Starting phenix.real_space_refine on Thu Mar 5 13:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9c_24256/03_2026/7n9c_24256.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9c_24256/03_2026/7n9c_24256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n9c_24256/03_2026/7n9c_24256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9c_24256/03_2026/7n9c_24256.map" model { file = "/net/cci-nas-00/data/ceres_data/7n9c_24256/03_2026/7n9c_24256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9c_24256/03_2026/7n9c_24256.cif" } resolution = 3.71 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 14499 2.51 5 N 3826 2.21 5 O 4311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22734 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7542 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 54, 'TRANS': 925} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 6220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6220 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 46, 'TRANS': 765} Chain breaks: 7 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 7018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7018 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 53, 'TRANS': 921} Chain breaks: 7 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 798 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 14, 'GLU:plan': 12, 'ASP:plan': 16, 'GLN:plan1': 8, 'PHE:plan': 10, 'TYR:plan': 13, 'ARG:plan': 7, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 370 Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.61, per 1000 atoms: 0.20 Number of scatterers: 22734 At special positions: 0 Unit cell: (136.74, 140.98, 182.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 4311 8.00 N 3826 7.00 C 14499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 258 " distance=2.05 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 524 " distance=2.02 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 763 " distance=2.02 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 852 " distance=2.02 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS A1124 " - pdb=" SG CYS A1135 " distance=2.01 Simple disulfide: pdb=" SG CYS A1174 " - pdb=" SG CYS A1218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 258 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 393 " distance=2.02 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 754 " - pdb=" SG CYS B 763 " distance=2.03 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 852 " distance=2.02 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 841 " distance=2.00 Simple disulfide: pdb=" SG CYS B1124 " - pdb=" SG CYS B1135 " distance=2.01 Simple disulfide: pdb=" SG CYS B1174 " - pdb=" SG CYS B1218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 223 " - pdb=" SG CYS C 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 428 " - pdb=" SG CYS C 453 " distance=2.01 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 524 " distance=1.99 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 682 " distance=2.02 Simple disulfide: pdb=" SG CYS C 709 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 754 " - pdb=" SG CYS C 763 " distance=2.02 Simple disulfide: pdb=" SG CYS C 830 " - pdb=" SG CYS C 852 " distance=2.01 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 841 " distance=2.02 Simple disulfide: pdb=" SG CYS C1124 " - pdb=" SG CYS C1135 " distance=2.01 Simple disulfide: pdb=" SG CYS C1174 " - pdb=" SG CYS C1218 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5644 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 48 sheets defined 26.1% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 457 through 463 removed outlier: 4.065A pdb=" N TYR A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.583A pdb=" N LEU A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 480 " --> pdb=" O THR A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 480' Processing helix chain 'A' and resid 495 through 502 removed outlier: 4.964A pdb=" N ARG A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.921A pdb=" N ASP A 512 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.573A pdb=" N GLN A 598 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.644A pdb=" N SER A 729 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 730 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 836 Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.883A pdb=" N GLN A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 874 removed outlier: 3.700A pdb=" N ASP A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 916 Processing helix chain 'A' and resid 958 through 977 removed outlier: 3.604A pdb=" N GLY A 977 " --> pdb=" O THR A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.598A pdb=" N GLY A 981 " --> pdb=" O TRP A 978 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 982 " --> pdb=" O THR A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 982' Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.733A pdb=" N TYR A 996 " --> pdb=" O MET A 992 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1010 removed outlier: 4.249A pdb=" N LEU A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1033 removed outlier: 3.681A pdb=" N GLN A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1049 Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1068 through 1074 Processing helix chain 'A' and resid 1077 through 1125 removed outlier: 4.535A pdb=" N VAL A1083 " --> pdb=" O PRO A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1239 Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 829 through 836 Processing helix chain 'B' and resid 838 through 847 removed outlier: 3.641A pdb=" N SER B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 875 removed outlier: 3.767A pdb=" N ASP B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 870 " --> pdb=" O GLN B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 918 Processing helix chain 'B' and resid 958 through 977 Processing helix chain 'B' and resid 978 through 983 removed outlier: 3.512A pdb=" N GLY B 981 " --> pdb=" O TRP B 978 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 983 " --> pdb=" O PHE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1001 Processing helix chain 'B' and resid 1005 through 1011 removed outlier: 3.710A pdb=" N TYR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1033 removed outlier: 3.815A pdb=" N GLN B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B1028 " --> pdb=" O GLY B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1049 Processing helix chain 'B' and resid 1051 through 1058 Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1077 through 1125 removed outlier: 4.443A pdb=" N VAL B1083 " --> pdb=" O PRO B1079 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B1108 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1240 removed outlier: 4.165A pdb=" N GLU B1236 " --> pdb=" O PRO B1232 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.903A pdb=" N VAL C 433 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 445 removed outlier: 3.574A pdb=" N ALA C 444 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 445' Processing helix chain 'C' and resid 456 through 462 removed outlier: 3.911A pdb=" N LEU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 481 removed outlier: 4.379A pdb=" N ASN C 480 " --> pdb=" O THR C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 530 through 535 Processing helix chain 'C' and resid 594 through 598 Processing helix chain 'C' and resid 711 through 716 Processing helix chain 'C' and resid 722 through 730 removed outlier: 4.584A pdb=" N TYR C 728 " --> pdb=" O THR C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 835 Processing helix chain 'C' and resid 839 through 846 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 850 through 875 removed outlier: 3.533A pdb=" N ASP C 867 " --> pdb=" O ALA C 863 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 870 " --> pdb=" O GLN C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 918 Processing helix chain 'C' and resid 958 through 977 Processing helix chain 'C' and resid 989 through 1001 Processing helix chain 'C' and resid 1005 through 1010 Processing helix chain 'C' and resid 1011 through 1032 removed outlier: 3.582A pdb=" N ILE C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN C1027 " --> pdb=" O ILE C1023 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP C1028 " --> pdb=" O GLY C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1036 removed outlier: 3.775A pdb=" N ALA C1036 " --> pdb=" O THR C1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1033 through 1036' Processing helix chain 'C' and resid 1037 through 1057 removed outlier: 3.723A pdb=" N VAL C1043 " --> pdb=" O LYS C1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1060 No H-bonds generated for 'chain 'C' and resid 1058 through 1060' Processing helix chain 'C' and resid 1068 through 1075 Processing helix chain 'C' and resid 1077 through 1125 removed outlier: 4.923A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN C1084 " --> pdb=" O GLU C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1232 through 1239 removed outlier: 3.551A pdb=" N GLU C1236 " --> pdb=" O PRO C1232 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.916A pdb=" N LYS E 65 " --> pdb=" O ASN E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.281A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 3.559A pdb=" N THR A 121 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN A 153 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR A 361 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER A 297 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N HIS A 299 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N LEU A 315 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 128 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.080A pdb=" N ALA C 667 " --> pdb=" O GLY C 658 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP C 666 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 144 removed outlier: 3.550A pdb=" N ASP A 379 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177 removed outlier: 3.532A pdb=" N LEU A 176 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 411 removed outlier: 6.737A pdb=" N VAL A 687 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A 409 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A 685 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY A 686 " --> pdb=" O GLN A 705 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 446 through 450 removed outlier: 3.546A pdb=" N VAL A 604 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 600 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 523 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 470 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR E 104 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 removed outlier: 6.227A pdb=" N CYS A 453 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AB1, first strand: chain 'A' and resid 657 through 658 removed outlier: 6.556A pdb=" N PHE A 657 " --> pdb=" O PHE B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 746 through 747 removed outlier: 6.384A pdb=" N ILE A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AB4, first strand: chain 'A' and resid 803 through 820 removed outlier: 6.157A pdb=" N GLN A1163 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 810 " --> pdb=" O PRO A1161 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 812 " --> pdb=" O TYR A1159 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A1159 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 814 " --> pdb=" O VAL A1157 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1157 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 816 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A1155 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 818 " --> pdb=" O VAL A1153 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A1153 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY A1151 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER A1147 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A1153 " --> pdb=" O PRO A1145 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A1155 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A1143 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A1157 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 803 through 820 removed outlier: 6.157A pdb=" N GLN A1163 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 810 " --> pdb=" O PRO A1161 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 812 " --> pdb=" O TYR A1159 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A1159 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 814 " --> pdb=" O VAL A1157 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1157 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 816 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A1155 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 818 " --> pdb=" O VAL A1153 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A1153 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY A1151 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A1168 " --> pdb=" O SER A1189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 828 Processing sheet with id=AB7, first strand: chain 'A' and resid 1212 through 1214 Processing sheet with id=AB8, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.596A pdb=" N SER B 152 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASN B 153 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 361 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER B 297 " --> pdb=" O PRO B 317 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N HIS B 299 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LEU B 315 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 128 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 140 through 147 removed outlier: 3.591A pdb=" N ASP B 145 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 379 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 176 through 177 removed outlier: 3.747A pdb=" N GLY B 195 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 403 through 411 removed outlier: 6.960A pdb=" N VAL B 687 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 409 " --> pdb=" O GLY B 685 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY B 685 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 686 " --> pdb=" O GLN B 705 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 417 through 419 removed outlier: 6.859A pdb=" N ILE B 418 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B 666 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY B 658 " --> pdb=" O ASP B 666 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 657 " --> pdb=" O PHE C 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 746 through 747 removed outlier: 6.405A pdb=" N ILE B 762 " --> pdb=" O ILE B 758 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 794 through 796 Processing sheet with id=AC6, first strand: chain 'B' and resid 806 through 807 Processing sheet with id=AC7, first strand: chain 'B' and resid 810 through 820 removed outlier: 5.722A pdb=" N TYR B1159 " --> pdb=" O HIS B1140 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS B1140 " --> pdb=" O TYR B1159 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.392A pdb=" N LYS B 825 " --> pdb=" O LEU B 953 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1168 through 1169 removed outlier: 3.889A pdb=" N THR B1168 " --> pdb=" O SER B1189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1212 through 1214 Processing sheet with id=AD2, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AD3, first strand: chain 'C' and resid 139 through 147 removed outlier: 3.598A pdb=" N ASP C 145 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR C 366 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP C 382 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C 368 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA C 380 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS C 370 " --> pdb=" O THR C 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.535A pdb=" N LYS C 221 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 316 through 321 removed outlier: 7.089A pdb=" N ILE C 295 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP C 320 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE C 293 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN C 280 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU C 188 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 282 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 182 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 403 through 411 removed outlier: 5.663A pdb=" N ILE C 404 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR C 691 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN C 406 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 689 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 408 " --> pdb=" O VAL C 687 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY C 686 " --> pdb=" O GLN C 705 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 446 through 450 removed outlier: 4.148A pdb=" N ASN C 446 " --> pdb=" O SER C 491 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 491 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 494 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 601 " --> pdb=" O TRP C 528 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 605 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C 524 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 453 through 454 removed outlier: 6.524A pdb=" N CYS C 453 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 544 through 546 Processing sheet with id=AE1, first strand: chain 'C' and resid 746 through 747 removed outlier: 6.886A pdb=" N GLU C 746 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N THR C 788 " --> pdb=" O GLU C 746 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 762 " --> pdb=" O ILE C 758 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 803 through 820 removed outlier: 6.651A pdb=" N SER C 803 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1168 " --> pdb=" O SER C 803 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 805 " --> pdb=" O ASN C1166 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN C1166 " --> pdb=" O ALA C 805 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU C1164 " --> pdb=" O PRO C 807 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C1151 " --> pdb=" O ALA C1148 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C1148 " --> pdb=" O GLY C1151 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR C1159 " --> pdb=" O HIS C1140 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N HIS C1140 " --> pdb=" O TYR C1159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 803 through 820 removed outlier: 6.651A pdb=" N SER C 803 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1168 " --> pdb=" O SER C 803 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 805 " --> pdb=" O ASN C1166 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN C1166 " --> pdb=" O ALA C 805 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU C1164 " --> pdb=" O PRO C 807 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR C1168 " --> pdb=" O SER C1189 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C1170 " --> pdb=" O PHE C1187 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE C1187 " --> pdb=" O ALA C1170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 826 through 828 Processing sheet with id=AE5, first strand: chain 'C' and resid 1212 through 1217 removed outlier: 4.013A pdb=" N ALA C1179 " --> pdb=" O SER C1215 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AE7, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.584A pdb=" N TYR D 59 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 97 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.584A pdb=" N TYR D 59 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 97 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 94 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 68 through 72 removed outlier: 3.882A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.521A pdb=" N TYR E 59 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN E 39 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR E 115 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.521A pdb=" N TYR E 59 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN E 39 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 70 through 73 removed outlier: 3.679A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2634 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 1850 1.24 - 1.38: 6917 1.38 - 1.53: 12315 1.53 - 1.67: 2029 1.67 - 1.82: 126 Bond restraints: 23237 Sorted by residual: bond pdb=" C GLY C 496 " pdb=" O GLY C 496 " ideal model delta sigma weight residual 1.234 1.091 0.142 1.21e-02 6.83e+03 1.38e+02 bond pdb=" C TYR D 106 " pdb=" O TYR D 106 " ideal model delta sigma weight residual 1.234 1.108 0.126 1.26e-02 6.30e+03 9.94e+01 bond pdb=" C PHE A 469 " pdb=" O PHE A 469 " ideal model delta sigma weight residual 1.235 1.120 0.115 1.22e-02 6.72e+03 8.81e+01 bond pdb=" C PHE C 469 " pdb=" O PHE C 469 " ideal model delta sigma weight residual 1.235 1.150 0.085 1.22e-02 6.72e+03 4.87e+01 bond pdb=" C VAL C 474 " pdb=" O VAL C 474 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.00e-02 1.00e+04 3.35e+01 ... (remaining 23232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 31668 6.87 - 13.73: 36 13.73 - 20.60: 1 20.60 - 27.47: 1 27.47 - 34.34: 1 Bond angle restraints: 31707 Sorted by residual: angle pdb=" CE2 TYR D 104 " pdb=" CZ TYR D 104 " pdb=" OH TYR D 104 " ideal model delta sigma weight residual 119.90 85.56 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N LEU A1051 " pdb=" CA LEU A1051 " pdb=" C LEU A1051 " ideal model delta sigma weight residual 113.97 101.58 12.39 1.28e+00 6.10e-01 9.37e+01 angle pdb=" C PRO C 476 " pdb=" CA PRO C 476 " pdb=" CB PRO C 476 " ideal model delta sigma weight residual 110.27 98.41 11.86 1.29e+00 6.01e-01 8.45e+01 angle pdb=" CE1 TYR D 104 " pdb=" CZ TYR D 104 " pdb=" OH TYR D 104 " ideal model delta sigma weight residual 119.90 147.28 -27.38 3.00e+00 1.11e-01 8.33e+01 angle pdb=" N LEU B1051 " pdb=" CA LEU B1051 " pdb=" C LEU B1051 " ideal model delta sigma weight residual 113.50 102.31 11.19 1.23e+00 6.61e-01 8.28e+01 ... (remaining 31702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12588 17.95 - 35.90: 1019 35.90 - 53.84: 135 53.84 - 71.79: 45 71.79 - 89.74: 33 Dihedral angle restraints: 13820 sinusoidal: 5063 harmonic: 8757 Sorted by residual: dihedral pdb=" CB CYS A 383 " pdb=" SG CYS A 383 " pdb=" SG CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sinusoidal sigma weight residual -86.00 -173.36 87.36 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS C 383 " pdb=" SG CYS C 383 " pdb=" SG CYS C 393 " pdb=" CB CYS C 393 " ideal model delta sinusoidal sigma weight residual 93.00 170.00 -77.00 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" C PHE C 469 " pdb=" N PHE C 469 " pdb=" CA PHE C 469 " pdb=" CB PHE C 469 " ideal model delta harmonic sigma weight residual -122.60 -143.51 20.91 0 2.50e+00 1.60e-01 7.00e+01 ... (remaining 13817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 3101 0.157 - 0.314: 560 0.314 - 0.471: 8 0.471 - 0.628: 0 0.628 - 0.785: 1 Chirality restraints: 3670 Sorted by residual: chirality pdb=" CA PHE C 469 " pdb=" N PHE C 469 " pdb=" C PHE C 469 " pdb=" CB PHE C 469 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA GLN B1234 " pdb=" N GLN B1234 " pdb=" C GLN B1234 " pdb=" CB GLN B1234 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA TYR D 103 " pdb=" N TYR D 103 " pdb=" C TYR D 103 " pdb=" CB TYR D 103 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 3667 not shown) Planarity restraints: 4133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 104 " -0.011 2.00e-02 2.50e+03 8.74e-02 1.53e+02 pdb=" CG TYR D 104 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR D 104 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 104 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR D 104 " 0.126 2.00e-02 2.50e+03 pdb=" CE2 TYR D 104 " 0.101 2.00e-02 2.50e+03 pdb=" CZ TYR D 104 " -0.169 2.00e-02 2.50e+03 pdb=" OH TYR D 104 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 474 " -0.028 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C VAL C 474 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL C 474 " -0.039 2.00e-02 2.50e+03 pdb=" N SER C 475 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 109 " -0.000 2.00e-02 2.50e+03 3.67e-02 2.36e+01 pdb=" CG PHE E 109 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE E 109 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 109 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE E 109 " 0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE E 109 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 109 " -0.058 2.00e-02 2.50e+03 ... (remaining 4130 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1948 2.73 - 3.27: 22984 3.27 - 3.81: 35970 3.81 - 4.36: 45872 4.36 - 4.90: 76148 Nonbonded interactions: 182922 Sorted by model distance: nonbonded pdb=" O PHE C 466 " pdb=" OH TYR D 59 " model vdw 2.185 3.040 nonbonded pdb=" O ALA A 464 " pdb=" OH TYR E 59 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 461 " pdb=" O PRO A 476 " model vdw 2.229 3.040 nonbonded pdb=" O SER C 976 " pdb=" OG1 THR C 979 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR B 848 " pdb=" OD2 ASP B1086 " model vdw 2.283 3.040 ... (remaining 182917 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 119 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 158 or resid 174 through 178 o \ r (resid 179 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 80 through 185 or (resid 186 through 192 and (name N or name CA or name C or nam \ e O or name CB )) or resid 193 through 199 or (resid 200 through 208 and (name N \ or name CA or name C or name O or name CB )) or resid 209 through 211 or (resid \ 212 and (name N or name CA or name C or name O or name CB )) or resid 213 throu \ gh 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or \ resid 219 through 225 or (resid 226 and (name N or name CA or name C or name O \ or name CB )) or resid 227 through 229 or (resid 230 and (name N or name CA or n \ ame C or name O or name CB )) or resid 231 or (resid 232 and (name N or name CA \ or name C or name O or name CB )) or resid 258 or (resid 259 through 282 and (na \ me N or name CA or name C or name O or name CB )) or resid 283 through 289 or (r \ esid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 296 or (resid 297 and (name N or name CA or name C or name O or name CB ) \ ) or resid 298 through 299 or (resid 300 and (name N or name CA or name C or nam \ e O or name CB )) or resid 301 through 309 or (resid 310 and (name N or name CA \ or name C or name O or name CB )) or resid 311 through 320 or (resid 321 and (na \ me N or name CA or name C or name O or name CB )) or resid 322 through 372 or (r \ esid 373 and (name N or name CA or name C or name O or name CB )) or resid 374 t \ hrough 415 or (resid 416 and (name N or name CA or name C or name O or name CB ) \ ) or resid 417 through 423 or (resid 424 through 427 and (name N or name CA or n \ ame C or name O or name CB )) or resid 428 through 431 or (resid 432 through 434 \ and (name N or name CA or name C or name O or name CB )) or resid 435 through 4 \ 36 or (resid 437 through 438 and (name N or name CA or name C or name O or name \ CB )) or resid 439 through 440 or (resid 441 through 444 and (name N or name CA \ or name C or name O or name CB )) or resid 445 through 448 or (resid 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 or (resid 451 thr \ ough 452 and (name N or name CA or name C or name O or name CB )) or resid 453 t \ hrough 455 or (resid 456 through 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 or (resid 467 through 470 and (name N or name CA or n \ ame C or name O or name CB )) or resid 471 or (resid 472 and (name N or name CA \ or name C or name O or name CB )) or resid 473 or (resid 474 through 475 and (na \ me N or name CA or name C or name O or name CB )) or resid 476 or (resid 477 thr \ ough 482 and (name N or name CA or name C or name O or name CB )) or resid 483 t \ hrough 489 or (resid 490 through 495 and (name N or name CA or name C or name O \ or name CB )) or resid 496 or (resid 497 through 503 and (name N or name CA or n \ ame C or name O or name CB )) or resid 504 through 505 or (resid 506 through 507 \ and (name N or name CA or name C or name O or name CB )) or resid 508 or (resid \ 509 through 517 and (name N or name CA or name C or name O or name CB )) or res \ id 518 or (resid 519 through 522 and (name N or name CA or name C or name O or n \ ame CB )) or resid 523 through 524 or (resid 525 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 533 or (resid 534 thr \ ough 537 and (name N or name CA or name C or name O or name CB )) or resid 538 t \ hrough 539 or (resid 540 through 587 and (name N or name CA or name C or name O \ or name CB )) or resid 588 or (resid 589 through 590 and (name N or name CA or n \ ame C or name O or name CB )) or resid 591 or (resid 592 through 593 and (name N \ or name CA or name C or name O or name CB )) or resid 594 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throu \ gh 599 or (resid 600 through 612 and (name N or name CA or name C or name O or n \ ame CB )) or resid 613 through 614 or (resid 615 through 616 and (name N or name \ CA or name C or name O or name CB )) or resid 617 through 619 or (resid 620 thr \ ough 623 and (name N or name CA or name C or name O or name CB )) or resid 624 t \ hrough 628 or (resid 629 and (name N or name CA or name C or name O or name CB ) \ ) or resid 630 through 672 or (resid 673 and (name N or name CA or name C or nam \ e O or name CB )) or resid 674 through 745 or (resid 746 and (name N or name CA \ or name C or name O or name CB )) or resid 747 through 836 or (resid 837 through \ 838 and (name N or name CA or name C or name O or name CB )) or resid 839 or (r \ esid 840 and (name N or name CA or name C or name O or name CB )) or resid 841 o \ r (resid 842 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 43 through 849 or (resid 850 and (name N or name CA or name C or name O or name \ CB )) or resid 851 through 902 or (resid 903 and (name N or name CA or name C or \ name O or name CB )) or resid 904 through 905 or (resid 906 and (name N or name \ CA or name C or name O or name CB )) or resid 907 through 919 or resid 948 thro \ ugh 1028 or (resid 1029 and (name N or name CA or name C or name O or name CB )) \ or resid 1030 or (resid 1031 through 1033 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1034 through 1065 or (resid 1066 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1067 through 1079 or (resid 1080 \ through 1081 and (name N or name CA or name C or name O or name CB )) or resid \ 1082 through 1218 or (resid 1219 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1220 through 1233 or (resid 1234 and (name N or name CA or na \ me C or name O or name CB )) or resid 1235 through 1239)) selection = (chain 'C' and (resid 119 through 232 or resid 258 through 264 or (resid 279 thr \ ough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 t \ hrough 312 or (resid 313 through 314 and (name N or name CA or name C or name O \ or name CB )) or resid 315 through 319 or (resid 320 through 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 through 328 or (resid 329 \ and (name N or name CA or name C or name O or name CB )) or resid 330 through 5 \ 47 or resid 584 through 645 or (resid 646 and (name N or name CA or name C or na \ me O or name CB )) or resid 647 through 659 or (resid 660 and (name N or name CA \ or name C or name O or name CB )) or resid 661 through 767 or (resid 768 and (n \ ame N or name CA or name C or name O or name CB )) or resid 782 through 793 or ( \ resid 794 and (name N or name CA or name C or name O or name CB )) or resid 795 \ through 885 or (resid 886 and (name N or name CA or name C or name O or name CB \ )) or resid 887 through 904 or (resid 905 through 906 and (name N or name CA or \ name C or name O or name CB )) or resid 907 through 1238 or (resid 1239 and (nam \ e N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 1 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 126)) selection = (chain 'E' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 126)) } 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.880 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.013 0.142 23272 Z= 0.953 Angle : 1.630 34.337 31777 Z= 1.175 Chirality : 0.112 0.785 3670 Planarity : 0.009 0.087 4133 Dihedral : 13.879 89.738 8071 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.21 % Allowed : 4.40 % Favored : 95.39 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 2967 helix: 1.40 (0.20), residues: 657 sheet: -0.32 (0.20), residues: 631 loop : -1.39 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 669 TYR 0.169 0.005 TYR D 104 PHE 0.061 0.003 PHE E 109 TRP 0.018 0.003 TRP A 528 HIS 0.007 0.002 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.01320 (23237) covalent geometry : angle 1.62857 (31707) SS BOND : bond 0.01325 ( 35) SS BOND : angle 2.02844 ( 70) hydrogen bonds : bond 0.22061 ( 934) hydrogen bonds : angle 9.04588 ( 2634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 239 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6588 (p0) REVERT: B 306 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7384 (mtp-110) REVERT: B 1062 PHE cc_start: 0.8363 (m-80) cc_final: 0.8105 (m-80) REVERT: B 1214 VAL cc_start: 0.8826 (t) cc_final: 0.8555 (m) REVERT: C 331 GLN cc_start: 0.6543 (mm110) cc_final: 0.6282 (tp40) REVERT: C 423 ASN cc_start: 0.5366 (t0) cc_final: 0.4924 (p0) REVERT: C 466 PHE cc_start: 0.2445 (t80) cc_final: 0.2175 (t80) REVERT: C 834 ILE cc_start: 0.9286 (mt) cc_final: 0.8985 (mt) REVERT: E 34 MET cc_start: 0.3956 (ppp) cc_final: 0.3293 (ppp) outliers start: 5 outliers final: 0 residues processed: 243 average time/residue: 0.1364 time to fit residues: 54.5554 Evaluate side-chains 180 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 879 GLN A1041 GLN ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS ** B 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN C 843 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.129638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097199 restraints weight = 58145.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096054 restraints weight = 37909.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096555 restraints weight = 29366.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096978 restraints weight = 25260.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097061 restraints weight = 21566.263| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23272 Z= 0.146 Angle : 0.609 9.862 31777 Z= 0.329 Chirality : 0.046 0.187 3670 Planarity : 0.005 0.051 4133 Dihedral : 5.198 58.161 3203 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.09 % Allowed : 8.22 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 2967 helix: 1.28 (0.20), residues: 675 sheet: -0.47 (0.19), residues: 705 loop : -1.31 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 136 TYR 0.023 0.002 TYR C1159 PHE 0.015 0.001 PHE E 47 TRP 0.015 0.001 TRP C 156 HIS 0.004 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00309 (23237) covalent geometry : angle 0.60567 (31707) SS BOND : bond 0.00308 ( 35) SS BOND : angle 1.49339 ( 70) hydrogen bonds : bond 0.04913 ( 934) hydrogen bonds : angle 6.77050 ( 2634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6425 (p0) REVERT: A 879 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: A 956 LEU cc_start: 0.8706 (tp) cc_final: 0.8365 (tt) REVERT: B 306 ARG cc_start: 0.7477 (mmm-85) cc_final: 0.7237 (mtp-110) REVERT: B 1043 VAL cc_start: 0.9061 (t) cc_final: 0.8551 (p) REVERT: B 1047 ASN cc_start: 0.8068 (m110) cc_final: 0.7575 (m110) REVERT: B 1057 GLN cc_start: 0.8050 (mm110) cc_final: 0.7539 (mm-40) REVERT: B 1062 PHE cc_start: 0.8175 (m-80) cc_final: 0.7269 (m-80) REVERT: B 1214 VAL cc_start: 0.8690 (t) cc_final: 0.8487 (m) REVERT: C 156 TRP cc_start: 0.5783 (t60) cc_final: 0.5536 (t60) REVERT: C 157 PHE cc_start: 0.6260 (m-80) cc_final: 0.6014 (m-80) REVERT: C 331 GLN cc_start: 0.6737 (mm110) cc_final: 0.6086 (tp40) REVERT: C 423 ASN cc_start: 0.5328 (t0) cc_final: 0.4781 (p0) REVERT: D 59 TYR cc_start: 0.5778 (t80) cc_final: 0.5562 (t80) REVERT: E 34 MET cc_start: 0.4288 (ppp) cc_final: 0.3853 (ppp) outliers start: 26 outliers final: 13 residues processed: 247 average time/residue: 0.1400 time to fit residues: 56.2573 Evaluate side-chains 205 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 173 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 204 optimal weight: 0.0010 chunk 189 optimal weight: 40.0000 chunk 88 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 chunk 4 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN B 288 ASN ** B 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1198 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.130072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097385 restraints weight = 58347.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.097054 restraints weight = 37243.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.097121 restraints weight = 27513.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.097399 restraints weight = 27076.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097545 restraints weight = 22437.621| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23272 Z= 0.110 Angle : 0.552 12.307 31777 Z= 0.291 Chirality : 0.044 0.172 3670 Planarity : 0.004 0.054 4133 Dihedral : 4.779 58.615 3203 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.13 % Allowed : 10.19 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 2967 helix: 1.50 (0.21), residues: 658 sheet: -0.42 (0.19), residues: 737 loop : -1.18 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1075 TYR 0.018 0.001 TYR C1159 PHE 0.014 0.001 PHE B 151 TRP 0.018 0.001 TRP A 156 HIS 0.003 0.000 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00233 (23237) covalent geometry : angle 0.54841 (31707) SS BOND : bond 0.00250 ( 35) SS BOND : angle 1.39496 ( 70) hydrogen bonds : bond 0.04027 ( 934) hydrogen bonds : angle 6.02155 ( 2634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 LEU cc_start: 0.8784 (tp) cc_final: 0.8405 (tt) REVERT: B 306 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7415 (mtp-110) REVERT: B 1057 GLN cc_start: 0.8079 (mm110) cc_final: 0.7489 (mm-40) REVERT: B 1062 PHE cc_start: 0.8013 (m-80) cc_final: 0.6965 (m-80) REVERT: B 1214 VAL cc_start: 0.8723 (t) cc_final: 0.8510 (m) REVERT: B 1231 ASP cc_start: 0.7852 (t0) cc_final: 0.7438 (t70) REVERT: C 294 LYS cc_start: 0.6780 (mppt) cc_final: 0.6489 (mppt) REVERT: C 361 TYR cc_start: 0.5910 (m-80) cc_final: 0.5705 (m-80) REVERT: C 423 ASN cc_start: 0.5273 (t0) cc_final: 0.4621 (p0) REVERT: C 755 ASP cc_start: 0.7475 (p0) cc_final: 0.6838 (m-30) REVERT: E 34 MET cc_start: 0.4225 (ppp) cc_final: 0.3721 (ppp) outliers start: 27 outliers final: 14 residues processed: 244 average time/residue: 0.1367 time to fit residues: 54.7915 Evaluate side-chains 206 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 18 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 271 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B1047 ASN B1103 GLN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 ASN C 869 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.129833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096989 restraints weight = 57942.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095906 restraints weight = 40556.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096170 restraints weight = 31159.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096510 restraints weight = 28077.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096617 restraints weight = 24889.965| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23272 Z= 0.220 Angle : 0.618 10.981 31777 Z= 0.326 Chirality : 0.046 0.173 3670 Planarity : 0.005 0.054 4133 Dihedral : 4.990 28.976 3201 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.85 % Allowed : 13.05 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 2967 helix: 1.15 (0.20), residues: 670 sheet: -0.63 (0.18), residues: 724 loop : -1.36 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 420 TYR 0.036 0.002 TYR D 104 PHE 0.024 0.002 PHE A 998 TRP 0.019 0.002 TRP C 156 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00500 (23237) covalent geometry : angle 0.61552 (31707) SS BOND : bond 0.00364 ( 35) SS BOND : angle 1.31044 ( 70) hydrogen bonds : bond 0.04309 ( 934) hydrogen bonds : angle 6.08854 ( 2634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 956 LEU cc_start: 0.8800 (tp) cc_final: 0.8409 (tt) REVERT: A 1109 GLU cc_start: 0.7543 (tt0) cc_final: 0.7275 (tp30) REVERT: B 1057 GLN cc_start: 0.8117 (mm110) cc_final: 0.7542 (mm-40) REVERT: B 1062 PHE cc_start: 0.8067 (m-80) cc_final: 0.7137 (m-80) REVERT: B 1214 VAL cc_start: 0.8768 (t) cc_final: 0.8545 (m) REVERT: B 1231 ASP cc_start: 0.7988 (t0) cc_final: 0.7590 (t0) REVERT: C 423 ASN cc_start: 0.5637 (t0) cc_final: 0.4694 (p0) REVERT: C 755 ASP cc_start: 0.7432 (p0) cc_final: 0.6959 (m-30) REVERT: D 50 THR cc_start: 0.1468 (OUTLIER) cc_final: 0.1257 (m) REVERT: E 34 MET cc_start: 0.4398 (ppp) cc_final: 0.3954 (ppp) outliers start: 44 outliers final: 29 residues processed: 226 average time/residue: 0.1319 time to fit residues: 49.6609 Evaluate side-chains 216 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 258 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 283 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 GLN A1146 GLN B 717 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.128237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095438 restraints weight = 58326.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094168 restraints weight = 40788.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094608 restraints weight = 32250.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.094953 restraints weight = 26557.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095069 restraints weight = 23678.031| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23272 Z= 0.206 Angle : 0.599 11.747 31777 Z= 0.315 Chirality : 0.045 0.170 3670 Planarity : 0.004 0.053 4133 Dihedral : 5.006 28.408 3201 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.68 % Allowed : 13.72 % Favored : 83.60 % 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: -1.01 (0.15), residues: 2967 helix: 1.07 (0.20), residues: 671 sheet: -0.68 (0.19), residues: 697 loop : -1.45 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 38 TYR 0.019 0.002 TYR C1159 PHE 0.020 0.002 PHE A 998 TRP 0.017 0.002 TRP A 156 HIS 0.004 0.001 HIS C1193 Details of bonding type rmsd covalent geometry : bond 0.00466 (23237) covalent geometry : angle 0.59691 (31707) SS BOND : bond 0.00293 ( 35) SS BOND : angle 1.26618 ( 70) hydrogen bonds : bond 0.04165 ( 934) hydrogen bonds : angle 6.01744 ( 2634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.6195 (mmtt) cc_final: 0.5947 (mmmt) REVERT: A 705 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: A 956 LEU cc_start: 0.8776 (tp) cc_final: 0.8376 (tt) REVERT: A 1121 MET cc_start: 0.8474 (tpp) cc_final: 0.8184 (tpp) REVERT: B 287 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7551 (ttpt) REVERT: B 306 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6452 (ttp-110) REVERT: B 413 GLN cc_start: 0.5884 (mp10) cc_final: 0.5649 (mp10) REVERT: B 876 GLN cc_start: 0.7708 (mt0) cc_final: 0.7497 (mt0) REVERT: B 1057 GLN cc_start: 0.8078 (mm110) cc_final: 0.7546 (mm-40) REVERT: B 1062 PHE cc_start: 0.8058 (m-80) cc_final: 0.7101 (m-80) REVERT: B 1214 VAL cc_start: 0.8789 (t) cc_final: 0.8562 (m) REVERT: B 1231 ASP cc_start: 0.7943 (t0) cc_final: 0.7393 (t0) REVERT: C 755 ASP cc_start: 0.7401 (p0) cc_final: 0.6861 (m-30) REVERT: D 50 THR cc_start: 0.1638 (OUTLIER) cc_final: 0.1408 (m) REVERT: E 34 MET cc_start: 0.4486 (ppp) cc_final: 0.4039 (ppp) outliers start: 64 outliers final: 40 residues processed: 240 average time/residue: 0.1307 time to fit residues: 52.7529 Evaluate side-chains 221 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 698 ASN Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 201 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 750 ASN B 993 GLN B1047 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.130245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097144 restraints weight = 57192.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096352 restraints weight = 38734.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096657 restraints weight = 28561.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096854 restraints weight = 26196.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096990 restraints weight = 23405.794| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23272 Z= 0.164 Angle : 0.571 11.197 31777 Z= 0.299 Chirality : 0.045 0.295 3670 Planarity : 0.004 0.057 4133 Dihedral : 4.853 26.886 3201 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.64 % Allowed : 14.72 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 2967 helix: 1.21 (0.20), residues: 665 sheet: -0.65 (0.18), residues: 731 loop : -1.47 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1075 TYR 0.020 0.001 TYR C 296 PHE 0.024 0.001 PHE C 284 TRP 0.017 0.001 TRP A 156 HIS 0.003 0.001 HIS C1193 Details of bonding type rmsd covalent geometry : bond 0.00370 (23237) covalent geometry : angle 0.56554 (31707) SS BOND : bond 0.00301 ( 35) SS BOND : angle 1.77490 ( 70) hydrogen bonds : bond 0.03935 ( 934) hydrogen bonds : angle 5.88192 ( 2634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.6176 (mmtt) cc_final: 0.5620 (mptt) REVERT: A 705 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: A 956 LEU cc_start: 0.8721 (tp) cc_final: 0.8336 (tt) REVERT: A 1121 MET cc_start: 0.8427 (tpp) cc_final: 0.8160 (tpp) REVERT: B 287 LYS cc_start: 0.7941 (ptmt) cc_final: 0.7574 (ttpt) REVERT: B 306 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6578 (ttp-110) REVERT: B 413 GLN cc_start: 0.5957 (mp10) cc_final: 0.5748 (mp10) REVERT: B 1057 GLN cc_start: 0.8014 (mm110) cc_final: 0.7523 (mm-40) REVERT: B 1062 PHE cc_start: 0.8031 (m-80) cc_final: 0.7045 (m-80) REVERT: B 1214 VAL cc_start: 0.8794 (t) cc_final: 0.8578 (m) REVERT: B 1231 ASP cc_start: 0.7929 (t0) cc_final: 0.7307 (t0) REVERT: C 755 ASP cc_start: 0.7407 (p0) cc_final: 0.6873 (m-30) REVERT: D 50 THR cc_start: 0.1545 (OUTLIER) cc_final: 0.1301 (m) REVERT: E 34 MET cc_start: 0.4467 (ppp) cc_final: 0.4035 (ppp) outliers start: 63 outliers final: 41 residues processed: 253 average time/residue: 0.1337 time to fit residues: 56.6639 Evaluate side-chains 233 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 852 CYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 698 ASN Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 80 optimal weight: 0.0870 chunk 118 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 214 optimal weight: 50.0000 chunk 87 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 276 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.132264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098320 restraints weight = 56882.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.098367 restraints weight = 38236.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099209 restraints weight = 26181.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098951 restraints weight = 24180.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099364 restraints weight = 22275.120| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23272 Z= 0.110 Angle : 0.537 9.431 31777 Z= 0.278 Chirality : 0.044 0.199 3670 Planarity : 0.004 0.054 4133 Dihedral : 4.529 23.929 3201 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 15.35 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 2967 helix: 1.49 (0.21), residues: 659 sheet: -0.58 (0.19), residues: 704 loop : -1.25 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 38 TYR 0.017 0.001 TYR A 357 PHE 0.020 0.001 PHE C 284 TRP 0.019 0.001 TRP A 156 HIS 0.002 0.000 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00243 (23237) covalent geometry : angle 0.53203 (31707) SS BOND : bond 0.00292 ( 35) SS BOND : angle 1.59357 ( 70) hydrogen bonds : bond 0.03568 ( 934) hydrogen bonds : angle 5.54425 ( 2634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 TYR cc_start: 0.5060 (p90) cc_final: 0.4021 (t80) REVERT: A 621 LYS cc_start: 0.6094 (mmtt) cc_final: 0.5615 (mptt) REVERT: A 677 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 705 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: A 956 LEU cc_start: 0.8658 (tp) cc_final: 0.8328 (tt) REVERT: B 287 LYS cc_start: 0.7907 (ptmt) cc_final: 0.7563 (ttpt) REVERT: B 306 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6679 (ttp-110) REVERT: B 1047 ASN cc_start: 0.7735 (m110) cc_final: 0.7528 (m-40) REVERT: B 1057 GLN cc_start: 0.7925 (mm110) cc_final: 0.7418 (mm-40) REVERT: B 1062 PHE cc_start: 0.7951 (m-80) cc_final: 0.7048 (m-80) REVERT: B 1214 VAL cc_start: 0.8787 (t) cc_final: 0.8576 (m) REVERT: B 1231 ASP cc_start: 0.7869 (t0) cc_final: 0.7245 (t70) REVERT: C 657 PHE cc_start: 0.7663 (p90) cc_final: 0.7341 (p90) REVERT: D 50 THR cc_start: 0.1478 (OUTLIER) cc_final: 0.1147 (m) REVERT: E 34 MET cc_start: 0.4593 (ppp) cc_final: 0.4237 (ppp) outliers start: 45 outliers final: 32 residues processed: 238 average time/residue: 0.1297 time to fit residues: 51.4004 Evaluate side-chains 226 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 268 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 189 optimal weight: 40.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN B 406 GLN B 876 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095552 restraints weight = 58020.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094556 restraints weight = 39668.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095087 restraints weight = 28430.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095359 restraints weight = 25762.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095509 restraints weight = 22606.730| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23272 Z= 0.173 Angle : 0.572 10.471 31777 Z= 0.298 Chirality : 0.044 0.193 3670 Planarity : 0.004 0.054 4133 Dihedral : 4.689 27.228 3201 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.14 % Allowed : 15.77 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 2967 helix: 1.26 (0.20), residues: 667 sheet: -0.60 (0.19), residues: 720 loop : -1.31 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 495 TYR 0.017 0.001 TYR C1159 PHE 0.018 0.002 PHE C 286 TRP 0.016 0.001 TRP A 156 HIS 0.004 0.001 HIS C1193 Details of bonding type rmsd covalent geometry : bond 0.00391 (23237) covalent geometry : angle 0.56759 (31707) SS BOND : bond 0.00353 ( 35) SS BOND : angle 1.67582 ( 70) hydrogen bonds : bond 0.03817 ( 934) hydrogen bonds : angle 5.63651 ( 2634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.6129 (mmtt) cc_final: 0.5665 (mptt) REVERT: A 705 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7160 (mp10) REVERT: A 956 LEU cc_start: 0.8733 (tp) cc_final: 0.8373 (tt) REVERT: A 1121 MET cc_start: 0.8417 (tpp) cc_final: 0.8133 (tpp) REVERT: A 1220 VAL cc_start: 0.6740 (p) cc_final: 0.6351 (t) REVERT: B 287 LYS cc_start: 0.7864 (ptmt) cc_final: 0.7462 (ttpt) REVERT: B 306 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6564 (ttp-110) REVERT: B 1057 GLN cc_start: 0.7961 (mm110) cc_final: 0.7635 (mm-40) REVERT: B 1062 PHE cc_start: 0.8006 (m-80) cc_final: 0.7169 (m-80) REVERT: B 1214 VAL cc_start: 0.8801 (t) cc_final: 0.8588 (m) REVERT: B 1231 ASP cc_start: 0.7958 (t0) cc_final: 0.7312 (t0) REVERT: D 34 MET cc_start: 0.2463 (ptt) cc_final: 0.1946 (mmp) REVERT: D 50 THR cc_start: 0.1613 (OUTLIER) cc_final: 0.1393 (m) REVERT: E 34 MET cc_start: 0.4732 (ppp) cc_final: 0.4340 (ppp) outliers start: 51 outliers final: 42 residues processed: 227 average time/residue: 0.1341 time to fit residues: 50.3299 Evaluate side-chains 228 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 284 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 211 optimal weight: 50.0000 chunk 296 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.134864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103197 restraints weight = 59380.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101842 restraints weight = 38397.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101983 restraints weight = 29630.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102336 restraints weight = 27574.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103008 restraints weight = 23078.426| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23272 Z= 0.132 Angle : 0.549 9.972 31777 Z= 0.285 Chirality : 0.044 0.191 3670 Planarity : 0.004 0.056 4133 Dihedral : 4.583 26.749 3201 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.01 % Allowed : 16.07 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 2967 helix: 1.36 (0.21), residues: 661 sheet: -0.59 (0.19), residues: 720 loop : -1.29 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 38 TYR 0.017 0.001 TYR C1159 PHE 0.022 0.001 PHE C 284 TRP 0.017 0.001 TRP A 156 HIS 0.003 0.001 HIS B 717 Details of bonding type rmsd covalent geometry : bond 0.00297 (23237) covalent geometry : angle 0.54372 (31707) SS BOND : bond 0.00470 ( 35) SS BOND : angle 1.64309 ( 70) hydrogen bonds : bond 0.03650 ( 934) hydrogen bonds : angle 5.53798 ( 2634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 TYR cc_start: 0.5281 (p90) cc_final: 0.4250 (t80) REVERT: A 621 LYS cc_start: 0.6117 (mmtt) cc_final: 0.5676 (mptt) REVERT: A 705 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: A 956 LEU cc_start: 0.8660 (tp) cc_final: 0.8337 (tt) REVERT: A 1121 MET cc_start: 0.8271 (tpp) cc_final: 0.7985 (tpp) REVERT: A 1220 VAL cc_start: 0.6465 (p) cc_final: 0.6156 (t) REVERT: B 287 LYS cc_start: 0.7933 (ptmt) cc_final: 0.7522 (ttpt) REVERT: B 306 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6637 (ttp-110) REVERT: B 1047 ASN cc_start: 0.7727 (m110) cc_final: 0.7446 (m-40) REVERT: B 1057 GLN cc_start: 0.7914 (mm110) cc_final: 0.7616 (mm-40) REVERT: B 1062 PHE cc_start: 0.7981 (m-80) cc_final: 0.7185 (m-80) REVERT: B 1214 VAL cc_start: 0.8804 (t) cc_final: 0.8591 (m) REVERT: B 1231 ASP cc_start: 0.7889 (t0) cc_final: 0.7224 (t0) REVERT: C 657 PHE cc_start: 0.7628 (p90) cc_final: 0.7324 (p90) REVERT: C 992 MET cc_start: 0.7704 (mtp) cc_final: 0.7475 (mtm) REVERT: D 34 MET cc_start: 0.2499 (ptt) cc_final: 0.1955 (mmp) REVERT: D 50 THR cc_start: 0.1963 (OUTLIER) cc_final: 0.1747 (m) REVERT: E 34 MET cc_start: 0.4831 (ppp) cc_final: 0.4410 (ppp) outliers start: 48 outliers final: 42 residues processed: 226 average time/residue: 0.1329 time to fit residues: 50.2484 Evaluate side-chains 229 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 101 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 232 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104308 restraints weight = 59208.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103692 restraints weight = 37245.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104063 restraints weight = 26802.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.104355 restraints weight = 24799.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.104405 restraints weight = 22198.538| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23272 Z= 0.116 Angle : 0.538 9.034 31777 Z= 0.278 Chirality : 0.043 0.179 3670 Planarity : 0.004 0.058 4133 Dihedral : 4.443 24.707 3201 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.97 % Allowed : 16.11 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 2967 helix: 1.49 (0.21), residues: 658 sheet: -0.54 (0.19), residues: 720 loop : -1.23 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.017 0.001 TYR C1159 PHE 0.033 0.001 PHE C 286 TRP 0.019 0.001 TRP A 156 HIS 0.003 0.001 HIS B 717 Details of bonding type rmsd covalent geometry : bond 0.00262 (23237) covalent geometry : angle 0.53397 (31707) SS BOND : bond 0.00353 ( 35) SS BOND : angle 1.42606 ( 70) hydrogen bonds : bond 0.03526 ( 934) hydrogen bonds : angle 5.40356 ( 2634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8333 (tt) cc_final: 0.8132 (tp) REVERT: A 443 TYR cc_start: 0.5155 (p90) cc_final: 0.4122 (t80) REVERT: A 621 LYS cc_start: 0.6137 (mmtt) cc_final: 0.5675 (mptt) REVERT: A 956 LEU cc_start: 0.8626 (tp) cc_final: 0.8325 (tt) REVERT: A 1220 VAL cc_start: 0.6576 (p) cc_final: 0.6228 (t) REVERT: B 287 LYS cc_start: 0.7984 (ptmt) cc_final: 0.7564 (ttpt) REVERT: B 306 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6641 (ttp-110) REVERT: B 1047 ASN cc_start: 0.7641 (m110) cc_final: 0.7333 (m-40) REVERT: B 1057 GLN cc_start: 0.7838 (mm110) cc_final: 0.7578 (mm-40) REVERT: B 1062 PHE cc_start: 0.7942 (m-80) cc_final: 0.7131 (m-80) REVERT: C 361 TYR cc_start: 0.5737 (OUTLIER) cc_final: 0.4992 (t80) REVERT: C 657 PHE cc_start: 0.7619 (p90) cc_final: 0.7324 (p90) REVERT: E 34 MET cc_start: 0.4803 (ppp) cc_final: 0.4404 (ppp) outliers start: 47 outliers final: 37 residues processed: 234 average time/residue: 0.1393 time to fit residues: 54.3039 Evaluate side-chains 226 residues out of total 2641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 162 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 283 optimal weight: 20.0000 chunk 260 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 274 optimal weight: 0.2980 chunk 296 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 847 GLN ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.129462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096739 restraints weight = 58001.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.096013 restraints weight = 36296.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096224 restraints weight = 26321.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096542 restraints weight = 26319.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096747 restraints weight = 21602.226| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23272 Z= 0.103 Angle : 0.525 8.018 31777 Z= 0.271 Chirality : 0.043 0.184 3670 Planarity : 0.004 0.059 4133 Dihedral : 4.293 23.085 3201 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 16.19 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 2967 helix: 1.61 (0.21), residues: 658 sheet: -0.52 (0.19), residues: 725 loop : -1.16 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.017 0.001 TYR C1159 PHE 0.024 0.001 PHE C 147 TRP 0.019 0.001 TRP A 156 HIS 0.003 0.000 HIS B 717 Details of bonding type rmsd covalent geometry : bond 0.00228 (23237) covalent geometry : angle 0.52234 (31707) SS BOND : bond 0.00313 ( 35) SS BOND : angle 1.25384 ( 70) hydrogen bonds : bond 0.03380 ( 934) hydrogen bonds : angle 5.27268 ( 2634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.59 seconds wall clock time: 57 minutes 13.39 seconds (3433.39 seconds total)