_start: 0.8861 (t80) cc_final: 0.8583 (t80) REVERT: A 779 LEU cc_start: 0.6811 (tp) cc_final: 0.6056 (pt) REVERT: A 881 MET cc_start: 0.9010 (tpp) cc_final: 0.8201 (mmt) REVERT: A 882 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7192 (pt) REVERT: A 1035 ILE cc_start: 0.7090 (mt) cc_final: 0.6792 (mt) REVERT: B 353 VAL cc_start: 0.7057 (p) cc_final: 0.6773 (t) REVERT: B 429 MET cc_start: 0.6713 (ppp) cc_final: 0.6300 (ppp) REVERT: B 523 ASP cc_start: 0.6525 (m-30) cc_final: 0.6274 (m-30) REVERT: B 532 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7652 (tp) REVERT: B 561 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8071 (mttm) REVERT: B 1036 ARG cc_start: 0.8420 (tmm-80) cc_final: 0.8085 (ttp-170) REVERT: B 1044 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7831 (mm-40) REVERT: C 246 MET cc_start: 0.6510 (ppp) cc_final: 0.5948 (ppp) REVERT: C 257 ARG cc_start: 0.7456 (mtp180) cc_final: 0.7212 (mtm-85) REVERT: C 378 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7736 (mttm) REVERT: C 575 PHE cc_start: 0.8432 (m-80) cc_final: 0.8231 (m-80) REVERT: C 651 MET cc_start: 0.8542 (ttm) cc_final: 0.8294 (mtt) REVERT: C 708 ILE cc_start: 0.8848 (mt) cc_final: 0.8631 (mt) REVERT: C 728 THR cc_start: 0.9508 (OUTLIER) cc_final: 0.9275 (m) REVERT: C 823 LYS cc_start: 0.8480 (mttt) cc_final: 0.8033 (tppt) REVERT: C 824 LYS cc_start: 0.8576 (mttt) cc_final: 0.8019 (tmtt) REVERT: C 853 ARG cc_start: 0.8152 (tmm-80) cc_final: 0.7803 (tmm160) REVERT: D 375 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.6126 (t80) REVERT: D 400 HIS cc_start: 0.5998 (m-70) cc_final: 0.5728 (m-70) REVERT: D 561 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7857 (mttm) REVERT: D 598 LYS cc_start: 0.7997 (mttt) cc_final: 0.7632 (ptmm) REVERT: D 818 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9018 (tp) REVERT: D 834 MET cc_start: 0.8511 (ttm) cc_final: 0.8225 (mtt) REVERT: D 911 THR cc_start: 0.9578 (OUTLIER) cc_final: 0.9240 (m) REVERT: D 1017 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7433 (tm-30) REVERT: D 1021 ASP cc_start: 0.8064 (m-30) cc_final: 0.7863 (m-30) REVERT: D 1043 GLU cc_start: 0.5911 (mm-30) cc_final: 0.5322 (mm-30) outliers start: 91 outliers final: 50 residues processed: 507 average time/residue: 0.1411 time to fit residues: 114.7568 Evaluate side-chains 447 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 391 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 500 MET Chi-restraints excluded: chain A residue 562 LEU 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 818 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 926 MET 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 464 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 691 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 131 GLU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 HIS 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 614 VAL Chi-restraints excluded: chain C residue 635 LEU 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 864 ILE Chi-restraints excluded: chain C residue 865 GLN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 521 SER 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 874 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 242 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 304 optimal weight: 7.9990 chunk 307 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 806 ASN A 837 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN C 713 ASN D 482 HIS D 935 ASN D1057 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.163922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133934 restraints weight = 33748.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136404 restraints weight = 23376.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138146 restraints weight = 14518.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138452 restraints weight = 11163.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138866 restraints weight = 10625.847| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 23649 Z= 0.243 Angle : 0.986 14.684 32237 Z= 0.494 Chirality : 0.051 0.308 3775 Planarity : 0.005 0.063 3968 Dihedral : 10.048 93.406 4668 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.75 % Allowed : 10.09 % Favored : 89.16 % Rotamer: Outliers : 5.15 % Allowed : 16.68 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.31 % Twisted Proline : 0.93 % Twisted General : 0.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.16), residues: 2528 helix: -0.96 (0.13), residues: 1651 sheet: None (None), residues: 0 loop : -3.66 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1034 TYR 0.018 0.002 TYR C 525 PHE 0.036 0.002 PHE B 777 TRP 0.023 0.002 TRP D 480 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00553 (23645) covalent geometry : angle 0.98643 (32229) SS BOND : bond 0.00377 ( 4) SS BOND : angle 1.13784 ( 8) hydrogen bonds : bond 0.03987 ( 994) hydrogen bonds : angle 4.36847 ( 2856) *********************** 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 530 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 431 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.6892 (p0) cc_final: 0.6368 (t70) REVERT: A 353 VAL cc_start: 0.8214 (p) cc_final: 0.7550 (p) REVERT: A 429 MET cc_start: 0.5681 (ppp) cc_final: 0.4908 (ppp) REVERT: A 470 MET cc_start: 0.8732 (mmm) cc_final: 0.8447 (mmm) REVERT: A 505 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7513 (mmtm) REVERT: A 561 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7840 (mttp) REVERT: A 591 MET cc_start: 0.5619 (ptp) cc_final: 0.5132 (ptp) REVERT: A 837 ASN cc_start: 0.8244 (t160) cc_final: 0.8002 (t160) REVERT: A 872 LYS cc_start: 0.6996 (mttt) cc_final: 0.6240 (tptp) REVERT: A 881 MET cc_start: 0.9269 (tpp) cc_final: 0.8410 (mmt) REVERT: A 882 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7384 (pt) REVERT: B 429 MET cc_start: 0.7037 (ppp) cc_final: 0.6445 (ppp) REVERT: B 561 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8160 (mttm) REVERT: B 847 LEU cc_start: 0.9149 (tp) cc_final: 0.8949 (tp) REVERT: B 872 LYS cc_start: 0.7168 (mttt) cc_final: 0.6739 (tptp) REVERT: B 882 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7551 (pt) REVERT: B 1006 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8202 (ttpt) REVERT: B 1009 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7734 (t-90) REVERT: B 1036 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8233 (ttp-170) REVERT: B 1044 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8230 (tm-30) REVERT: C 246 MET cc_start: 0.6525 (ppp) cc_final: 0.5953 (ppp) REVERT: C 257 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7309 (mtm-85) REVERT: C 378 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8088 (mttm) REVERT: C 699 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7583 (pt) REVERT: C 728 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9103 (m) REVERT: C 775 MET cc_start: 0.8818 (mmm) cc_final: 0.8518 (mmm) REVERT: C 823 LYS cc_start: 0.8306 (mttt) cc_final: 0.7954 (tppt) REVERT: C 824 LYS cc_start: 0.8581 (mttt) cc_final: 0.8310 (tmtt) REVERT: C 853 ARG cc_start: 0.8196 (tmm-80) cc_final: 0.7886 (tmm160) REVERT: D 375 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.6186 (t80) REVERT: D 533 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 561 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8105 (mttm) REVERT: D 845 MET cc_start: 0.8380 (ttm) cc_final: 0.8070 (ttm) REVERT: D 882 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7579 (pt) REVERT: D 935 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8130 (t0) REVERT: D 1006 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7432 (tppt) REVERT: D 1007 LYS cc_start: 0.8475 (mttt) cc_final: 0.8190 (tmtt) REVERT: D 1017 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7521 (tm-30) REVERT: D 1043 GLU cc_start: 0.5709 (mm-30) cc_final: 0.5269 (mm-30) outliers start: 99 outliers final: 66 residues processed: 493 average time/residue: 0.1346 time to fit residues: 107.7431 Evaluate side-chains 473 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 399 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 927 VAL Chi-restraints excluded: chain A residue 999 PHE 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 482 HIS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 736 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 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 999 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU 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 553 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 585 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 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 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 463 LEU Chi-restraints excluded: chain D residue 482 HIS 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 754 ILE Chi-restraints excluded: chain D residue 768 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 830 MET 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 935 ASN Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1049 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 18 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 288 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 292 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN B1044 GLN B1048 GLN C 861 GLN C 865 GLN D 481 GLN D 935 ASN D 936 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135146 restraints weight = 33641.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137748 restraints weight = 22361.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138934 restraints weight = 14199.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139374 restraints weight = 11580.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139724 restraints weight = 10631.563| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23649 Z= 0.198 Angle : 0.943 14.274 32237 Z= 0.471 Chirality : 0.050 0.293 3775 Planarity : 0.004 0.055 3968 Dihedral : 9.719 88.168 4668 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.73 % Favored : 89.52 % Rotamer: Outliers : 4.73 % Allowed : 20.06 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.35 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.16), residues: 2528 helix: -0.66 (0.13), residues: 1639 sheet: None (None), residues: 0 loop : -3.65 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 569 TYR 0.021 0.001 TYR C 525 PHE 0.032 0.002 PHE A 777 TRP 0.029 0.002 TRP D 480 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00448 (23645) covalent geometry : angle 0.94260 (32229) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.60416 ( 8) hydrogen bonds : bond 0.03637 ( 994) hydrogen bonds : angle 4.20835 ( 2856) *********************** 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 506 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 415 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 312 LEU cc_start: 0.8807 (mt) cc_final: 0.8600 (mt) REVERT: A 429 MET cc_start: 0.5825 (ppp) cc_final: 0.5078 (ppp) REVERT: A 470 MET cc_start: 0.8707 (mmm) cc_final: 0.8464 (mmm) REVERT: A 505 LYS cc_start: 0.7616 (mmtm) cc_final: 0.7348 (mmtm) REVERT: A 561 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8043 (mttp) REVERT: A 591 MET cc_start: 0.5394 (ptp) cc_final: 0.4893 (ptp) REVERT: A 872 LYS cc_start: 0.6920 (mttt) cc_final: 0.6254 (tttp) REVERT: A 881 MET cc_start: 0.9277 (tpp) cc_final: 0.8243 (mmt) REVERT: A 882 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7325 (pt) REVERT: A 933 PHE cc_start: 0.8580 (t80) cc_final: 0.8106 (t80) REVERT: B 429 MET cc_start: 0.7203 (ppp) cc_final: 0.6597 (ppp) REVERT: B 545 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7574 (mmtm) REVERT: B 561 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8121 (mttm) REVERT: B 591 MET cc_start: 0.6337 (mmm) cc_final: 0.6101 (mmm) REVERT: B 847 LEU cc_start: 0.9112 (tp) cc_final: 0.8868 (tp) REVERT: B 872 LYS cc_start: 0.7179 (mttt) cc_final: 0.6713 (tptp) REVERT: B 882 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7530 (pt) REVERT: B 1006 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7349 (tppt) REVERT: B 1036 ARG cc_start: 0.8441 (tmm-80) cc_final: 0.8188 (ttp-170) REVERT: B 1044 GLN cc_start: 0.8524 (tm130) cc_final: 0.8308 (tm-30) REVERT: C 246 MET cc_start: 0.6563 (ppp) cc_final: 0.5925 (ppp) REVERT: C 287 MET cc_start: 0.8676 (mmm) cc_final: 0.8301 (mmp) REVERT: C 336 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8043 (tm-30) REVERT: C 378 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8117 (mttm) REVERT: C 699 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7417 (pt) REVERT: C 728 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9148 (m) REVERT: C 823 LYS cc_start: 0.8351 (mttt) cc_final: 0.7988 (tppt) REVERT: C 824 LYS cc_start: 0.8589 (mttt) cc_final: 0.8328 (tmtt) REVERT: C 853 ARG cc_start: 0.8101 (tmm-80) cc_final: 0.7769 (tmm160) REVERT: D 375 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6329 (t80) REVERT: D 533 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7359 (tm-30) REVERT: D 561 LYS cc_start: 0.8357 (mtmt) cc_final: 0.8111 (mttm) REVERT: D 818 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8982 (tp) REVERT: D 882 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7489 (pt) REVERT: D 911 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9119 (m) REVERT: D 935 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7784 (t0) REVERT: D 1006 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7227 (tppt) REVERT: D 1007 LYS cc_start: 0.8416 (mttt) cc_final: 0.8173 (tmtt) REVERT: D 1043 GLU cc_start: 0.5876 (mm-30) cc_final: 0.5431 (mm-30) outliers start: 91 outliers final: 72 residues processed: 473 average time/residue: 0.1402 time to fit residues: 107.4511 Evaluate side-chains 476 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 394 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 716 MET 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 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 418 PHE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 545 LYS 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 828 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 935 ASN Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain C residue 235 PHE 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 338 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 585 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 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 C residue 859 VAL Chi-restraints excluded: chain D residue 308 THR 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 463 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 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 589 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 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 935 ASN Chi-restraints excluded: chain D residue 936 ASN 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 169 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 216 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 136 optimal weight: 0.0980 chunk 242 optimal weight: 20.0000 chunk 292 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 806 ASN A 936 ASN A1005 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 935 ASN D 473 GLN D 590 ASN D 763 ASN D 935 ASN D 936 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.170119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140838 restraints weight = 33523.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142303 restraints weight = 20936.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143829 restraints weight = 14251.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144050 restraints weight = 12204.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144221 restraints weight = 10883.057| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23649 Z= 0.154 Angle : 0.891 13.333 32237 Z= 0.448 Chirality : 0.047 0.257 3775 Planarity : 0.004 0.056 3968 Dihedral : 9.180 71.398 4668 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.38 % Favored : 89.87 % Rotamer: Outliers : 4.99 % Allowed : 21.00 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.47 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.17), residues: 2528 helix: -0.38 (0.13), residues: 1652 sheet: None (None), residues: 0 loop : -3.53 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 498 TYR 0.016 0.001 TYR D 708 PHE 0.038 0.002 PHE B 934 TRP 0.029 0.002 TRP A 480 HIS 0.004 0.000 HIS D 482 Details of bonding type rmsd covalent geometry : bond 0.00318 (23645) covalent geometry : angle 0.89137 (32229) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.23697 ( 8) hydrogen bonds : bond 0.03319 ( 994) hydrogen bonds : angle 3.95948 ( 2856) *********************** 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 535 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 439 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5759 (ppp) cc_final: 0.5028 (ppp) REVERT: A 470 MET cc_start: 0.8753 (mmm) cc_final: 0.8481 (mmm) REVERT: A 1025 ASP cc_start: 0.6985 (t70) cc_final: 0.6738 (t70) REVERT: B 429 MET cc_start: 0.6901 (ppp) cc_final: 0.6314 (ppp) REVERT: B 523 ASP cc_start: 0.6551 (m-30) cc_final: 0.6233 (m-30) REVERT: B 561 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8161 (mttm) REVERT: B 777 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7302 (m-10) REVERT: B 847 LEU cc_start: 0.9108 (tp) cc_final: 0.8808 (tp) REVERT: B 872 LYS cc_start: 0.7152 (mttt) cc_final: 0.6536 (tptt) REVERT: B 1006 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7753 (tppt) REVERT: B 1009 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7547 (t-90) REVERT: B 1041 ARG cc_start: 0.8612 (tpp80) cc_final: 0.7959 (tpp80) REVERT: B 1044 GLN cc_start: 0.8508 (tm130) cc_final: 0.7868 (mm-40) REVERT: C 246 MET cc_start: 0.6543 (ppp) cc_final: 0.5860 (ppp) REVERT: C 257 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7247 (mtm-85) REVERT: C 287 MET cc_start: 0.8677 (mmm) cc_final: 0.8288 (mmp) REVERT: C 336 GLN cc_start: 0.8267 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 378 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8049 (mttm) REVERT: C 385 LEU cc_start: 0.0321 (OUTLIER) cc_final: 0.0093 (pt) REVERT: C 635 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8798 (tp) REVERT: C 651 MET cc_start: 0.8494 (ttm) cc_final: 0.8210 (mtt) REVERT: C 699 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7048 (pt) REVERT: C 728 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9224 (m) REVERT: C 739 GLN cc_start: 0.8609 (mm110) cc_final: 0.8297 (tp40) REVERT: C 823 LYS cc_start: 0.8394 (mttt) cc_final: 0.7995 (tppt) REVERT: C 824 LYS cc_start: 0.8623 (mttt) cc_final: 0.8304 (tmtt) REVERT: C 853 ARG cc_start: 0.8014 (tmm-80) cc_final: 0.7661 (tmm160) REVERT: D 375 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.6379 (t80) REVERT: D 429 MET cc_start: 0.7613 (ppp) cc_final: 0.7219 (ppp) REVERT: D 470 MET cc_start: 0.8576 (mmm) cc_final: 0.8230 (mmp) REVERT: D 568 LEU cc_start: 0.0691 (OUTLIER) cc_final: 0.0470 (pt) REVERT: D 591 MET cc_start: 0.6505 (mmm) cc_final: 0.6299 (mmt) REVERT: D 818 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8922 (tp) REVERT: D 834 MET cc_start: 0.8356 (ttm) cc_final: 0.8141 (mtt) REVERT: D 882 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7290 (pt) REVERT: D 911 THR cc_start: 0.9529 (OUTLIER) cc_final: 0.9196 (m) REVERT: D 935 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7649 (t0) REVERT: D 1006 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7297 (tppt) REVERT: D 1007 LYS cc_start: 0.8345 (mttt) cc_final: 0.8076 (tmtt) REVERT: D 1041 ARG cc_start: 0.8568 (tpp80) cc_final: 0.7937 (mtt-85) REVERT: D 1043 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5491 (mm-30) outliers start: 96 outliers final: 64 residues processed: 501 average time/residue: 0.1478 time to fit residues: 118.3641 Evaluate side-chains 464 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 388 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE 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 521 SER 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 849 LEU 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 377 SER Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 418 PHE 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 568 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 777 PHE 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 937 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 PHE 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 299 HIS 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 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 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 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 521 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 719 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 849 LEU 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 935 ASN Chi-restraints excluded: chain D residue 936 ASN Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 268 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 139 optimal weight: 0.0870 chunk 233 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 158 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 935 ASN C 739 GLN C 745 ASN ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 935 ASN D 936 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.167646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137215 restraints weight = 33501.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138798 restraints weight = 20221.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140052 restraints weight = 14104.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140721 restraints weight = 12049.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140833 restraints weight = 10600.718| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23649 Z= 0.154 Angle : 0.891 13.293 32237 Z= 0.446 Chirality : 0.047 0.263 3775 Planarity : 0.004 0.053 3968 Dihedral : 8.784 68.901 4666 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.73 % Favored : 89.68 % Rotamer: Outliers : 4.94 % Allowed : 22.51 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.51 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.17), residues: 2528 helix: -0.20 (0.13), residues: 1635 sheet: None (None), residues: 0 loop : -3.35 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 569 TYR 0.013 0.001 TYR A 840 PHE 0.026 0.002 PHE A 934 TRP 0.027 0.002 TRP A 480 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00327 (23645) covalent geometry : angle 0.89111 (32229) SS BOND : bond 0.00153 ( 4) SS BOND : angle 0.27976 ( 8) hydrogen bonds : bond 0.03307 ( 994) hydrogen bonds : angle 3.87244 ( 2856) *********************** 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 498 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 403 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5914 (ppp) cc_final: 0.5098 (ppp) REVERT: A 470 MET cc_start: 0.8701 (mmm) cc_final: 0.8418 (mmm) REVERT: A 474 VAL cc_start: 0.9338 (t) cc_final: 0.9134 (p) REVERT: A 524 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.7085 (t80) REVERT: A 882 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7242 (pt) REVERT: A 1004 ASP cc_start: 0.6713 (m-30) cc_final: 0.6341 (m-30) REVERT: B 429 MET cc_start: 0.6878 (ppp) cc_final: 0.6287 (ppp) REVERT: B 523 ASP cc_start: 0.6702 (m-30) cc_final: 0.6384 (m-30) REVERT: B 561 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8117 (mttm) REVERT: B 568 LEU cc_start: 0.0486 (OUTLIER) cc_final: 0.0117 (pt) REVERT: B 777 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: B 847 LEU cc_start: 0.9023 (tp) cc_final: 0.8694 (tp) REVERT: B 882 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7112 (pt) REVERT: B 1006 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7719 (tppt) REVERT: B 1044 GLN cc_start: 0.8460 (tm130) cc_final: 0.8256 (tm-30) REVERT: C 246 MET cc_start: 0.6587 (ppp) cc_final: 0.5925 (ppp) REVERT: C 257 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7233 (mtm-85) REVERT: C 336 GLN cc_start: 0.8265 (tm-30) cc_final: 0.8001 (tm-30) REVERT: C 385 LEU cc_start: 0.1171 (OUTLIER) cc_final: 0.0943 (pt) REVERT: C 699 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7215 (pt) REVERT: C 728 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9228 (m) REVERT: C 823 LYS cc_start: 0.8405 (mttt) cc_final: 0.8058 (tppt) REVERT: C 824 LYS cc_start: 0.8674 (mttt) cc_final: 0.8295 (tmtt) REVERT: D 375 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6479 (t80) REVERT: D 470 MET cc_start: 0.8653 (mmm) cc_final: 0.8286 (mmp) REVERT: D 568 LEU cc_start: 0.0542 (OUTLIER) cc_final: 0.0244 (pt) REVERT: D 845 MET cc_start: 0.8748 (ttm) cc_final: 0.8376 (ttp) REVERT: D 882 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7338 (pt) REVERT: D 911 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9213 (m) REVERT: D 935 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.7867 (t0) REVERT: D 1006 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7259 (tppt) REVERT: D 1007 LYS cc_start: 0.8465 (mttt) cc_final: 0.8106 (tmtt) REVERT: D 1041 ARG cc_start: 0.8500 (tpp80) cc_final: 0.7845 (mtt-85) REVERT: D 1043 GLU cc_start: 0.5886 (mm-30) cc_final: 0.5481 (mm-30) outliers start: 95 outliers final: 64 residues processed: 465 average time/residue: 0.1426 time to fit residues: 106.6867 Evaluate side-chains 463 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 386 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 524 PHE 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 882 ILE 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 377 SER Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 418 PHE 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 568 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 777 PHE 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 937 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 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 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 647 MET Chi-restraints excluded: chain C residue 666 LEU 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 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 377 SER 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 521 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 768 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 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 935 ASN Chi-restraints excluded: chain D residue 936 ASN Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 153 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN A 806 ASN A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 935 ASN C 623 ASN ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN D 936 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.154675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124211 restraints weight = 34068.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126889 restraints weight = 23694.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127535 restraints weight = 15826.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129428 restraints weight = 13047.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129414 restraints weight = 10659.335| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 23649 Z= 0.316 Angle : 1.050 14.445 32237 Z= 0.522 Chirality : 0.055 0.313 3775 Planarity : 0.005 0.064 3968 Dihedral : 9.650 76.615 4666 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.72 % Favored : 88.49 % Rotamer: Outliers : 5.87 % Allowed : 22.71 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.39 % Twisted Proline : 1.85 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.17), residues: 2528 helix: -0.53 (0.13), residues: 1659 sheet: None (None), residues: 0 loop : -3.44 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 397 TYR 0.020 0.002 TYR C 657 PHE 0.033 0.003 PHE A 478 TRP 0.028 0.002 TRP B 480 HIS 0.007 0.002 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00740 (23645) covalent geometry : angle 1.04952 (32229) SS BOND : bond 0.00375 ( 4) SS BOND : angle 1.25422 ( 8) hydrogen bonds : bond 0.04052 ( 994) hydrogen bonds : angle 4.28717 ( 2856) *********************** 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 539 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 426 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.6393 (ppp) cc_final: 0.5699 (ppp) REVERT: A 470 MET cc_start: 0.8686 (mmm) cc_final: 0.8334 (mmm) REVERT: A 505 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7503 (mmtm) REVERT: A 524 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 568 LEU cc_start: 0.0606 (OUTLIER) cc_final: 0.0305 (pt) REVERT: A 834 MET cc_start: 0.8520 (ttm) cc_final: 0.8242 (mtm) REVERT: A 872 LYS cc_start: 0.6783 (mttt) cc_final: 0.6075 (tttp) REVERT: A 1004 ASP cc_start: 0.6748 (m-30) cc_final: 0.6491 (m-30) REVERT: B 429 MET cc_start: 0.7359 (ppp) cc_final: 0.6683 (ppp) REVERT: B 524 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.7803 (t80) REVERT: B 561 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8175 (mttm) REVERT: B 568 LEU cc_start: 0.0841 (OUTLIER) cc_final: 0.0386 (pt) REVERT: B 777 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: B 872 LYS cc_start: 0.7195 (mttt) cc_final: 0.6421 (tttp) REVERT: B 882 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7578 (pt) REVERT: B 1006 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7753 (tppt) REVERT: B 1032 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7455 (mm-30) REVERT: C 180 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7940 (ttm110) REVERT: C 242 TYR cc_start: 0.7870 (m-80) cc_final: 0.7513 (m-80) REVERT: C 246 MET cc_start: 0.6814 (ppp) cc_final: 0.6100 (ppp) REVERT: C 341 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.7409 (t80) REVERT: C 350 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7815 (tm-30) REVERT: C 378 LYS cc_start: 0.8362 (mtmt) cc_final: 0.8047 (mttm) REVERT: C 385 LEU cc_start: 0.0666 (OUTLIER) cc_final: 0.0295 (pt) REVERT: C 623 ASN cc_start: 0.9076 (t0) cc_final: 0.8632 (t0) REVERT: C 699 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7669 (pt) REVERT: C 728 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9074 (m) REVERT: C 748 ILE cc_start: 0.8900 (mm) cc_final: 0.8613 (mt) REVERT: C 823 LYS cc_start: 0.8332 (mttt) cc_final: 0.7922 (tppt) REVERT: C 824 LYS cc_start: 0.8647 (mttt) cc_final: 0.8282 (tmtt) REVERT: D 375 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6424 (t80) REVERT: D 470 MET cc_start: 0.8773 (mmm) cc_final: 0.8411 (mmp) REVERT: D 524 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.7208 (t80) REVERT: D 533 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 561 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7912 (mttp) REVERT: D 568 LEU cc_start: 0.0749 (OUTLIER) cc_final: 0.0356 (pt) REVERT: D 911 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9118 (m) REVERT: D 935 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8241 (t0) REVERT: D 1006 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7355 (tppt) REVERT: D 1007 LYS cc_start: 0.8481 (mttt) cc_final: 0.8193 (tmtt) REVERT: D 1043 GLU cc_start: 0.6043 (mm-30) cc_final: 0.5600 (mm-30) outliers start: 113 outliers final: 81 residues processed: 497 average time/residue: 0.1519 time to fit residues: 121.8435 Evaluate side-chains 493 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 397 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 716 MET 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 807 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 883 PHE 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 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 463 LEU 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 524 PHE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 777 PHE 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 883 PHE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1042 VAL 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 191 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 217 HIS 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 338 SER Chi-restraints excluded: chain C residue 341 PHE 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 700 PHE 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 377 SER Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 465 ILE 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 524 PHE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 604 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 768 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 883 PHE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 936 ASN Chi-restraints excluded: chain D residue 999 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 46 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 291 optimal weight: 0.5980 chunk 180 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN C 336 GLN C 623 ASN ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN D1044 GLN D1048 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.164620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134247 restraints weight = 33594.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136389 restraints weight = 20961.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137508 restraints weight = 14802.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137928 restraints weight = 11716.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138040 restraints weight = 10703.436| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23649 Z= 0.163 Angle : 0.915 13.277 32237 Z= 0.458 Chirality : 0.047 0.263 3775 Planarity : 0.005 0.053 3968 Dihedral : 8.920 70.460 4666 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.77 % Favored : 89.48 % Rotamer: Outliers : 4.21 % Allowed : 25.42 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.43 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.17), residues: 2528 helix: -0.22 (0.13), residues: 1672 sheet: None (None), residues: 0 loop : -3.55 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 800 TYR 0.015 0.001 TYR C 657 PHE 0.024 0.002 PHE D1039 TRP 0.026 0.001 TRP A 480 HIS 0.003 0.001 HIS D 482 Details of bonding type rmsd covalent geometry : bond 0.00352 (23645) covalent geometry : angle 0.91508 (32229) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.34687 ( 8) hydrogen bonds : bond 0.03376 ( 994) hydrogen bonds : angle 3.95880 ( 2856) *********************** 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 506 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 425 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.6097 (ppp) cc_final: 0.5369 (ppp) REVERT: A 470 MET cc_start: 0.8725 (mmm) cc_final: 0.8478 (mmm) REVERT: A 524 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.7242 (t80) REVERT: A 834 MET cc_start: 0.8340 (ttm) cc_final: 0.8047 (mtm) REVERT: A 1007 LYS cc_start: 0.7608 (tmtt) cc_final: 0.7237 (tptp) REVERT: B 429 MET cc_start: 0.6897 (ppp) cc_final: 0.6318 (ppp) REVERT: B 523 ASP cc_start: 0.6691 (m-30) cc_final: 0.6414 (m-30) REVERT: B 561 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7980 (mttp) REVERT: B 568 LEU cc_start: 0.1022 (OUTLIER) cc_final: 0.0777 (pt) REVERT: B 777 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: B 872 LYS cc_start: 0.7201 (mttt) cc_final: 0.6489 (tttp) REVERT: B 882 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7234 (pt) REVERT: B 1006 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7357 (tppt) REVERT: C 246 MET cc_start: 0.6601 (ppp) cc_final: 0.5947 (ppp) REVERT: C 250 MET cc_start: 0.8120 (ptp) cc_final: 0.7670 (pmm) REVERT: C 350 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 385 LEU cc_start: 0.0754 (OUTLIER) cc_final: 0.0527 (pt) REVERT: C 699 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7154 (pt) REVERT: C 728 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9142 (m) REVERT: C 823 LYS cc_start: 0.8255 (mttt) cc_final: 0.7766 (tppt) REVERT: C 824 LYS cc_start: 0.8592 (mttt) cc_final: 0.8213 (tmtt) REVERT: C 835 MET cc_start: 0.8103 (ttm) cc_final: 0.7806 (ttm) REVERT: C 851 ARG cc_start: 0.7199 (mtt-85) cc_final: 0.6869 (mtt-85) REVERT: D 375 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6624 (t80) REVERT: D 429 MET cc_start: 0.7659 (ppp) cc_final: 0.7307 (ppp) REVERT: D 470 MET cc_start: 0.8656 (mmm) cc_final: 0.8270 (mmp) REVERT: D 533 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7529 (tm-30) REVERT: D 568 LEU cc_start: 0.0855 (OUTLIER) cc_final: 0.0576 (pt) REVERT: D 911 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9172 (m) REVERT: D 935 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7801 (t0) REVERT: D 1004 ASP cc_start: 0.6830 (m-30) cc_final: 0.6548 (m-30) REVERT: D 1006 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7263 (tppt) REVERT: D 1007 LYS cc_start: 0.8546 (mttt) cc_final: 0.8128 (tmtt) REVERT: D 1039 PHE cc_start: 0.8998 (t80) cc_final: 0.8796 (t80) REVERT: D 1041 ARG cc_start: 0.8614 (tpp80) cc_final: 0.7999 (tpp80) REVERT: D 1043 GLU cc_start: 0.5945 (mm-30) cc_final: 0.5465 (mm-30) outliers start: 81 outliers final: 55 residues processed: 476 average time/residue: 0.1504 time to fit residues: 115.2928 Evaluate side-chains 479 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 413 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 524 PHE 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 849 LEU Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 937 VAL 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 463 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 777 PHE 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 999 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1042 VAL 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 280 LEU Chi-restraints excluded: chain C residue 299 HIS 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 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 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 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 463 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 719 LEU 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 883 PHE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 999 PHE Chi-restraints excluded: chain D residue 1048 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 142 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 275 optimal weight: 0.6980 chunk 193 optimal weight: 4.9990 chunk 287 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 935 ASN ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 896 ASN D 935 ASN D 936 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132115 restraints weight = 33719.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134995 restraints weight = 22357.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136182 restraints weight = 13613.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137195 restraints weight = 11111.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137642 restraints weight = 10032.664| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23649 Z= 0.171 Angle : 0.924 14.154 32237 Z= 0.461 Chirality : 0.048 0.263 3775 Planarity : 0.005 0.073 3968 Dihedral : 8.738 70.255 4666 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.45 % Favored : 89.72 % Rotamer: Outliers : 4.11 % Allowed : 25.99 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.47 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.17), residues: 2528 helix: -0.17 (0.13), residues: 1668 sheet: None (None), residues: 0 loop : -3.30 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 800 TYR 0.017 0.001 TYR C 657 PHE 0.023 0.002 PHE A 934 TRP 0.021 0.002 TRP A 480 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00378 (23645) covalent geometry : angle 0.92367 (32229) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.36167 ( 8) hydrogen bonds : bond 0.03370 ( 994) hydrogen bonds : angle 3.88592 ( 2856) ********************** 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 492 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 413 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.6138 (ppp) cc_final: 0.5404 (ppp) REVERT: A 470 MET cc_start: 0.8797 (mmm) cc_final: 0.8539 (mmm) REVERT: A 524 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.7259 (t80) REVERT: A 1007 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7246 (tptp) REVERT: B 429 MET cc_start: 0.6892 (ppp) cc_final: 0.6324 (ppp) REVERT: B 523 ASP cc_start: 0.6737 (m-30) cc_final: 0.6441 (m-30) REVERT: B 568 LEU cc_start: 0.1050 (OUTLIER) cc_final: 0.0816 (pt) REVERT: B 719 LEU cc_start: 0.8051 (mt) cc_final: 0.7824 (mp) REVERT: B 777 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: B 882 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7263 (pt) REVERT: B 1006 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7791 (tppt) REVERT: B 1043 GLU cc_start: 0.6256 (mm-30) cc_final: 0.6045 (mm-30) REVERT: C 246 MET cc_start: 0.6563 (ppp) cc_final: 0.5938 (ppp) REVERT: C 350 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 385 LEU cc_start: 0.0869 (OUTLIER) cc_final: 0.0580 (pt) REVERT: C 699 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7171 (pt) REVERT: C 728 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9166 (m) REVERT: C 823 LYS cc_start: 0.8127 (mttt) cc_final: 0.7822 (tppt) REVERT: C 824 LYS cc_start: 0.8588 (mttt) cc_final: 0.8226 (tmtt) REVERT: C 835 MET cc_start: 0.8093 (ttm) cc_final: 0.7799 (ttm) REVERT: D 375 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6607 (t80) REVERT: D 429 MET cc_start: 0.7661 (ppp) cc_final: 0.7282 (ppp) REVERT: D 470 MET cc_start: 0.8715 (mmm) cc_final: 0.8353 (mmp) REVERT: D 524 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.6747 (t80) REVERT: D 533 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7452 (tm-30) REVERT: D 568 LEU cc_start: 0.1179 (OUTLIER) cc_final: 0.0924 (pt) REVERT: D 845 MET cc_start: 0.8649 (ttm) cc_final: 0.8331 (ttm) REVERT: D 911 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9199 (m) REVERT: D 935 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7501 (t0) REVERT: D 1004 ASP cc_start: 0.6709 (m-30) cc_final: 0.6419 (m-30) REVERT: D 1006 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7267 (tppt) REVERT: D 1007 LYS cc_start: 0.8512 (mttt) cc_final: 0.8114 (tmtt) REVERT: D 1041 ARG cc_start: 0.8551 (tpp80) cc_final: 0.7854 (tpp80) REVERT: D 1043 GLU cc_start: 0.5918 (mm-30) cc_final: 0.5537 (mm-30) REVERT: D 1044 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8240 (mm110) outliers start: 79 outliers final: 63 residues processed: 466 average time/residue: 0.1534 time to fit residues: 116.2381 Evaluate side-chains 482 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 407 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 524 PHE 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 849 LEU Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 999 PHE 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 463 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 777 PHE 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 935 ASN Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1042 VAL 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 191 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 HIS 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 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 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 D residue 371 PHE Chi-restraints excluded: chain D residue 374 ILE 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 521 SER Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain D residue 568 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 803 TYR 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 883 PHE Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 935 ASN 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 154 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 211 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 189 optimal weight: 0.1980 chunk 83 optimal weight: 9.9990 chunk 249 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 ASN A 935 ASN B 461 ASN B 935 ASN ** B1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN ** D 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 936 ASN D 961 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132853 restraints weight = 33642.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134322 restraints weight = 20495.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135896 restraints weight = 14195.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136717 restraints weight = 11557.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136919 restraints weight = 10317.512| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 23649 Z= 0.203 Angle : 1.122 59.189 32237 Z= 0.605 Chirality : 0.051 0.744 3775 Planarity : 0.005 0.092 3968 Dihedral : 8.756 70.130 4666 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.65 % Favored : 89.52 % Rotamer: Outliers : 4.21 % Allowed : 25.42 % Favored : 70.37 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.47 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.17), residues: 2528 helix: -0.17 (0.13), residues: 1668 sheet: None (None), residues: 0 loop : -3.28 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 363 TYR 0.017 0.001 TYR C 657 PHE 0.021 0.002 PHE A 934 TRP 0.020 0.001 TRP A 480 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00419 (23645) covalent geometry : angle 1.12241 (32229) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.35692 ( 8) hydrogen bonds : bond 0.03376 ( 994) hydrogen bonds : angle 3.88604 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.90 seconds wall clock time: 65 minutes 28.47 seconds (3928.47 seconds total)