Starting phenix.real_space_refine on Tue Oct 27 06:33:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.map" model { file = "/net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bwi_7299/10_2026/6bwi_7299.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 92 5.16 5 Na 5 4.78 5 C 15310 2.51 5 N 4064 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23491 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5649 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'UNK:plan-1': 195, 'GLU:plan': 15, 'ASP:plan': 11, 'GLN:plan1': 6, 'ARG:plan': 10, 'TRP:plan': 1, 'PHE:plan': 4, 'HIS:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 435 Chain: "B" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5644 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'UNK:plan-1': 195, 'GLU:plan': 15, 'ASP:plan': 11, 'GLN:plan1': 6, 'ARG:plan': 10, 'TRP:plan': 1, 'PHE:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 440 Chain: "C" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5644 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'UNK:plan-1': 195, 'GLU:plan': 15, 'ASP:plan': 11, 'GLN:plan1': 6, 'ARG:plan': 10, 'TRP:plan': 1, 'PHE:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 440 Chain: "D" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5649 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'UNK:plan-1': 195, 'GLU:plan': 15, 'ASP:plan': 11, 'GLN:plan1': 6, 'ARG:plan': 10, 'TRP:plan': 1, 'PHE:plan': 4, 'HIS:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 435 Chain: "A" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 228 Unusual residues: {' NA': 3, 'NAG': 1, 'Y01': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 227 Unusual residues: {' NA': 2, 'NAG': 1, 'Y01': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 260 Unusual residues: {'NAG': 1, 'Y01': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 5.39, per 1000 atoms: 0.23 Number of scatterers: 23491 At special positions: 0 Unit cell: (131.61, 131.61, 153.75, 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 92 16.00 Na 5 11.00 O 4020 8.00 N 4064 7.00 C 15310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.18 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=1.89 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=1.51 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=1.54 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=4, symmetry=0 Links applied NAG-ASN " NAG A1210 " - " ASN A 992 " " NAG B1209 " - " ASN B 992 " " NAG D1208 " - " ASN D 992 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 871.7 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6280 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 8 sheets defined 83.1% alpha, 1.0% 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 5 through 9 removed outlier: 3.860A pdb=" N UNK A 9 " --> pdb=" O UNK A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 32 through 44 removed outlier: 3.973A pdb=" N UNK A 44 " --> pdb=" O UNK A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 4.042A pdb=" N UNK A 58 " --> pdb=" O UNK A 54 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK A 59 " --> pdb=" O UNK A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK A 232 " --> pdb=" O UNK A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.744A pdb=" N UNK A 241 " --> pdb=" O UNK A 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK A 242 " --> pdb=" O UNK A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 242' Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.519A pdb=" N TRP A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 3.766A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 removed outlier: 3.532A pdb=" N GLU A 439 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.526A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.673A pdb=" N SER A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 Processing helix chain 'A' and resid 610 through 634 removed outlier: 4.728A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 703 " --> pdb=" O CYS A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 698 through 703' Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 780 through 803 removed outlier: 3.962A pdb=" N VAL A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 832 removed outlier: 3.792A pdb=" N TYR A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 830 " --> pdb=" O CYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 removed outlier: 3.565A pdb=" N VAL A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 926 removed outlier: 3.900A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 952 removed outlier: 3.949A pdb=" N VAL A 930 " --> pdb=" O MET A 926 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 951 " --> pdb=" O ALA A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 1017 through 1031 removed outlier: 3.674A pdb=" N VAL A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1068 removed outlier: 4.285A pdb=" N ALA A1041 " --> pdb=" O ASN A1037 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A1049 " --> pdb=" O TYR A1045 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1090 removed outlier: 4.193A pdb=" N LEU A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1137 removed outlier: 4.000A pdb=" N ALA A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU A1172 " --> pdb=" O TYR A1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.862A pdb=" N UNK B 9 " --> pdb=" O UNK B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.973A pdb=" N UNK B 44 " --> pdb=" O UNK B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 4.043A pdb=" N UNK B 58 " --> pdb=" O UNK B 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N UNK B 59 " --> pdb=" O UNK B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK B 232 " --> pdb=" O UNK B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.744A pdb=" N UNK B 241 " --> pdb=" O UNK B 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK B 242 " --> pdb=" O UNK B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 261 through 276 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.519A pdb=" N TRP B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 3.765A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.531A pdb=" N GLU B 439 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.526A pdb=" N LEU B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 585 through 591 Processing helix chain 'B' and resid 595 through 602 Processing helix chain 'B' and resid 610 through 634 removed outlier: 4.728A pdb=" N ALA B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU B 657 " --> pdb=" O THR B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 668' Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU B 702 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 703 " --> pdb=" O CYS B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 698 through 703' Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 771 through 776 Processing helix chain 'B' and resid 780 through 803 removed outlier: 3.961A pdb=" N VAL B 803 " --> pdb=" O ARG B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 832 removed outlier: 3.792A pdb=" N TYR B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 830 " --> pdb=" O CYS B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 860 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 removed outlier: 3.565A pdb=" N VAL B 894 " --> pdb=" O LEU B 890 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 926 removed outlier: 3.901A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 952 removed outlier: 3.948A pdb=" N VAL B 930 " --> pdb=" O MET B 926 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 942 " --> pdb=" O GLY B 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 949 " --> pdb=" O GLY B 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY B 950 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 951 " --> pdb=" O ALA B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 1017 through 1034 removed outlier: 3.675A pdb=" N VAL B1021 " --> pdb=" O ASN B1017 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1069 removed outlier: 4.285A pdb=" N ALA B1041 " --> pdb=" O ASN B1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B1049 " --> pdb=" O TYR B1045 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1090 removed outlier: 4.192A pdb=" N LEU B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1137 removed outlier: 3.999A pdb=" N ALA B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU B1172 " --> pdb=" O TYR B1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.861A pdb=" N UNK C 9 " --> pdb=" O UNK C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 32 through 44 removed outlier: 3.972A pdb=" N UNK C 44 " --> pdb=" O UNK C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 4.043A pdb=" N UNK C 58 " --> pdb=" O UNK C 54 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK C 59 " --> pdb=" O UNK C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK C 232 " --> pdb=" O UNK C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.743A pdb=" N UNK C 241 " --> pdb=" O UNK C 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK C 242 " --> pdb=" O UNK C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 261 through 276 Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.518A pdb=" N TRP C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 3.765A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 440 removed outlier: 3.532A pdb=" N GLU C 439 " --> pdb=" O ASP C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 560 through 568 removed outlier: 3.526A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 585 through 591 Processing helix chain 'C' and resid 595 through 602 Processing helix chain 'C' and resid 610 through 634 removed outlier: 4.727A pdb=" N ALA C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU C 657 " --> pdb=" O THR C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 663 through 668' Processing helix chain 'C' and resid 672 through 681 Processing helix chain 'C' and resid 689 through 695 Processing helix chain 'C' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU C 702 " --> pdb=" O PHE C 698 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE C 703 " --> pdb=" O CYS C 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 698 through 703' Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 780 through 803 removed outlier: 3.961A pdb=" N VAL C 803 " --> pdb=" O ARG C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 832 removed outlier: 3.792A pdb=" N TYR C 818 " --> pdb=" O GLU C 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 830 " --> pdb=" O CYS C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 860 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU C 877 " --> pdb=" O THR C 873 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 910 removed outlier: 3.565A pdb=" N VAL C 894 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 926 removed outlier: 3.900A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 952 removed outlier: 3.949A pdb=" N VAL C 930 " --> pdb=" O MET C 926 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL C 942 " --> pdb=" O GLY C 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 949 " --> pdb=" O GLY C 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 951 " --> pdb=" O ALA C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 1017 through 1034 removed outlier: 3.675A pdb=" N VAL C1021 " --> pdb=" O ASN C1017 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C1032 " --> pdb=" O LEU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1068 removed outlier: 4.286A pdb=" N ALA C1041 " --> pdb=" O ASN C1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS C1049 " --> pdb=" O TYR C1045 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 4.193A pdb=" N LEU C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1137 removed outlier: 4.000A pdb=" N ALA C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU C1172 " --> pdb=" O TYR C1168 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.861A pdb=" N UNK D 9 " --> pdb=" O UNK D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.974A pdb=" N UNK D 44 " --> pdb=" O UNK D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 62 removed outlier: 4.042A pdb=" N UNK D 58 " --> pdb=" O UNK D 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N UNK D 59 " --> pdb=" O UNK D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 228 through 234 removed outlier: 3.531A pdb=" N UNK D 232 " --> pdb=" O UNK D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.743A pdb=" N UNK D 241 " --> pdb=" O UNK D 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N UNK D 242 " --> pdb=" O UNK D 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 237 through 242' Processing helix chain 'D' and resid 261 through 276 Processing helix chain 'D' and resid 396 through 403 removed outlier: 3.518A pdb=" N TRP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.765A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 removed outlier: 4.731A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 440 removed outlier: 3.531A pdb=" N GLU D 439 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 465 Processing helix chain 'D' and resid 473 through 479 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 560 through 568 removed outlier: 3.525A pdb=" N LEU D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP D 565 " --> pdb=" O ASP D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 585 through 591 Processing helix chain 'D' and resid 595 through 602 Processing helix chain 'D' and resid 610 through 634 removed outlier: 4.728A pdb=" N ALA D 616 " --> pdb=" O ARG D 612 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 634 " --> pdb=" O CYS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.590A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 658 removed outlier: 3.691A pdb=" N LEU D 657 " --> pdb=" O THR D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 668 removed outlier: 3.786A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 663 through 668' Processing helix chain 'D' and resid 672 through 681 Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 698 through 703 removed outlier: 3.551A pdb=" N LEU D 702 " --> pdb=" O PHE D 698 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE D 703 " --> pdb=" O CYS D 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 698 through 703' Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 771 through 776 Processing helix chain 'D' and resid 780 through 803 removed outlier: 3.961A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 832 removed outlier: 3.791A pdb=" N TYR D 818 " --> pdb=" O GLU D 814 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 830 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 860 Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.550A pdb=" N LEU D 877 " --> pdb=" O THR D 873 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 890 through 910 removed outlier: 3.564A pdb=" N VAL D 894 " --> pdb=" O LEU D 890 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 926 removed outlier: 3.901A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 952 removed outlier: 3.949A pdb=" N VAL D 930 " --> pdb=" O MET D 926 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 942 " --> pdb=" O GLY D 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY D 950 " --> pdb=" O VAL D 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU D 951 " --> pdb=" O ALA D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 966 Processing helix chain 'D' and resid 1017 through 1034 removed outlier: 3.675A pdb=" N VAL D1021 " --> pdb=" O ASN D1017 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D1032 " --> pdb=" O LEU D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1035 through 1068 removed outlier: 4.286A pdb=" N ALA D1041 " --> pdb=" O ASN D1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS D1049 " --> pdb=" O TYR D1045 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1090 removed outlier: 4.193A pdb=" N LEU D1085 " --> pdb=" O VAL D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1137 removed outlier: 4.000A pdb=" N ALA D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1172 removed outlier: 3.545A pdb=" N LEU D1172 " --> pdb=" O TYR D1168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA2, first strand: chain 'A' and resid 999 through 1000 removed outlier: 3.925A pdb=" N PHE A 999 " --> pdb=" O GLN A1014 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'B' and resid 999 through 1000 removed outlier: 3.925A pdb=" N PHE B 999 " --> pdb=" O GLN B1014 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA6, first strand: chain 'C' and resid 999 through 1000 removed outlier: 3.925A pdb=" N PHE C 999 " --> pdb=" O GLN C1014 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 101 through 103 Processing sheet with id=AA8, first strand: chain 'D' and resid 999 through 1000 removed outlier: 3.924A pdb=" N PHE D 999 " --> pdb=" O GLN D1014 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3552 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: 4.13 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6784 1.33 - 1.45: 4014 1.45 - 1.57: 13032 1.57 - 1.69: 2 1.69 - 1.81: 136 Bond restraints: 23968 Sorted by residual: bond pdb=" C GLU B1169 " pdb=" N GLN B1170 " ideal model delta sigma weight residual 1.334 1.590 -0.256 1.33e-02 5.65e+03 3.70e+02 bond pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 1.334 1.588 -0.254 1.32e-02 5.74e+03 3.70e+02 bond pdb=" C LEU B1162 " pdb=" N GLY B1163 " ideal model delta sigma weight residual 1.334 1.560 -0.226 1.32e-02 5.74e+03 2.92e+02 bond pdb=" C GLU A1169 " pdb=" N GLN A1170 " ideal model delta sigma weight residual 1.334 1.542 -0.208 1.33e-02 5.65e+03 2.43e+02 bond pdb=" C GLU D1169 " pdb=" N GLN D1170 " ideal model delta sigma weight residual 1.334 1.527 -0.192 1.33e-02 5.65e+03 2.09e+02 ... (remaining 23963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 31841 3.57 - 7.15: 913 7.15 - 10.72: 83 10.72 - 14.29: 22 14.29 - 17.87: 1 Bond angle restraints: 32860 Sorted by residual: angle pdb=" C LEU A1162 " pdb=" N GLY A1163 " pdb=" CA GLY A1163 " ideal model delta sigma weight residual 119.98 137.85 -17.87 1.11e+00 8.12e-01 2.59e+02 angle pdb=" O LEU A1162 " pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 122.12 108.93 13.19 1.06e+00 8.90e-01 1.55e+02 angle pdb=" CA LEU A1162 " pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 117.22 130.77 -13.55 1.17e+00 7.31e-01 1.34e+02 angle pdb=" C LEU B1162 " pdb=" N GLY B1163 " pdb=" CA GLY B1163 " ideal model delta sigma weight residual 119.98 132.24 -12.26 1.11e+00 8.12e-01 1.22e+02 angle pdb=" N PRO C 701 " pdb=" CA PRO C 701 " pdb=" CB PRO C 701 " ideal model delta sigma weight residual 103.25 113.65 -10.40 1.05e+00 9.07e-01 9.82e+01 ... (remaining 32855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 12800 15.58 - 31.16: 762 31.16 - 46.74: 194 46.74 - 62.32: 49 62.32 - 77.90: 15 Dihedral angle restraints: 13820 sinusoidal: 4276 harmonic: 9544 Sorted by residual: dihedral pdb=" CA UNK A 93 " pdb=" C UNK A 93 " pdb=" N UNK A 94 " pdb=" CA UNK A 94 " ideal model delta harmonic sigma weight residual -180.00 -138.03 -41.97 0 5.00e+00 4.00e-02 7.05e+01 dihedral pdb=" CA UNK D 93 " pdb=" C UNK D 93 " pdb=" N UNK D 94 " pdb=" CA UNK D 94 " ideal model delta harmonic sigma weight residual -180.00 -138.05 -41.95 0 5.00e+00 4.00e-02 7.04e+01 dihedral pdb=" CA UNK B 93 " pdb=" C UNK B 93 " pdb=" N UNK B 94 " pdb=" CA UNK B 94 " ideal model delta harmonic sigma weight residual -180.00 -138.11 -41.89 0 5.00e+00 4.00e-02 7.02e+01 ... (remaining 13817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 3921 0.224 - 0.447: 75 0.447 - 0.671: 16 0.671 - 0.894: 2 0.894 - 1.118: 1 Chirality restraints: 4015 Sorted by residual: chirality pdb=" C1 NAG D1208 " pdb=" ND2 ASN D 992 " pdb=" C2 NAG D1208 " pdb=" O5 NAG D1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" C1 NAG B1209 " pdb=" ND2 ASN B 992 " pdb=" C2 NAG B1209 " pdb=" O5 NAG B1209 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" C1 NAG A1210 " pdb=" ND2 ASN A 992 " pdb=" C2 NAG A1210 " pdb=" O5 NAG A1210 " both_signs ideal model delta sigma weight residual False -2.40 -3.07 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 4012 not shown) Planarity restraints: 4065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 992 " 0.561 2.00e-02 2.50e+03 5.54e-01 3.84e+03 pdb=" CG ASN A 992 " -0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN A 992 " 0.135 2.00e-02 2.50e+03 pdb=" ND2 ASN A 992 " -1.003 2.00e-02 2.50e+03 pdb=" C1 NAG A1210 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 992 " 0.490 2.00e-02 2.50e+03 4.96e-01 3.07e+03 pdb=" CG ASN D 992 " -0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN D 992 " 0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN D 992 " -0.890 2.00e-02 2.50e+03 pdb=" C1 NAG D1208 " 0.414 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 992 " -0.422 2.00e-02 2.50e+03 4.71e-01 2.77e+03 pdb=" CG ASN B 992 " 0.126 2.00e-02 2.50e+03 pdb=" OD1 ASN B 992 " -0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN B 992 " 0.831 2.00e-02 2.50e+03 pdb=" C1 NAG B1209 " -0.466 2.00e-02 2.50e+03 ... (remaining 4062 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 53 2.38 - 3.01: 11974 3.01 - 3.64: 34640 3.64 - 4.27: 49452 4.27 - 4.90: 78950 Nonbonded interactions: 175069 Sorted by model distance: nonbonded pdb=" CG ASN B 992 " pdb=" O1 NAG B1209 " model vdw 1.745 2.616 nonbonded pdb=" OD1 ASN B 992 " pdb=" O1 NAG B1209 " model vdw 1.857 3.040 nonbonded pdb=" O PHE D 975 " pdb=" N GLN D 977 " model vdw 1.917 3.120 nonbonded pdb=" CE3 TRP B 864 " pdb=" CAR Y01 B1207 " model vdw 1.975 2.992 nonbonded pdb=" CG ASN A 992 " pdb=" O1 NAG A1210 " model vdw 2.091 2.616 ... (remaining 175064 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 989 or (resid 990 and (name N or name CA or name \ C or name O or name CB )) or resid 991 through 1174 or resid 1204 through 1205) \ ) selection = (chain 'B' and (resid 1 through 1174 or resid 1204 through 1205)) selection = (chain 'C' and (resid 1 through 1174 or resid 1204 through 1205)) selection = (chain 'D' and (resid 1 through 989 or (resid 990 and (name N or name CA or name \ C or name O or name CB )) or resid 991 through 1174 or resid 1204 through 1205) \ ) } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.290 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.019 1.365 23979 Z= 1.102 Angle : 1.554 46.866 32877 Z= 0.782 Chirality : 0.085 1.118 4015 Planarity : 0.012 0.288 4062 Dihedral : 12.093 77.900 7528 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.11 % Favored : 91.52 % Rotamer: Outliers : 1.36 % Allowed : 6.02 % Favored : 92.62 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.08 (0.14), residues: 2428 helix: -3.41 (0.08), residues: 1572 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 644 TYR 0.020 0.002 TYR B 888 PHE 0.032 0.004 PHE D 710 TRP 0.038 0.004 TRP B 565 HIS 0.006 0.002 HIS B1128 Details of bonding type rmsd/Z covalent geometry : bond 0.01081 / 0.56 (23968) covalent geometry : angle 1.38753 / 0.73 (32860) SS BOND : bond 0.37308 / 18.66 ( 4) SS BOND : angle 31.76032 / 15.97 ( 8) hydrogen bonds : bond 0.17415 / 10.09 ( 1200) hydrogen bonds : angle 10.65826 / 6.71 ( 3552) Misc. bond : bond 0.51174 / 25.74 ( 4) link_NAG-ASN : bond 1.13271 / 57.73 ( 3) link_NAG-ASN : angle 29.89949 / 15.53 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 661 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 625 ASP cc_start: 0.7363 (m-30) cc_final: 0.7161 (m-30) REVERT: A 679 LYS cc_start: 0.8634 (mttt) cc_final: 0.8419 (ptmt) REVERT: A 815 LEU cc_start: 0.8539 (mt) cc_final: 0.8147 (mp) REVERT: A 828 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 854 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6223 (tt0) REVERT: A 859 TYR cc_start: 0.8530 (t80) cc_final: 0.8051 (t80) REVERT: A 944 TYR cc_start: 0.8540 (t80) cc_final: 0.8289 (t80) REVERT: B 439 GLU cc_start: 0.6628 (mt-10) cc_final: 0.5923 (mt-10) REVERT: B 679 LYS cc_start: 0.8626 (mttt) cc_final: 0.8315 (pttt) REVERT: B 815 LEU cc_start: 0.8651 (mt) cc_final: 0.8324 (mp) REVERT: B 828 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 859 TYR cc_start: 0.8602 (t80) cc_final: 0.8164 (t80) REVERT: B 944 TYR cc_start: 0.8659 (t80) cc_final: 0.8445 (t80) REVERT: C 576 MET cc_start: 0.7957 (mmm) cc_final: 0.7695 (mpp) REVERT: C 679 LYS cc_start: 0.8640 (mttt) cc_final: 0.8345 (pttt) REVERT: C 815 LEU cc_start: 0.8643 (mt) cc_final: 0.8352 (mp) REVERT: C 828 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7692 (mm-30) REVERT: C 859 TYR cc_start: 0.8539 (t80) cc_final: 0.8109 (t80) REVERT: D 679 LYS cc_start: 0.8636 (mttt) cc_final: 0.8426 (pttt) REVERT: D 815 LEU cc_start: 0.8572 (mt) cc_final: 0.8185 (mp) REVERT: D 828 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7767 (mm-30) REVERT: D 859 TYR cc_start: 0.8516 (t80) cc_final: 0.8098 (t80) REVERT: D 1014 GLN cc_start: 0.8275 (pp30) cc_final: 0.7898 (pp30) outliers start: 24 outliers final: 10 residues processed: 677 average time/residue: 0.1771 time to fit residues: 179.1607 Evaluate side-chains 371 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 360 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 854 GLN Chi-restraints excluded: chain A residue 955 ARG Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 955 ARG Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 955 ARG Chi-restraints excluded: chain C residue 1033 ILE Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 584 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 HIS ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 GLN A 908 HIS A 980 GLN A1032 ASN A1037 ASN A1161 GLN A1164 HIS B 447 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN B 908 HIS B1161 GLN B1164 HIS C 447 HIS C 584 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 ASN C1161 GLN C1164 HIS D 447 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN D 908 HIS D 977 GLN D1032 ASN D1161 GLN D1164 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125256 restraints weight = 39080.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126465 restraints weight = 30815.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127011 restraints weight = 25135.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127579 restraints weight = 22970.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127654 restraints weight = 21462.746| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 23979 Z= 0.414 Angle : 1.095 20.964 32877 Z= 0.517 Chirality : 0.064 1.487 4015 Planarity : 0.007 0.072 4062 Dihedral : 10.413 87.930 3761 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.23 % Favored : 90.40 % Rotamer: Outliers : 6.70 % Allowed : 15.95 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.15), residues: 2428 helix: -1.84 (0.11), residues: 1676 sheet: None (None), residues: 0 loop : -3.52 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 892 TYR 0.016 0.002 TYR B1063 PHE 0.036 0.004 PHE B 710 TRP 0.024 0.003 TRP C 864 HIS 0.010 0.002 HIS D1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00936 / 0.41 (23968) covalent geometry : angle 1.07540 / 0.51 (32860) SS BOND : bond 0.01162 / 0.58 ( 4) SS BOND : angle 1.64790 / 0.81 ( 8) hydrogen bonds : bond 0.05777 / 3.39 ( 1200) hydrogen bonds : angle 6.01269 / 3.85 ( 3552) Misc. bond : bond 0.00516 / 0.26 ( 4) link_NAG-ASN : bond 0.03207 / 1.61 ( 3) link_NAG-ASN : angle 12.31285 / 6.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 414 time to evaluate : 0.629 Fit side-chains REVERT: A 607 GLU cc_start: 0.8216 (tp30) cc_final: 0.8010 (tp30) REVERT: A 697 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: A 776 TRP cc_start: 0.4730 (t-100) cc_final: 0.4214 (t60) REVERT: A 815 LEU cc_start: 0.8710 (mt) cc_final: 0.8493 (mp) REVERT: B 607 GLU cc_start: 0.8102 (tp30) cc_final: 0.7900 (tp30) REVERT: B 697 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.7114 (m-10) REVERT: B 776 TRP cc_start: 0.4793 (t-100) cc_final: 0.4550 (t-100) REVERT: B 815 LEU cc_start: 0.8698 (mt) cc_final: 0.8490 (mp) REVERT: B 818 TYR cc_start: 0.7415 (m-80) cc_final: 0.7182 (m-80) REVERT: B 855 ARG cc_start: 0.6167 (tpt-90) cc_final: 0.5906 (tpt170) REVERT: B 944 TYR cc_start: 0.9126 (t80) cc_final: 0.8696 (t80) REVERT: B 952 LEU cc_start: 0.8861 (pp) cc_final: 0.8550 (mt) REVERT: B 955 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6946 (ttp-170) REVERT: B 1022 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9404 (tp) REVERT: B 1157 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8788 (mp) REVERT: B 1164 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7015 (t70) REVERT: C 697 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: C 776 TRP cc_start: 0.4809 (t-100) cc_final: 0.4578 (t-100) REVERT: C 855 ARG cc_start: 0.6248 (tpt-90) cc_final: 0.5906 (tpt170) REVERT: C 944 TYR cc_start: 0.9029 (t80) cc_final: 0.8665 (t80) REVERT: C 955 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.7005 (ttp-170) REVERT: C 1157 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8791 (mp) REVERT: C 1164 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6916 (t70) REVERT: D 697 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7103 (m-10) REVERT: D 776 TRP cc_start: 0.4729 (t-100) cc_final: 0.4522 (t-100) REVERT: D 815 LEU cc_start: 0.8699 (mt) cc_final: 0.8481 (mp) REVERT: D 952 LEU cc_start: 0.8795 (pp) cc_final: 0.8584 (mt) REVERT: D 1022 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9389 (tp) REVERT: D 1157 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8777 (mp) REVERT: D 1164 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6763 (t70) outliers start: 118 outliers final: 47 residues processed: 497 average time/residue: 0.1410 time to fit residues: 113.8968 Evaluate side-chains 389 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 328 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 955 ARG Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 697 PHE Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 955 ARG Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 863 SER Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 GLN B 419 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 GLN B 980 GLN ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 ASN B1164 HIS C 419 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN C 908 HIS ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 584 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 980 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126180 restraints weight = 39007.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126590 restraints weight = 34799.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127447 restraints weight = 27991.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127685 restraints weight = 22629.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127619 restraints weight = 21216.839| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 23979 Z= 0.404 Angle : 1.017 18.285 32877 Z= 0.483 Chirality : 0.058 1.147 4015 Planarity : 0.006 0.059 4062 Dihedral : 10.166 96.004 3752 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.53 % Favored : 88.30 % Rotamer: Outliers : 8.85 % Allowed : 17.14 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.16), residues: 2428 helix: -1.27 (0.12), residues: 1688 sheet: None (None), residues: 0 loop : -3.61 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 892 TYR 0.026 0.003 TYR C 859 PHE 0.035 0.003 PHE D 710 TRP 0.038 0.003 TRP C 864 HIS 0.020 0.003 HIS D1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00916 / 0.40 (23968) covalent geometry : angle 1.00584 / 0.48 (32860) SS BOND : bond 0.00192 / 0.10 ( 4) SS BOND : angle 1.10995 / 0.56 ( 8) hydrogen bonds : bond 0.05582 / 3.28 ( 1200) hydrogen bonds : angle 5.79185 / 3.69 ( 3552) Misc. bond : bond 0.00467 / 0.23 ( 4) link_NAG-ASN : bond 0.04205 / 2.10 ( 3) link_NAG-ASN : angle 9.09825 / 4.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 378 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 697 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: A 776 TRP cc_start: 0.4181 (t-100) cc_final: 0.3909 (t-100) REVERT: A 786 ASN cc_start: 0.8263 (t0) cc_final: 0.7819 (t0) REVERT: A 815 LEU cc_start: 0.8519 (mt) cc_final: 0.8315 (mp) REVERT: A 944 TYR cc_start: 0.8922 (t80) cc_final: 0.8589 (t80) REVERT: A 1125 GLU cc_start: 0.8486 (tt0) cc_final: 0.8226 (tt0) REVERT: A 1164 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.6863 (t-170) REVERT: B 675 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8314 (tp) REVERT: B 697 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: B 776 TRP cc_start: 0.4542 (t-100) cc_final: 0.4283 (t-100) REVERT: B 815 LEU cc_start: 0.8532 (mt) cc_final: 0.8303 (mp) REVERT: B 944 TYR cc_start: 0.8950 (t80) cc_final: 0.8620 (t80) REVERT: B 955 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7299 (ttp-170) REVERT: B 1149 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8154 (pttp) REVERT: B 1157 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8885 (mp) REVERT: B 1164 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.7038 (t70) REVERT: C 590 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5467 (tt) REVERT: C 697 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6964 (m-10) REVERT: C 776 TRP cc_start: 0.4550 (t-100) cc_final: 0.4316 (t-100) REVERT: C 859 TYR cc_start: 0.8850 (t80) cc_final: 0.8647 (t80) REVERT: C 944 TYR cc_start: 0.8823 (t80) cc_final: 0.8458 (t80) REVERT: C 955 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7178 (ttp-170) REVERT: C 1149 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8155 (pttp) REVERT: C 1157 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8927 (mp) REVERT: D 590 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5467 (tt) REVERT: D 675 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8258 (tp) REVERT: D 776 TRP cc_start: 0.4614 (t-100) cc_final: 0.4364 (t-100) REVERT: D 944 TYR cc_start: 0.8908 (t80) cc_final: 0.8586 (t80) REVERT: D 1149 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8174 (pttp) REVERT: D 1157 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8922 (mp) outliers start: 156 outliers final: 99 residues processed: 495 average time/residue: 0.1394 time to fit residues: 113.2639 Evaluate side-chains 447 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 331 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 955 ARG Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 PHE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 866 GLN Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 955 ARG Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 GLN A1164 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 GLN B 980 GLN ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 980 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124448 restraints weight = 39298.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124539 restraints weight = 32646.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124768 restraints weight = 28718.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124859 restraints weight = 26134.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124884 restraints weight = 25519.812| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 23979 Z= 0.399 Angle : 0.986 13.725 32877 Z= 0.470 Chirality : 0.055 0.839 4015 Planarity : 0.006 0.061 4062 Dihedral : 10.216 100.538 3752 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.03 % Favored : 87.81 % Rotamer: Outliers : 9.48 % Allowed : 19.92 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.16), residues: 2428 helix: -1.05 (0.12), residues: 1688 sheet: None (None), residues: 0 loop : -3.58 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 892 TYR 0.022 0.002 TYR C 859 PHE 0.033 0.003 PHE D 710 TRP 0.050 0.003 TRP C 864 HIS 0.016 0.002 HIS B1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.40 (23968) covalent geometry : angle 0.97753 / 0.47 (32860) SS BOND : bond 0.00418 / 0.21 ( 4) SS BOND : angle 1.20401 / 0.59 ( 8) hydrogen bonds : bond 0.05508 / 3.24 ( 1200) hydrogen bonds : angle 5.75834 / 3.66 ( 3552) Misc. bond : bond 0.00479 / 0.24 ( 4) link_NAG-ASN : bond 0.03450 / 1.72 ( 3) link_NAG-ASN : angle 7.82772 / 4.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 364 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASN cc_start: 0.7825 (m-40) cc_final: 0.7496 (t0) REVERT: A 648 LEU cc_start: 0.8133 (mt) cc_final: 0.7905 (mt) REVERT: A 776 TRP cc_start: 0.4165 (t-100) cc_final: 0.3872 (t-100) REVERT: A 786 ASN cc_start: 0.8220 (t0) cc_final: 0.7683 (t0) REVERT: A 815 LEU cc_start: 0.8607 (mt) cc_final: 0.8358 (mp) REVERT: A 944 TYR cc_start: 0.8960 (t80) cc_final: 0.8598 (t80) REVERT: B 475 ASN cc_start: 0.7739 (m-40) cc_final: 0.7448 (t0) REVERT: B 594 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6559 (tt) REVERT: B 675 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8324 (tp) REVERT: B 776 TRP cc_start: 0.4095 (t-100) cc_final: 0.3785 (t-100) REVERT: B 944 TYR cc_start: 0.8991 (t80) cc_final: 0.8631 (t80) REVERT: B 955 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7198 (ttp-170) REVERT: B 1149 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8164 (pttp) REVERT: B 1157 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8913 (mp) REVERT: B 1164 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6848 (t70) REVERT: C 475 ASN cc_start: 0.7692 (m-40) cc_final: 0.7369 (t0) REVERT: C 584 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7670 (m-40) REVERT: C 675 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8237 (tp) REVERT: C 706 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7324 (tmt170) REVERT: C 776 TRP cc_start: 0.4444 (t-100) cc_final: 0.4158 (t-100) REVERT: C 944 TYR cc_start: 0.8883 (t80) cc_final: 0.8515 (t80) REVERT: C 955 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7082 (ttp-170) REVERT: C 1149 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8134 (pttp) REVERT: C 1157 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8915 (mp) REVERT: C 1164 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6921 (t70) REVERT: D 475 ASN cc_start: 0.7830 (m-40) cc_final: 0.7526 (t0) REVERT: D 675 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8250 (tp) REVERT: D 706 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7409 (tmt170) REVERT: D 776 TRP cc_start: 0.4501 (t-100) cc_final: 0.4244 (t-100) REVERT: D 944 TYR cc_start: 0.9014 (t80) cc_final: 0.8664 (t80) REVERT: D 955 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7272 (ttp-170) REVERT: D 1032 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8614 (m110) REVERT: D 1149 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8126 (pttp) REVERT: D 1157 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8952 (mp) outliers start: 167 outliers final: 113 residues processed: 487 average time/residue: 0.1441 time to fit residues: 113.5431 Evaluate side-chains 475 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 343 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 955 ARG Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 706 ARG Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 955 ARG Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 706 ARG Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1062 ARG Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN C 980 GLN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 866 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122980 restraints weight = 39486.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123041 restraints weight = 31146.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123004 restraints weight = 28345.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122999 restraints weight = 27240.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123083 restraints weight = 25944.983| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 23979 Z= 0.396 Angle : 0.974 12.185 32877 Z= 0.463 Chirality : 0.055 0.869 4015 Planarity : 0.006 0.058 4062 Dihedral : 10.098 100.153 3752 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.27 % Favored : 87.56 % Rotamer: Outliers : 10.67 % Allowed : 19.86 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2428 helix: -0.95 (0.12), residues: 1704 sheet: None (None), residues: 0 loop : -3.53 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 892 TYR 0.019 0.002 TYR B 818 PHE 0.031 0.003 PHE D 710 TRP 0.033 0.003 TRP C 864 HIS 0.017 0.003 HIS D1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.40 (23968) covalent geometry : angle 0.96692 / 0.46 (32860) SS BOND : bond 0.00675 / 0.34 ( 4) SS BOND : angle 1.54565 / 0.75 ( 8) hydrogen bonds : bond 0.05529 / 3.25 ( 1200) hydrogen bonds : angle 5.74822 / 3.65 ( 3552) Misc. bond : bond 0.00391 / 0.20 ( 4) link_NAG-ASN : bond 0.03480 / 1.74 ( 3) link_NAG-ASN : angle 6.91286 / 3.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 362 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASN cc_start: 0.7761 (m-40) cc_final: 0.7447 (t0) REVERT: A 594 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6526 (tt) REVERT: A 776 TRP cc_start: 0.4177 (t-100) cc_final: 0.3890 (t-100) REVERT: A 786 ASN cc_start: 0.8212 (t0) cc_final: 0.7682 (t0) REVERT: A 815 LEU cc_start: 0.8608 (mt) cc_final: 0.8366 (mp) REVERT: A 944 TYR cc_start: 0.8954 (t80) cc_final: 0.8585 (t80) REVERT: B 475 ASN cc_start: 0.7672 (m-40) cc_final: 0.7373 (t0) REVERT: B 594 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6542 (tt) REVERT: B 675 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8354 (tp) REVERT: B 776 TRP cc_start: 0.4183 (t-100) cc_final: 0.3855 (t-100) REVERT: B 944 TYR cc_start: 0.8993 (t80) cc_final: 0.8671 (t80) REVERT: B 1068 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 1149 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8147 (pttp) REVERT: B 1157 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8871 (mp) REVERT: B 1164 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.6913 (t70) REVERT: C 475 ASN cc_start: 0.7630 (m-40) cc_final: 0.7288 (t0) REVERT: C 584 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7687 (m-40) REVERT: C 594 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6553 (tt) REVERT: C 675 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8253 (tp) REVERT: C 776 TRP cc_start: 0.4567 (t-100) cc_final: 0.4269 (t-100) REVERT: C 944 TYR cc_start: 0.8901 (t80) cc_final: 0.8551 (t80) REVERT: C 955 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7343 (tpm170) REVERT: C 1068 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7394 (tm-30) REVERT: C 1149 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8117 (pttp) REVERT: C 1157 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8936 (mt) REVERT: C 1164 HIS cc_start: 0.7497 (OUTLIER) cc_final: 0.7071 (t70) REVERT: D 475 ASN cc_start: 0.7698 (m-40) cc_final: 0.7372 (t0) REVERT: D 584 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7557 (m-40) REVERT: D 594 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6530 (tt) REVERT: D 675 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8244 (tp) REVERT: D 697 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7132 (m-10) REVERT: D 706 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7325 (tmt170) REVERT: D 776 TRP cc_start: 0.4626 (t-100) cc_final: 0.4310 (t-100) REVERT: D 944 TYR cc_start: 0.9037 (t80) cc_final: 0.8670 (t80) REVERT: D 955 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7315 (ttp-170) REVERT: D 969 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8131 (ttp80) REVERT: D 1149 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8123 (pttp) REVERT: D 1157 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8995 (mt) outliers start: 188 outliers final: 135 residues processed: 502 average time/residue: 0.1398 time to fit residues: 114.6848 Evaluate side-chains 501 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 344 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 955 ARG Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 706 ARG Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 969 ARG Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1062 ARG Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1155 VAL Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 GLN ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120081 restraints weight = 39656.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122749 restraints weight = 26765.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123699 restraints weight = 20590.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124277 restraints weight = 17477.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124670 restraints weight = 15870.075| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 23979 Z= 0.396 Angle : 0.970 12.373 32877 Z= 0.461 Chirality : 0.055 0.813 4015 Planarity : 0.006 0.061 4062 Dihedral : 10.027 100.052 3748 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.23 % Favored : 87.60 % Rotamer: Outliers : 11.63 % Allowed : 20.72 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.16), residues: 2428 helix: -0.88 (0.12), residues: 1704 sheet: None (None), residues: 0 loop : -3.54 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 892 TYR 0.018 0.002 TYR B 818 PHE 0.031 0.003 PHE B 710 TRP 0.059 0.003 TRP C 864 HIS 0.015 0.003 HIS D1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.40 (23968) covalent geometry : angle 0.96416 / 0.46 (32860) SS BOND : bond 0.00201 / 0.10 ( 4) SS BOND : angle 1.38624 / 0.68 ( 8) hydrogen bonds : bond 0.05558 / 3.27 ( 1200) hydrogen bonds : angle 5.78789 / 3.68 ( 3552) Misc. bond : bond 0.00358 / 0.18 ( 4) link_NAG-ASN : bond 0.03220 / 1.61 ( 3) link_NAG-ASN : angle 6.38568 / 3.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 350 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASN cc_start: 0.7730 (m-40) cc_final: 0.7287 (t0) REVERT: A 476 LEU cc_start: 0.9518 (mp) cc_final: 0.9277 (mp) REVERT: A 594 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6494 (tt) REVERT: A 641 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8910 (tp) REVERT: A 697 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: A 776 TRP cc_start: 0.3982 (t-100) cc_final: 0.3685 (t-100) REVERT: A 786 ASN cc_start: 0.8379 (t0) cc_final: 0.7823 (t0) REVERT: A 815 LEU cc_start: 0.8732 (mt) cc_final: 0.8470 (mp) REVERT: A 944 TYR cc_start: 0.9012 (t80) cc_final: 0.8658 (t80) REVERT: A 1164 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7153 (t-170) REVERT: B 475 ASN cc_start: 0.7676 (m-40) cc_final: 0.7274 (t0) REVERT: B 594 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6464 (tt) REVERT: B 675 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8372 (tp) REVERT: B 697 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: B 776 TRP cc_start: 0.4165 (t-100) cc_final: 0.3818 (t-100) REVERT: B 782 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8847 (tp) REVERT: B 944 TYR cc_start: 0.9060 (t80) cc_final: 0.8728 (t80) REVERT: B 1068 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 1149 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8031 (pttp) REVERT: B 1157 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8771 (mp) REVERT: C 475 ASN cc_start: 0.7660 (m-40) cc_final: 0.7263 (t0) REVERT: C 584 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7652 (m-40) REVERT: C 594 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6563 (tt) REVERT: C 641 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8958 (tp) REVERT: C 675 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8294 (tp) REVERT: C 697 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: C 776 TRP cc_start: 0.4444 (t-100) cc_final: 0.4146 (t-100) REVERT: C 944 TYR cc_start: 0.8961 (t80) cc_final: 0.8609 (t80) REVERT: C 949 GLU cc_start: 0.8033 (mp0) cc_final: 0.7673 (mm-30) REVERT: C 955 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7272 (tpm170) REVERT: C 1149 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8004 (pttp) REVERT: C 1157 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8838 (mt) REVERT: C 1164 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6849 (t70) REVERT: D 475 ASN cc_start: 0.7666 (m-40) cc_final: 0.7280 (t0) REVERT: D 594 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6434 (tt) REVERT: D 656 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: D 675 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8290 (tp) REVERT: D 697 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7250 (m-10) REVERT: D 706 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7337 (tmt170) REVERT: D 776 TRP cc_start: 0.4459 (t-100) cc_final: 0.4181 (t-100) REVERT: D 944 TYR cc_start: 0.9094 (t80) cc_final: 0.8741 (t80) REVERT: D 955 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7293 (ttp-170) REVERT: D 969 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8113 (ttp80) REVERT: D 1149 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7994 (pttp) REVERT: D 1157 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8875 (mt) outliers start: 205 outliers final: 144 residues processed: 509 average time/residue: 0.1392 time to fit residues: 115.5763 Evaluate side-chains 516 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 344 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 PHE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 955 ARG Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1066 ILE Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 706 ARG Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 969 ARG Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1062 ARG Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1155 VAL Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 866 GLN ** A 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS C 980 GLN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126425 restraints weight = 39496.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127113 restraints weight = 36264.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126822 restraints weight = 25803.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126630 restraints weight = 22327.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126662 restraints weight = 22649.296| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 23979 Z= 0.395 Angle : 0.964 12.162 32877 Z= 0.458 Chirality : 0.054 0.723 4015 Planarity : 0.006 0.062 4062 Dihedral : 9.925 99.231 3748 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.60 % Favored : 87.23 % Rotamer: Outliers : 12.32 % Allowed : 20.49 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.17), residues: 2428 helix: -0.84 (0.12), residues: 1700 sheet: None (None), residues: 0 loop : -3.45 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 892 TYR 0.018 0.002 TYR B 818 PHE 0.031 0.003 PHE C 710 TRP 0.042 0.003 TRP C 864 HIS 0.018 0.003 HIS B1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00901 / 0.39 (23968) covalent geometry : angle 0.95886 / 0.46 (32860) SS BOND : bond 0.00580 / 0.29 ( 4) SS BOND : angle 1.37385 / 0.68 ( 8) hydrogen bonds : bond 0.05553 / 3.27 ( 1200) hydrogen bonds : angle 5.80998 / 3.69 ( 3552) Misc. bond : bond 0.00368 / 0.18 ( 4) link_NAG-ASN : bond 0.02995 / 1.50 ( 3) link_NAG-ASN : angle 5.89395 / 2.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 360 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASN cc_start: 0.7550 (m-40) cc_final: 0.7291 (t0) REVERT: A 594 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6431 (tt) REVERT: A 697 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: A 776 TRP cc_start: 0.4156 (t-100) cc_final: 0.3855 (t-100) REVERT: A 786 ASN cc_start: 0.8178 (t0) cc_final: 0.7649 (t0) REVERT: A 815 LEU cc_start: 0.8574 (mt) cc_final: 0.8330 (mp) REVERT: A 944 TYR cc_start: 0.8953 (t80) cc_final: 0.8597 (t80) REVERT: A 949 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 973 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: B 475 ASN cc_start: 0.7517 (m-40) cc_final: 0.7264 (t0) REVERT: B 594 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6553 (tt) REVERT: B 675 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 697 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: B 776 TRP cc_start: 0.4025 (t-100) cc_final: 0.3689 (t-100) REVERT: B 782 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8786 (tp) REVERT: B 944 TYR cc_start: 0.9015 (t80) cc_final: 0.8689 (t80) REVERT: B 973 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: B 1068 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 1157 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8894 (mp) REVERT: B 1164 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6781 (t70) REVERT: C 475 ASN cc_start: 0.7542 (m-40) cc_final: 0.7285 (t0) REVERT: C 584 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7625 (m-40) REVERT: C 594 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6557 (tt) REVERT: C 641 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8888 (tp) REVERT: C 675 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8266 (tp) REVERT: C 697 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7302 (m-10) REVERT: C 776 TRP cc_start: 0.4679 (t-100) cc_final: 0.4444 (t-100) REVERT: C 944 TYR cc_start: 0.8928 (t80) cc_final: 0.8580 (t80) REVERT: C 949 GLU cc_start: 0.8019 (mp0) cc_final: 0.7603 (mm-30) REVERT: C 1149 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8109 (pttp) REVERT: C 1157 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9023 (mt) REVERT: C 1164 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.6936 (t70) REVERT: D 475 ASN cc_start: 0.7554 (m-40) cc_final: 0.7288 (t0) REVERT: D 594 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6371 (tt) REVERT: D 675 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8262 (tp) REVERT: D 697 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7336 (m-10) REVERT: D 776 TRP cc_start: 0.4725 (t-100) cc_final: 0.4464 (t-100) REVERT: D 782 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 944 TYR cc_start: 0.9044 (t80) cc_final: 0.8687 (t80) REVERT: D 955 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7414 (ttp-170) REVERT: D 969 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8118 (ttp80) REVERT: D 973 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8209 (mt0) REVERT: D 1149 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (pttp) REVERT: D 1157 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9019 (mt) REVERT: D 1164 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.6752 (t70) outliers start: 217 outliers final: 153 residues processed: 526 average time/residue: 0.1337 time to fit residues: 115.1766 Evaluate side-chains 523 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 342 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 973 GLN Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 973 GLN Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 697 PHE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1066 ILE Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1148 LEU Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 969 ARG Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1062 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1155 VAL Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN C1164 HIS ** D 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN ** D1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123761 restraints weight = 39100.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124021 restraints weight = 33943.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124212 restraints weight = 28557.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124311 restraints weight = 25610.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124375 restraints weight = 25101.439| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 23979 Z= 0.394 Angle : 0.965 12.408 32877 Z= 0.459 Chirality : 0.054 0.702 4015 Planarity : 0.006 0.063 4062 Dihedral : 9.862 98.822 3742 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.11 % Favored : 87.73 % Rotamer: Outliers : 11.63 % Allowed : 21.40 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.17), residues: 2428 helix: -0.82 (0.12), residues: 1700 sheet: None (None), residues: 0 loop : -3.41 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 969 TYR 0.017 0.002 TYR B 818 PHE 0.031 0.003 PHE C 710 TRP 0.035 0.003 TRP C 864 HIS 0.014 0.003 HIS D1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00899 / 0.39 (23968) covalent geometry : angle 0.96089 / 0.46 (32860) SS BOND : bond 0.00288 / 0.15 ( 4) SS BOND : angle 1.33076 / 0.69 ( 8) hydrogen bonds : bond 0.05572 / 3.27 ( 1200) hydrogen bonds : angle 5.83499 / 3.71 ( 3552) Misc. bond : bond 0.00353 / 0.18 ( 4) link_NAG-ASN : bond 0.02793 / 1.40 ( 3) link_NAG-ASN : angle 5.59595 / 2.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 350 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6446 (tt) REVERT: A 675 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 697 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7291 (m-10) REVERT: A 776 TRP cc_start: 0.4200 (t-100) cc_final: 0.3902 (t-100) REVERT: A 786 ASN cc_start: 0.8186 (t0) cc_final: 0.7708 (t0) REVERT: A 815 LEU cc_start: 0.8649 (mt) cc_final: 0.8379 (mp) REVERT: A 817 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7660 (tp) REVERT: A 944 TYR cc_start: 0.8960 (t80) cc_final: 0.8601 (t80) REVERT: A 973 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: A 1164 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.6601 (t-170) REVERT: B 475 ASN cc_start: 0.7575 (m-40) cc_final: 0.7248 (t0) REVERT: B 590 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5506 (tt) REVERT: B 594 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6529 (tt) REVERT: B 675 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8369 (tp) REVERT: B 697 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: B 776 TRP cc_start: 0.4400 (t-100) cc_final: 0.4092 (t-100) REVERT: B 944 TYR cc_start: 0.9037 (t80) cc_final: 0.8708 (t80) REVERT: B 973 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: B 1157 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8901 (mp) REVERT: C 475 ASN cc_start: 0.7564 (m-40) cc_final: 0.7184 (t0) REVERT: C 584 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7612 (m-40) REVERT: C 594 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6522 (tt) REVERT: C 641 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8959 (tp) REVERT: C 675 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8264 (tp) REVERT: C 697 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: C 776 TRP cc_start: 0.4444 (t-100) cc_final: 0.4195 (t-100) REVERT: C 817 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7864 (tp) REVERT: C 944 TYR cc_start: 0.8957 (t80) cc_final: 0.8593 (t80) REVERT: C 949 GLU cc_start: 0.8072 (mp0) cc_final: 0.7708 (mm-30) REVERT: C 1068 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7453 (tm-30) REVERT: C 1149 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8081 (pttp) REVERT: C 1157 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9016 (mt) REVERT: C 1164 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6908 (t70) REVERT: D 594 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6405 (tt) REVERT: D 641 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9041 (tp) REVERT: D 675 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8252 (tp) REVERT: D 697 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: D 776 TRP cc_start: 0.4540 (t-100) cc_final: 0.4269 (t-100) REVERT: D 782 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8772 (tp) REVERT: D 817 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7907 (tp) REVERT: D 944 TYR cc_start: 0.9056 (t80) cc_final: 0.8689 (t80) REVERT: D 955 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7366 (ttp-170) REVERT: D 969 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8123 (ttp80) REVERT: D 973 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: D 1149 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8095 (pttp) REVERT: D 1157 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9038 (mt) outliers start: 205 outliers final: 156 residues processed: 509 average time/residue: 0.1361 time to fit residues: 113.8130 Evaluate side-chains 520 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 332 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 973 GLN Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 973 GLN Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 PHE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1066 ILE Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1148 LEU Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 969 ARG Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1062 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1155 VAL Chi-restraints excluded: chain D residue 1157 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN A1164 HIS ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS C1017 ASN C1164 HIS ** D 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1164 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122649 restraints weight = 39555.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122789 restraints weight = 33324.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123119 restraints weight = 28159.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123201 restraints weight = 25889.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123230 restraints weight = 25361.346| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 23979 Z= 0.394 Angle : 0.967 12.203 32877 Z= 0.460 Chirality : 0.054 0.693 4015 Planarity : 0.006 0.062 4062 Dihedral : 9.867 98.517 3742 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.56 % Favored : 87.27 % Rotamer: Outliers : 11.80 % Allowed : 21.34 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.17), residues: 2428 helix: -0.79 (0.12), residues: 1708 sheet: None (None), residues: 0 loop : -3.45 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 969 TYR 0.017 0.002 TYR B 818 PHE 0.031 0.003 PHE C 710 TRP 0.032 0.003 TRP C 864 HIS 0.016 0.002 HIS C1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00899 / 0.39 (23968) covalent geometry : angle 0.96315 / 0.46 (32860) SS BOND : bond 0.00363 / 0.18 ( 4) SS BOND : angle 1.18925 / 0.62 ( 8) hydrogen bonds : bond 0.05561 / 3.27 ( 1200) hydrogen bonds : angle 5.83988 / 3.71 ( 3552) Misc. bond : bond 0.00350 / 0.18 ( 4) link_NAG-ASN : bond 0.02593 / 1.30 ( 3) link_NAG-ASN : angle 5.22011 / 2.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 341 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 594 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6438 (tt) REVERT: A 697 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7213 (m-10) REVERT: A 776 TRP cc_start: 0.4335 (t-100) cc_final: 0.3974 (t-100) REVERT: A 815 LEU cc_start: 0.8640 (mt) cc_final: 0.8367 (mp) REVERT: A 817 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7804 (tp) REVERT: A 944 TYR cc_start: 0.8939 (t80) cc_final: 0.8590 (t80) REVERT: A 973 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: B 475 ASN cc_start: 0.7613 (m-40) cc_final: 0.7275 (t0) REVERT: B 594 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6352 (tt) REVERT: B 675 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8364 (tp) REVERT: B 697 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: B 875 PHE cc_start: 0.8086 (t80) cc_final: 0.7830 (t80) REVERT: B 944 TYR cc_start: 0.9001 (t80) cc_final: 0.8665 (t80) REVERT: B 973 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: B 1157 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8914 (mp) REVERT: C 475 ASN cc_start: 0.7618 (m-40) cc_final: 0.7266 (t0) REVERT: C 594 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6483 (tt) REVERT: C 641 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8965 (tp) REVERT: C 675 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8256 (tp) REVERT: C 697 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: C 817 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7871 (tp) REVERT: C 944 TYR cc_start: 0.8965 (t80) cc_final: 0.8584 (t80) REVERT: C 949 GLU cc_start: 0.8049 (mp0) cc_final: 0.7721 (mm-30) REVERT: C 1068 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7429 (tm-30) REVERT: C 1149 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8106 (pttp) REVERT: C 1157 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9010 (mt) REVERT: C 1164 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.6995 (t70) REVERT: D 594 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6385 (tt) REVERT: D 641 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8941 (tp) REVERT: D 675 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8237 (tp) REVERT: D 697 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: D 782 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8754 (tp) REVERT: D 817 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7910 (tp) REVERT: D 944 TYR cc_start: 0.9040 (t80) cc_final: 0.8677 (t80) REVERT: D 955 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7328 (ttp-170) REVERT: D 969 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8132 (ttp80) REVERT: D 973 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: D 1149 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8085 (pttp) outliers start: 208 outliers final: 158 residues processed: 503 average time/residue: 0.1317 time to fit residues: 109.3559 Evaluate side-chains 516 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 331 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 973 GLN Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 973 GLN Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 PHE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1066 ILE Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1148 LEU Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 969 ARG Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1062 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1155 VAL Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS C1017 ASN C1164 HIS ** D 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1164 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123370 restraints weight = 39445.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124059 restraints weight = 31281.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124155 restraints weight = 25938.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124172 restraints weight = 24023.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124214 restraints weight = 23692.799| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 23979 Z= 0.393 Angle : 0.971 12.247 32877 Z= 0.461 Chirality : 0.054 0.685 4015 Planarity : 0.006 0.063 4062 Dihedral : 9.830 98.201 3738 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.36 % Favored : 87.48 % Rotamer: Outliers : 10.95 % Allowed : 22.25 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.17), residues: 2428 helix: -0.80 (0.12), residues: 1700 sheet: None (None), residues: 0 loop : -3.41 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 969 TYR 0.018 0.002 TYR B 818 PHE 0.031 0.003 PHE C 710 TRP 0.081 0.003 TRP C 864 HIS 0.010 0.002 HIS D1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.39 (23968) covalent geometry : angle 0.96767 / 0.46 (32860) SS BOND : bond 0.00271 / 0.13 ( 4) SS BOND : angle 1.15535 / 0.60 ( 8) hydrogen bonds : bond 0.05570 / 3.28 ( 1200) hydrogen bonds : angle 5.85259 / 3.72 ( 3552) Misc. bond : bond 0.00468 / 0.23 ( 4) link_NAG-ASN : bond 0.02467 / 1.24 ( 3) link_NAG-ASN : angle 4.92938 / 2.51 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 340 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6442 (tt) REVERT: A 675 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8316 (tp) REVERT: A 697 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: A 776 TRP cc_start: 0.4330 (t-100) cc_final: 0.3974 (t-100) REVERT: A 817 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7636 (tp) REVERT: A 944 TYR cc_start: 0.8939 (t80) cc_final: 0.8589 (t80) REVERT: A 973 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: B 594 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6351 (tt) REVERT: B 675 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 697 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: B 875 PHE cc_start: 0.8068 (t80) cc_final: 0.7835 (t80) REVERT: B 944 TYR cc_start: 0.9006 (t80) cc_final: 0.8668 (t80) REVERT: B 1157 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8906 (mp) REVERT: C 475 ASN cc_start: 0.7563 (m-40) cc_final: 0.7205 (t0) REVERT: C 594 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6489 (tt) REVERT: C 641 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8958 (tp) REVERT: C 675 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8262 (tp) REVERT: C 697 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7421 (m-10) REVERT: C 817 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7874 (tp) REVERT: C 944 TYR cc_start: 0.8952 (t80) cc_final: 0.8585 (t80) REVERT: C 949 GLU cc_start: 0.8042 (mp0) cc_final: 0.7716 (mm-30) REVERT: C 1068 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7429 (tm-30) REVERT: C 1149 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8083 (pttp) REVERT: D 594 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6394 (tt) REVERT: D 641 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8993 (tp) REVERT: D 675 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8272 (tp) REVERT: D 697 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7354 (m-10) REVERT: D 782 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8760 (tp) REVERT: D 817 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7930 (tp) REVERT: D 944 TYR cc_start: 0.9049 (t80) cc_final: 0.8685 (t80) REVERT: D 955 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7345 (ttp-170) REVERT: D 969 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8120 (ttp80) REVERT: D 973 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: D 1149 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8102 (pttp) outliers start: 193 outliers final: 159 residues processed: 490 average time/residue: 0.1351 time to fit residues: 108.9569 Evaluate side-chains 528 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 344 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 973 GLN Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 697 PHE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 PHE Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain B residue 1143 SER Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 697 PHE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1066 ILE Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1148 LEU Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 697 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 969 ARG Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1062 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1139 ASP Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1149 LYS Chi-restraints excluded: chain D residue 1155 VAL Chi-restraints excluded: chain D residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 GLN C1017 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN D1164 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122869 restraints weight = 39480.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123222 restraints weight = 28998.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123166 restraints weight = 24361.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123198 restraints weight = 24484.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123215 restraints weight = 23497.353| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 23979 Z= 0.393 Angle : 0.971 12.199 32877 Z= 0.461 Chirality : 0.054 0.673 4015 Planarity : 0.006 0.063 4062 Dihedral : 9.840 98.338 3738 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.64 % Favored : 87.19 % Rotamer: Outliers : 11.18 % Allowed : 21.79 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.17), residues: 2428 helix: -0.79 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -3.40 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 969 TYR 0.015 0.002 TYR B1063 PHE 0.031 0.003 PHE C 710 TRP 0.069 0.003 TRP C 864 HIS 0.008 0.002 HIS C1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.39 (23968) covalent geometry : angle 0.96833 / 0.46 (32860) SS BOND : bond 0.00262 / 0.13 ( 4) SS BOND : angle 1.09380 / 0.56 ( 8) hydrogen bonds : bond 0.05542 / 3.26 ( 1200) hydrogen bonds : angle 5.88579 / 3.74 ( 3552) Misc. bond : bond 0.00458 / 0.23 ( 4) link_NAG-ASN : bond 0.02264 / 1.14 ( 3) link_NAG-ASN : angle 4.44219 / 2.29 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5739.39 seconds wall clock time: 98 minutes 30.19 seconds (5910.19 seconds total)