Starting phenix.real_space_refine on Mon Aug 25 13:28:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e05_27817/08_2025/8e05_27817_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e05_27817/08_2025/8e05_27817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e05_27817/08_2025/8e05_27817_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e05_27817/08_2025/8e05_27817_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e05_27817/08_2025/8e05_27817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e05_27817/08_2025/8e05_27817.map" } resolution = 4.6 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 174 5.16 5 C 17680 2.51 5 N 4774 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27730 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1749, 13837 Classifications: {'peptide': 1749} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 89, 'TRANS': 1657} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 13837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1749, 13837 Classifications: {'peptide': 1749} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 89, 'TRANS': 1657} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.61, per 1000 atoms: 0.24 Number of scatterers: 27730 At special positions: 0 Unit cell: (170.52, 154.28, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 174 16.00 P 4 15.00 O 5098 8.00 N 4774 7.00 C 17680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 36 sheets defined 39.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.535A pdb=" N GLU A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 98 Proline residue: A 94 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 132 through 142 removed outlier: 3.685A pdb=" N SER A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.360A pdb=" N LEU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.592A pdb=" N PHE A 348 " --> pdb=" O PRO A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.534A pdb=" N LEU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 466 through 471 removed outlier: 4.423A pdb=" N PHE A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 729 through 745 removed outlier: 3.892A pdb=" N ASN A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 739 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 781 removed outlier: 4.456A pdb=" N VAL A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLU A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 773 " --> pdb=" O GLU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 799 No H-bonds generated for 'chain 'A' and resid 797 through 799' Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 844 through 865 Processing helix chain 'A' and resid 872 through 882 Processing helix chain 'A' and resid 889 through 903 removed outlier: 3.834A pdb=" N LEU A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.536A pdb=" N GLY A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 937 removed outlier: 3.550A pdb=" N ILE A 937 " --> pdb=" O ARG A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 958 Processing helix chain 'A' and resid 967 through 978 Processing helix chain 'A' and resid 992 through 995 removed outlier: 3.652A pdb=" N LEU A 995 " --> pdb=" O PRO A 992 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 992 through 995' Processing helix chain 'A' and resid 1026 through 1047 Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 3.657A pdb=" N ALA A1131 " --> pdb=" O PHE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1149 Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1190 through 1200 removed outlier: 4.110A pdb=" N GLU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 Processing helix chain 'A' and resid 1228 through 1232 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1286 through 1313 Processing helix chain 'A' and resid 1341 through 1351 removed outlier: 3.587A pdb=" N VAL A1345 " --> pdb=" O SER A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1380 Processing helix chain 'A' and resid 1442 through 1460 Processing helix chain 'A' and resid 1468 through 1478 Processing helix chain 'A' and resid 1486 through 1491 Processing helix chain 'A' and resid 1492 through 1503 Processing helix chain 'A' and resid 1506 through 1510 Processing helix chain 'A' and resid 1512 through 1521 removed outlier: 3.929A pdb=" N LYS A1521 " --> pdb=" O VAL A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1527 removed outlier: 3.509A pdb=" N ALA A1526 " --> pdb=" O ASP A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1559 Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1670 through 1678 Processing helix chain 'A' and resid 1685 through 1689 Processing helix chain 'A' and resid 1904 through 1908 Processing helix chain 'A' and resid 1950 through 1957 Proline residue: A1955 - end of helix Processing helix chain 'A' and resid 1990 through 2007 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.535A pdb=" N GLU B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 83 through 98 Proline residue: B 94 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.686A pdb=" N SER B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 228 through 239 Processing helix chain 'B' and resid 269 through 274 removed outlier: 4.360A pdb=" N LEU B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.592A pdb=" N PHE B 348 " --> pdb=" O PRO B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.534A pdb=" N LEU B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 466 through 471 removed outlier: 4.422A pdb=" N PHE B 470 " --> pdb=" O PRO B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 564 through 570 Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 611 through 618 Processing helix chain 'B' and resid 618 through 631 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 729 through 745 removed outlier: 3.892A pdb=" N ASN B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B 739 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 781 removed outlier: 4.456A pdb=" N VAL B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 773 " --> pdb=" O GLU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 799 No H-bonds generated for 'chain 'B' and resid 797 through 799' Processing helix chain 'B' and resid 811 through 825 Processing helix chain 'B' and resid 844 through 865 Processing helix chain 'B' and resid 872 through 882 Processing helix chain 'B' and resid 889 through 903 removed outlier: 3.833A pdb=" N LEU B 893 " --> pdb=" O ASP B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.536A pdb=" N GLY B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 937 removed outlier: 3.550A pdb=" N ILE B 937 " --> pdb=" O ARG B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 958 Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 992 through 995 removed outlier: 3.652A pdb=" N LEU B 995 " --> pdb=" O PRO B 992 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 992 through 995' Processing helix chain 'B' and resid 1026 through 1047 Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'B' and resid 1127 through 1145 removed outlier: 3.658A pdb=" N ALA B1131 " --> pdb=" O PHE B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1149 Processing helix chain 'B' and resid 1165 through 1173 Processing helix chain 'B' and resid 1190 through 1200 removed outlier: 4.110A pdb=" N GLU B1199 " --> pdb=" O LEU B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1223 Processing helix chain 'B' and resid 1228 through 1232 Processing helix chain 'B' and resid 1234 through 1238 Processing helix chain 'B' and resid 1243 through 1245 No H-bonds generated for 'chain 'B' and resid 1243 through 1245' Processing helix chain 'B' and resid 1286 through 1313 Processing helix chain 'B' and resid 1341 through 1351 removed outlier: 3.588A pdb=" N VAL B1345 " --> pdb=" O SER B1341 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1380 Processing helix chain 'B' and resid 1442 through 1460 Processing helix chain 'B' and resid 1468 through 1478 Processing helix chain 'B' and resid 1486 through 1491 Processing helix chain 'B' and resid 1492 through 1503 Processing helix chain 'B' and resid 1506 through 1510 Processing helix chain 'B' and resid 1512 through 1521 removed outlier: 3.929A pdb=" N LYS B1521 " --> pdb=" O VAL B1517 " (cutoff:3.500A) Processing helix chain 'B' and resid 1522 through 1527 removed outlier: 3.509A pdb=" N ALA B1526 " --> pdb=" O ASP B1522 " (cutoff:3.500A) Processing helix chain 'B' and resid 1556 through 1559 Processing helix chain 'B' and resid 1609 through 1611 No H-bonds generated for 'chain 'B' and resid 1609 through 1611' Processing helix chain 'B' and resid 1670 through 1678 Processing helix chain 'B' and resid 1685 through 1689 Processing helix chain 'B' and resid 1904 through 1908 Processing helix chain 'B' and resid 1950 through 1957 Proline residue: B1955 - end of helix Processing helix chain 'B' and resid 1990 through 2007 Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.743A pdb=" N LEU A 307 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 334 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 357 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 385 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 409 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU A 478 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 502 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU A 576 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 634 through 636 Processing sheet with id=AA4, first strand: chain 'A' and resid 673 through 681 removed outlier: 6.718A pdb=" N MET A 639 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TRP A 698 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N MET A 641 " --> pdb=" O TRP A 698 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 700 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 643 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N LEU A 719 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS A 640 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 721 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 642 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL A 723 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 644 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASN A 725 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 720 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 755 " --> pdb=" O TYR A 720 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 722 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR A 757 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP A 724 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 870 through 871 Processing sheet with id=AA6, first strand: chain 'A' and resid 948 through 950 Processing sheet with id=AA7, first strand: chain 'A' and resid 1080 through 1086 removed outlier: 6.663A pdb=" N THR A1093 " --> pdb=" O ASN A1081 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR A1083 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A1091 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR A1085 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY A1089 " --> pdb=" O TYR A1085 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN A1015 " --> pdb=" O PRO A1164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1202 through 1203 removed outlier: 4.032A pdb=" N ILE A1203 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A1213 " --> pdb=" O ILE A1203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1247 through 1250 removed outlier: 6.716A pdb=" N ILE A1257 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A1324 " --> pdb=" O ALA A1333 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU A1335 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A1322 " --> pdb=" O GLU A1335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1392 through 1394 Processing sheet with id=AB2, first strand: chain 'A' and resid 1528 through 1536 removed outlier: 6.209A pdb=" N PHE A1528 " --> pdb=" O ARG A1987 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG A1987 " --> pdb=" O PHE A1528 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A1530 " --> pdb=" O VAL A1985 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP A1981 " --> pdb=" O CYS A1534 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR A1969 " --> pdb=" O VAL A1965 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU A1975 " --> pdb=" O LEU A1959 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A1959 " --> pdb=" O GLU A1975 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1539 through 1542 removed outlier: 7.083A pdb=" N VAL A1564 " --> pdb=" O GLN A1575 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN A1575 " --> pdb=" O VAL A1564 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASN A1566 " --> pdb=" O GLU A1573 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLU A1573 " --> pdb=" O ASN A1566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1584 through 1590 removed outlier: 4.145A pdb=" N CYS A1586 " --> pdb=" O ALA A1597 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A1602 " --> pdb=" O THR A1598 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY A1646 " --> pdb=" O THR A1628 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A1630 " --> pdb=" O LEU A1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A1644 " --> pdb=" O PHE A1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A1632 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A1642 " --> pdb=" O ALA A1632 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A1640 " --> pdb=" O PRO A1634 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY A1646 " --> pdb=" O THR A1628 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A1630 " --> pdb=" O LEU A1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A1644 " --> pdb=" O PHE A1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A1632 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A1642 " --> pdb=" O ALA A1632 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A1640 " --> pdb=" O PRO A1634 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1696 through 1699 removed outlier: 6.266A pdb=" N ASP A1717 " --> pdb=" O ILE A1723 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A1723 " --> pdb=" O ASP A1717 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1736 through 1743 removed outlier: 3.614A pdb=" N SER A1738 " --> pdb=" O LEU A1754 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A1760 " --> pdb=" O ASP A1755 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A1761 " --> pdb=" O ARG A1774 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG A1774 " --> pdb=" O LEU A1761 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET A1763 " --> pdb=" O CYS A1772 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1786 through 1789 removed outlier: 7.208A pdb=" N VAL A1930 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL A1947 " --> pdb=" O VAL A1928 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A1928 " --> pdb=" O VAL A1947 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AC2, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.744A pdb=" N LEU B 307 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 334 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 357 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 385 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 409 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 478 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU B 502 " --> pdb=" O CYS B 554 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU B 576 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 634 through 636 Processing sheet with id=AC4, first strand: chain 'B' and resid 673 through 681 removed outlier: 6.718A pdb=" N MET B 639 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TRP B 698 " --> pdb=" O MET B 639 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N MET B 641 " --> pdb=" O TRP B 698 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE B 700 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 643 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N LEU B 719 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS B 640 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL B 721 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE B 642 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL B 723 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 644 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ASN B 725 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR B 720 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 755 " --> pdb=" O TYR B 720 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 722 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR B 757 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP B 724 " --> pdb=" O THR B 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 870 through 871 Processing sheet with id=AC6, first strand: chain 'B' and resid 948 through 950 Processing sheet with id=AC7, first strand: chain 'B' and resid 1080 through 1086 removed outlier: 6.663A pdb=" N THR B1093 " --> pdb=" O ASN B1081 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR B1083 " --> pdb=" O LEU B1091 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B1091 " --> pdb=" O THR B1083 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B1085 " --> pdb=" O GLY B1089 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B1089 " --> pdb=" O TYR B1085 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLN B1015 " --> pdb=" O PRO B1164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1202 through 1203 removed outlier: 4.032A pdb=" N ILE B1203 " --> pdb=" O VAL B1213 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B1213 " --> pdb=" O ILE B1203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1247 through 1250 removed outlier: 6.715A pdb=" N ILE B1257 " --> pdb=" O LEU B1248 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B1324 " --> pdb=" O ALA B1333 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU B1335 " --> pdb=" O LEU B1322 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU B1322 " --> pdb=" O GLU B1335 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1392 through 1394 Processing sheet with id=AD2, first strand: chain 'B' and resid 1528 through 1536 removed outlier: 6.209A pdb=" N PHE B1528 " --> pdb=" O ARG B1987 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG B1987 " --> pdb=" O PHE B1528 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B1530 " --> pdb=" O VAL B1985 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP B1981 " --> pdb=" O CYS B1534 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B1969 " --> pdb=" O VAL B1965 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU B1975 " --> pdb=" O LEU B1959 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU B1959 " --> pdb=" O GLU B1975 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1539 through 1542 removed outlier: 7.083A pdb=" N VAL B1564 " --> pdb=" O GLN B1575 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN B1575 " --> pdb=" O VAL B1564 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASN B1566 " --> pdb=" O GLU B1573 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU B1573 " --> pdb=" O ASN B1566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1584 through 1590 removed outlier: 4.144A pdb=" N CYS B1586 " --> pdb=" O ALA B1597 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B1602 " --> pdb=" O THR B1598 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY B1646 " --> pdb=" O THR B1628 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE B1630 " --> pdb=" O LEU B1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B1644 " --> pdb=" O PHE B1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B1632 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B1642 " --> pdb=" O ALA B1632 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER B1640 " --> pdb=" O PRO B1634 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1627 through 1635 removed outlier: 6.789A pdb=" N GLY B1646 " --> pdb=" O THR B1628 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE B1630 " --> pdb=" O LEU B1644 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B1644 " --> pdb=" O PHE B1630 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B1632 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B1642 " --> pdb=" O ALA B1632 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER B1640 " --> pdb=" O PRO B1634 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1696 through 1699 removed outlier: 6.267A pdb=" N ASP B1717 " --> pdb=" O ILE B1723 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B1723 " --> pdb=" O ASP B1717 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1736 through 1743 removed outlier: 3.614A pdb=" N SER B1738 " --> pdb=" O LEU B1754 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B1760 " --> pdb=" O ASP B1755 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B1761 " --> pdb=" O ARG B1774 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG B1774 " --> pdb=" O LEU B1761 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET B1763 " --> pdb=" O CYS B1772 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1786 through 1789 removed outlier: 7.209A pdb=" N VAL B1930 " --> pdb=" O ILE B1945 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL B1947 " --> pdb=" O VAL B1928 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1928 " --> pdb=" O VAL B1947 " (cutoff:3.500A) 1160 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4589 1.31 - 1.44: 7277 1.44 - 1.56: 16210 1.56 - 1.69: 6 1.69 - 1.81: 250 Bond restraints: 28332 Sorted by residual: bond pdb=" C PRO A1220 " pdb=" O PRO A1220 " ideal model delta sigma weight residual 1.238 1.187 0.051 1.36e-02 5.41e+03 1.41e+01 bond pdb=" N MET A1224 " pdb=" CA MET A1224 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.28e-02 6.10e+03 7.01e+00 bond pdb=" N ARG A1016 " pdb=" CA ARG A1016 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.25e-02 6.40e+03 4.41e+00 bond pdb=" N VAL A1219 " pdb=" CA VAL A1219 " ideal model delta sigma weight residual 1.461 1.485 -0.024 1.23e-02 6.61e+03 3.89e+00 bond pdb=" N PRO A1220 " pdb=" CD PRO A1220 " ideal model delta sigma weight residual 1.473 1.447 0.026 1.40e-02 5.10e+03 3.50e+00 ... (remaining 28327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 36985 1.63 - 3.26: 1140 3.26 - 4.89: 266 4.89 - 6.52: 31 6.52 - 8.15: 12 Bond angle restraints: 38434 Sorted by residual: angle pdb=" N THR A1225 " pdb=" CA THR A1225 " pdb=" C THR A1225 " ideal model delta sigma weight residual 112.88 104.73 8.15 1.29e+00 6.01e-01 3.99e+01 angle pdb=" N ASP A1226 " pdb=" CA ASP A1226 " pdb=" C ASP A1226 " ideal model delta sigma weight residual 113.97 107.60 6.37 1.28e+00 6.10e-01 2.48e+01 angle pdb=" C PRO A1220 " pdb=" CA PRO A1220 " pdb=" CB PRO A1220 " ideal model delta sigma weight residual 113.06 105.23 7.83 1.59e+00 3.96e-01 2.42e+01 angle pdb=" N PHE A1223 " pdb=" CA PHE A1223 " pdb=" C PHE A1223 " ideal model delta sigma weight residual 110.32 103.57 6.75 1.59e+00 3.96e-01 1.80e+01 angle pdb=" N ILE A 377 " pdb=" CA ILE A 377 " pdb=" C ILE A 377 " ideal model delta sigma weight residual 113.53 109.89 3.64 9.80e-01 1.04e+00 1.38e+01 ... (remaining 38429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 15915 16.93 - 33.86: 1011 33.86 - 50.79: 157 50.79 - 67.71: 61 67.71 - 84.64: 20 Dihedral angle restraints: 17164 sinusoidal: 6974 harmonic: 10190 Sorted by residual: dihedral pdb=" CA ARG A1592 " pdb=" C ARG A1592 " pdb=" N SER A1593 " pdb=" CA SER A1593 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG B1592 " pdb=" C ARG B1592 " pdb=" N SER B1593 " pdb=" CA SER B1593 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN B1591 " pdb=" C GLN B1591 " pdb=" N ARG B1592 " pdb=" CA ARG B1592 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 17161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3887 0.074 - 0.148: 439 0.148 - 0.223: 12 0.223 - 0.297: 4 0.297 - 0.371: 2 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CA ARG A1016 " pdb=" N ARG A1016 " pdb=" C ARG A1016 " pdb=" CB ARG A1016 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA VAL A1219 " pdb=" N VAL A1219 " pdb=" C VAL A1219 " pdb=" CB VAL A1219 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA THR A1225 " pdb=" N THR A1225 " pdb=" C THR A1225 " pdb=" CB THR A1225 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4341 not shown) Planarity restraints: 4922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1655 " -0.066 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO B1656 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B1656 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B1656 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1655 " 0.066 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO A1656 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A1656 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1656 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1784 " 0.256 9.50e-02 1.11e+02 1.15e-01 9.66e+00 pdb=" NE ARG B1784 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B1784 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B1784 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B1784 " 0.002 2.00e-02 2.50e+03 ... (remaining 4919 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1094 2.72 - 3.26: 29014 3.26 - 3.81: 46086 3.81 - 4.35: 59849 4.35 - 4.90: 95874 Nonbonded interactions: 231917 Sorted by model distance: nonbonded pdb=" OG SER A 458 " pdb=" OE1 GLU A 459 " model vdw 2.169 3.040 nonbonded pdb=" O PHE A 457 " pdb=" ND2 ASN A 460 " model vdw 2.198 3.120 nonbonded pdb=" O PHE B 457 " pdb=" ND2 ASN B 460 " model vdw 2.198 3.120 nonbonded pdb=" OG SER B 388 " pdb=" O SER B 412 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 388 " pdb=" O SER A 412 " model vdw 2.199 3.040 ... (remaining 231912 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.690 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28332 Z= 0.171 Angle : 0.730 8.152 38434 Z= 0.405 Chirality : 0.045 0.371 4344 Planarity : 0.006 0.116 4922 Dihedral : 11.908 84.643 10548 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.27 (0.14), residues: 3462 helix: 0.29 (0.15), residues: 1118 sheet: -0.65 (0.20), residues: 590 loop : -0.18 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B1784 TYR 0.046 0.002 TYR A 869 PHE 0.027 0.002 PHE A1132 TRP 0.048 0.002 TRP B1503 HIS 0.007 0.001 HIS B1956 Details of bonding type rmsd covalent geometry : bond 0.00352 (28332) covalent geometry : angle 0.72967 (38434) hydrogen bonds : bond 0.14374 ( 1146) hydrogen bonds : angle 7.03135 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8493 (mmt) cc_final: 0.8252 (mmt) REVERT: A 143 LEU cc_start: 0.7891 (mt) cc_final: 0.7658 (mp) REVERT: A 152 LEU cc_start: 0.9453 (tp) cc_final: 0.9082 (tp) REVERT: A 156 MET cc_start: 0.9594 (ptp) cc_final: 0.9071 (ptp) REVERT: A 196 LEU cc_start: 0.9364 (tt) cc_final: 0.8971 (mt) REVERT: A 215 ARG cc_start: 0.8935 (mtm180) cc_final: 0.8526 (mtm-85) REVERT: A 262 HIS cc_start: 0.9496 (m90) cc_final: 0.9252 (m90) REVERT: A 367 LEU cc_start: 0.8901 (tp) cc_final: 0.8508 (tp) REVERT: A 386 ASP cc_start: 0.8243 (t0) cc_final: 0.7876 (t0) REVERT: A 421 ASP cc_start: 0.8611 (t70) cc_final: 0.8261 (p0) REVERT: A 427 LEU cc_start: 0.9337 (mt) cc_final: 0.9009 (mt) REVERT: A 469 LEU cc_start: 0.8756 (tp) cc_final: 0.8467 (mt) REVERT: A 470 PHE cc_start: 0.9168 (m-10) cc_final: 0.8531 (m-80) REVERT: A 472 LEU cc_start: 0.9078 (mt) cc_final: 0.8789 (mt) REVERT: A 479 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.7573 (ttm110) REVERT: A 556 ASN cc_start: 0.9344 (p0) cc_final: 0.9098 (p0) REVERT: A 557 ASP cc_start: 0.8929 (t0) cc_final: 0.8729 (t0) REVERT: A 601 ASP cc_start: 0.8378 (t0) cc_final: 0.7799 (t0) REVERT: A 622 MET cc_start: 0.9195 (mtm) cc_final: 0.8940 (mtp) REVERT: A 641 MET cc_start: 0.7853 (ttm) cc_final: 0.7367 (mtt) REVERT: A 700 ILE cc_start: 0.8919 (mp) cc_final: 0.8620 (mp) REVERT: A 793 PHE cc_start: 0.8729 (m-10) cc_final: 0.7977 (m-10) REVERT: A 873 ARG cc_start: 0.8576 (mmp80) cc_final: 0.8241 (mmp-170) REVERT: A 876 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8904 (mt-10) REVERT: A 897 ILE cc_start: 0.9257 (mt) cc_final: 0.8996 (mt) REVERT: A 909 PHE cc_start: 0.7434 (t80) cc_final: 0.7183 (t80) REVERT: A 929 GLU cc_start: 0.9409 (tt0) cc_final: 0.8979 (tm-30) REVERT: A 969 GLU cc_start: 0.9290 (mp0) cc_final: 0.8921 (pp20) REVERT: A 1027 PHE cc_start: 0.9058 (t80) cc_final: 0.8803 (t80) REVERT: A 1035 MET cc_start: 0.9682 (mpp) cc_final: 0.9259 (mpp) REVERT: A 1042 MET cc_start: 0.9080 (tpt) cc_final: 0.8871 (tpt) REVERT: A 1118 ILE cc_start: 0.9383 (mp) cc_final: 0.8858 (mp) REVERT: A 1130 MET cc_start: 0.8764 (ttm) cc_final: 0.8547 (ttm) REVERT: A 1237 LYS cc_start: 0.9246 (mttt) cc_final: 0.8908 (mtpt) REVERT: A 1244 GLU cc_start: 0.8468 (pm20) cc_final: 0.8248 (pm20) REVERT: A 1303 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8840 (mt-10) REVERT: A 1307 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9072 (mt-10) REVERT: A 1404 ASN cc_start: 0.8478 (m110) cc_final: 0.8131 (m-40) REVERT: A 1527 THR cc_start: 0.8792 (p) cc_final: 0.8305 (t) REVERT: A 1529 MET cc_start: 0.6774 (mtm) cc_final: 0.6453 (mtm) REVERT: A 1577 MET cc_start: 0.7367 (tpp) cc_final: 0.7056 (tpp) REVERT: A 1595 TRP cc_start: 0.8636 (m-10) cc_final: 0.7921 (m100) REVERT: A 1655 PHE cc_start: 0.7107 (m-10) cc_final: 0.6145 (m-80) REVERT: A 1706 TRP cc_start: 0.8924 (m-10) cc_final: 0.8573 (m100) REVERT: A 1739 VAL cc_start: 0.8732 (t) cc_final: 0.8097 (p) REVERT: A 1784 ARG cc_start: 0.8839 (mtm110) cc_final: 0.8311 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.1002 time to fit residues: 52.9306 Evaluate side-chains 279 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 559 HIS A 868 GLN ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 HIS A1404 ASN ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.090090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068435 restraints weight = 60265.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071080 restraints weight = 37942.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.072965 restraints weight = 27074.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.074318 restraints weight = 20949.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075337 restraints weight = 17239.103| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28332 Z= 0.121 Angle : 0.593 8.490 38434 Z= 0.308 Chirality : 0.043 0.159 4344 Planarity : 0.005 0.074 4922 Dihedral : 4.571 36.401 3790 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: 0.05 (0.15), residues: 3462 helix: 0.71 (0.15), residues: 1132 sheet: -0.68 (0.19), residues: 624 loop : -0.00 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1784 TYR 0.026 0.002 TYR B1376 PHE 0.019 0.002 PHE B1132 TRP 0.028 0.002 TRP A1503 HIS 0.005 0.001 HIS B1312 Details of bonding type rmsd covalent geometry : bond 0.00259 (28332) covalent geometry : angle 0.59339 (38434) hydrogen bonds : bond 0.04594 ( 1146) hydrogen bonds : angle 5.77485 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8331 (mmt) cc_final: 0.8128 (mmt) REVERT: A 143 LEU cc_start: 0.7874 (mt) cc_final: 0.7665 (mp) REVERT: A 166 LEU cc_start: 0.9078 (tt) cc_final: 0.8876 (tt) REVERT: A 196 LEU cc_start: 0.9424 (tt) cc_final: 0.8979 (mt) REVERT: A 215 ARG cc_start: 0.8967 (mtm180) cc_final: 0.8511 (mtm-85) REVERT: A 262 HIS cc_start: 0.9461 (m90) cc_final: 0.9226 (m90) REVERT: A 334 ILE cc_start: 0.9338 (tp) cc_final: 0.9108 (tp) REVERT: A 421 ASP cc_start: 0.8504 (t70) cc_final: 0.8202 (p0) REVERT: A 427 LEU cc_start: 0.9420 (mt) cc_final: 0.9041 (mt) REVERT: A 469 LEU cc_start: 0.8868 (tp) cc_final: 0.8327 (mm) REVERT: A 470 PHE cc_start: 0.9245 (m-10) cc_final: 0.8481 (m-80) REVERT: A 472 LEU cc_start: 0.9067 (mt) cc_final: 0.8842 (mt) REVERT: A 496 CYS cc_start: 0.9058 (p) cc_final: 0.8599 (p) REVERT: A 499 LEU cc_start: 0.8938 (tp) cc_final: 0.8716 (tp) REVERT: A 556 ASN cc_start: 0.9344 (p0) cc_final: 0.9131 (p0) REVERT: A 557 ASP cc_start: 0.8688 (t0) cc_final: 0.8411 (t0) REVERT: A 568 CYS cc_start: 0.8885 (p) cc_final: 0.8552 (t) REVERT: A 601 ASP cc_start: 0.8431 (t0) cc_final: 0.7816 (t0) REVERT: A 622 MET cc_start: 0.9238 (mtm) cc_final: 0.8883 (mtp) REVERT: A 641 MET cc_start: 0.7909 (ttm) cc_final: 0.7575 (mtt) REVERT: A 658 LEU cc_start: 0.8516 (mt) cc_final: 0.8261 (mt) REVERT: A 793 PHE cc_start: 0.8428 (m-10) cc_final: 0.7786 (m-10) REVERT: A 826 MET cc_start: 0.7069 (tpp) cc_final: 0.6279 (mmm) REVERT: A 873 ARG cc_start: 0.8502 (mmp80) cc_final: 0.8117 (mmm160) REVERT: A 876 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8823 (mt-10) REVERT: A 909 PHE cc_start: 0.7433 (t80) cc_final: 0.7128 (t80) REVERT: A 929 GLU cc_start: 0.9283 (tt0) cc_final: 0.8829 (tm-30) REVERT: A 969 GLU cc_start: 0.9251 (mp0) cc_final: 0.8880 (pp20) REVERT: A 979 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8926 (mt-10) REVERT: A 1006 MET cc_start: 0.7665 (tmm) cc_final: 0.7353 (ppp) REVERT: A 1027 PHE cc_start: 0.8892 (t80) cc_final: 0.8548 (t80) REVERT: A 1042 MET cc_start: 0.8919 (tpt) cc_final: 0.8574 (tpt) REVERT: A 1086 TRP cc_start: 0.8546 (p90) cc_final: 0.8173 (p90) REVERT: A 1116 MET cc_start: 0.9036 (ppp) cc_final: 0.8644 (ppp) REVERT: A 1237 LYS cc_start: 0.9089 (mttt) cc_final: 0.8818 (mtpt) REVERT: A 1238 LEU cc_start: 0.9040 (tp) cc_final: 0.8721 (tp) REVERT: A 1270 LYS cc_start: 0.9411 (ttmt) cc_final: 0.9210 (ttmt) REVERT: A 1303 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8782 (mt-10) REVERT: A 1307 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8985 (mt-10) REVERT: A 1377 LEU cc_start: 0.9414 (mp) cc_final: 0.8999 (tp) REVERT: A 1391 ASN cc_start: 0.9260 (p0) cc_final: 0.8157 (t0) REVERT: A 1407 LEU cc_start: 0.9492 (mp) cc_final: 0.9290 (mp) REVERT: A 1410 TYR cc_start: 0.8980 (p90) cc_final: 0.8655 (p90) REVERT: A 1502 CYS cc_start: 0.8394 (m) cc_final: 0.7903 (m) REVERT: A 1520 MET cc_start: 0.7191 (tpp) cc_final: 0.6917 (tpp) REVERT: A 1595 TRP cc_start: 0.8590 (m-10) cc_final: 0.7749 (m100) REVERT: A 1655 PHE cc_start: 0.7239 (m-10) cc_final: 0.6196 (m-80) REVERT: A 1706 TRP cc_start: 0.9007 (m-10) cc_final: 0.8682 (m100) REVERT: A 1739 VAL cc_start: 0.8894 (t) cc_final: 0.8444 (p) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.1013 time to fit residues: 50.2567 Evaluate side-chains 270 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 265 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 327 optimal weight: 0.1980 chunk 190 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 29 optimal weight: 0.0270 chunk 34 optimal weight: 0.0010 chunk 226 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.6448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS ** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1349 ASN ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068286 restraints weight = 60060.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070943 restraints weight = 37734.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072867 restraints weight = 26821.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074259 restraints weight = 20675.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.075248 restraints weight = 16942.985| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28332 Z= 0.113 Angle : 0.580 9.774 38434 Z= 0.299 Chirality : 0.043 0.159 4344 Planarity : 0.004 0.061 4922 Dihedral : 4.393 23.009 3790 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.02 (0.15), residues: 3462 helix: 0.64 (0.15), residues: 1132 sheet: -0.67 (0.19), residues: 628 loop : -0.06 (0.16), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.027 0.001 TYR B1376 PHE 0.044 0.002 PHE A1492 TRP 0.055 0.002 TRP A1503 HIS 0.003 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00240 (28332) covalent geometry : angle 0.57981 (38434) hydrogen bonds : bond 0.04055 ( 1146) hydrogen bonds : angle 5.57742 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8296 (mmt) cc_final: 0.8053 (mmt) REVERT: A 143 LEU cc_start: 0.7873 (mt) cc_final: 0.7660 (mp) REVERT: A 196 LEU cc_start: 0.9459 (tt) cc_final: 0.9026 (mt) REVERT: A 209 ILE cc_start: 0.8087 (mt) cc_final: 0.7622 (mt) REVERT: A 219 TYR cc_start: 0.8005 (m-80) cc_final: 0.7690 (m-80) REVERT: A 262 HIS cc_start: 0.9476 (m90) cc_final: 0.9271 (m90) REVERT: A 410 ASN cc_start: 0.8186 (t0) cc_final: 0.7886 (t0) REVERT: A 421 ASP cc_start: 0.8427 (t70) cc_final: 0.8138 (p0) REVERT: A 469 LEU cc_start: 0.8934 (tp) cc_final: 0.8670 (tp) REVERT: A 470 PHE cc_start: 0.9233 (m-10) cc_final: 0.8589 (m-80) REVERT: A 472 LEU cc_start: 0.9083 (mt) cc_final: 0.8859 (mt) REVERT: A 496 CYS cc_start: 0.8816 (p) cc_final: 0.8318 (p) REVERT: A 499 LEU cc_start: 0.8943 (tp) cc_final: 0.8668 (tp) REVERT: A 556 ASN cc_start: 0.9386 (p0) cc_final: 0.9134 (p0) REVERT: A 557 ASP cc_start: 0.8590 (t0) cc_final: 0.8286 (t0) REVERT: A 568 CYS cc_start: 0.8819 (p) cc_final: 0.8566 (t) REVERT: A 601 ASP cc_start: 0.8523 (t0) cc_final: 0.7816 (t0) REVERT: A 622 MET cc_start: 0.9337 (mtm) cc_final: 0.8976 (mtp) REVERT: A 640 LYS cc_start: 0.6909 (mmmt) cc_final: 0.6485 (mmmt) REVERT: A 658 LEU cc_start: 0.8557 (mt) cc_final: 0.8319 (mt) REVERT: A 793 PHE cc_start: 0.8147 (m-10) cc_final: 0.7598 (m-10) REVERT: A 873 ARG cc_start: 0.8482 (mmp80) cc_final: 0.8058 (mmm160) REVERT: A 876 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 891 GLU cc_start: 0.9006 (pm20) cc_final: 0.8766 (pm20) REVERT: A 909 PHE cc_start: 0.7370 (t80) cc_final: 0.7162 (t80) REVERT: A 929 GLU cc_start: 0.9297 (tt0) cc_final: 0.8832 (tm-30) REVERT: A 969 GLU cc_start: 0.9196 (mp0) cc_final: 0.8749 (pp20) REVERT: A 979 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8858 (mt-10) REVERT: A 1027 PHE cc_start: 0.8867 (t80) cc_final: 0.8405 (t80) REVERT: A 1042 MET cc_start: 0.8877 (tpt) cc_final: 0.8598 (tpt) REVERT: A 1086 TRP cc_start: 0.8522 (p90) cc_final: 0.7778 (p90) REVERT: A 1116 MET cc_start: 0.9067 (ppp) cc_final: 0.8679 (ppp) REVERT: A 1130 MET cc_start: 0.8638 (tmm) cc_final: 0.8358 (ppp) REVERT: A 1237 LYS cc_start: 0.9149 (mttt) cc_final: 0.8896 (mtpt) REVERT: A 1275 LYS cc_start: 0.8848 (pptt) cc_final: 0.8642 (tmmt) REVERT: A 1303 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8705 (mt-10) REVERT: A 1307 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8933 (mt-10) REVERT: A 1325 ILE cc_start: 0.9024 (pt) cc_final: 0.8823 (pt) REVERT: A 1377 LEU cc_start: 0.9415 (mp) cc_final: 0.9069 (tp) REVERT: A 1391 ASN cc_start: 0.9240 (p0) cc_final: 0.8174 (t0) REVERT: A 1407 LEU cc_start: 0.9494 (mp) cc_final: 0.9286 (mp) REVERT: A 1410 TYR cc_start: 0.9017 (p90) cc_final: 0.8746 (p90) REVERT: A 1520 MET cc_start: 0.7697 (tpp) cc_final: 0.7179 (tpt) REVERT: A 1541 PHE cc_start: 0.8410 (t80) cc_final: 0.8179 (t80) REVERT: A 1595 TRP cc_start: 0.8649 (m-10) cc_final: 0.7935 (m100) REVERT: A 1655 PHE cc_start: 0.7149 (m-10) cc_final: 0.6232 (m-80) REVERT: A 1706 TRP cc_start: 0.8949 (m-10) cc_final: 0.8702 (m100) REVERT: A 1775 TYR cc_start: 0.9526 (t80) cc_final: 0.9010 (t80) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1015 time to fit residues: 48.8661 Evaluate side-chains 252 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 279 optimal weight: 0.0070 chunk 113 optimal weight: 0.0040 chunk 334 optimal weight: 7.9990 chunk 66 optimal weight: 0.3980 chunk 236 optimal weight: 0.0060 chunk 312 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 247 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 132 optimal weight: 0.0570 overall best weight: 0.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 GLN B1291 HIS ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.091348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069336 restraints weight = 59536.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.071991 restraints weight = 37720.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073889 restraints weight = 26975.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075224 restraints weight = 20927.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.076256 restraints weight = 17292.192| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28332 Z= 0.110 Angle : 0.570 8.999 38434 Z= 0.289 Chirality : 0.043 0.168 4344 Planarity : 0.004 0.060 4922 Dihedral : 4.239 21.869 3790 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.07 % Allowed : 1.37 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.07 (0.15), residues: 3462 helix: 0.59 (0.15), residues: 1130 sheet: -0.73 (0.20), residues: 654 loop : -0.05 (0.17), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 110 TYR 0.026 0.001 TYR A1376 PHE 0.026 0.002 PHE A1492 TRP 0.041 0.001 TRP B1503 HIS 0.003 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00233 (28332) covalent geometry : angle 0.57035 (38434) hydrogen bonds : bond 0.03754 ( 1146) hydrogen bonds : angle 5.35618 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 LEU cc_start: 0.7973 (mt) cc_final: 0.7752 (mp) REVERT: B 196 LEU cc_start: 0.9415 (tt) cc_final: 0.8997 (mt) REVERT: B 209 ILE cc_start: 0.8024 (mt) cc_final: 0.7578 (mt) REVERT: B 219 TYR cc_start: 0.7968 (m-80) cc_final: 0.7726 (m-80) REVERT: B 386 ASP cc_start: 0.7871 (t0) cc_final: 0.7463 (t0) REVERT: B 410 ASN cc_start: 0.8084 (t0) cc_final: 0.7845 (t0) REVERT: B 421 ASP cc_start: 0.8339 (t70) cc_final: 0.8050 (p0) REVERT: B 469 LEU cc_start: 0.8988 (tp) cc_final: 0.8749 (tp) REVERT: B 470 PHE cc_start: 0.9283 (m-10) cc_final: 0.8730 (m-80) REVERT: B 496 CYS cc_start: 0.8820 (p) cc_final: 0.8224 (p) REVERT: B 499 LEU cc_start: 0.8904 (tp) cc_final: 0.8674 (tp) REVERT: B 551 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 556 ASN cc_start: 0.9317 (p0) cc_final: 0.9087 (p0) REVERT: B 557 ASP cc_start: 0.8356 (t0) cc_final: 0.8046 (t0) REVERT: B 601 ASP cc_start: 0.8583 (t0) cc_final: 0.7889 (t0) REVERT: B 622 MET cc_start: 0.9383 (mtm) cc_final: 0.9028 (mtp) REVERT: B 658 LEU cc_start: 0.8523 (mt) cc_final: 0.8276 (mt) REVERT: B 793 PHE cc_start: 0.8075 (m-10) cc_final: 0.7489 (m-10) REVERT: B 873 ARG cc_start: 0.8377 (mmp80) cc_final: 0.7929 (mmm160) REVERT: B 876 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8745 (mt-10) REVERT: B 891 GLU cc_start: 0.8925 (pm20) cc_final: 0.8665 (pm20) REVERT: B 909 PHE cc_start: 0.7306 (t80) cc_final: 0.6752 (t80) REVERT: B 929 GLU cc_start: 0.9276 (tt0) cc_final: 0.8826 (tm-30) REVERT: B 979 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8929 (mt-10) REVERT: B 1027 PHE cc_start: 0.8728 (t80) cc_final: 0.8212 (t80) REVERT: B 1042 MET cc_start: 0.8854 (tpt) cc_final: 0.8564 (tpt) REVERT: B 1116 MET cc_start: 0.9054 (ppp) cc_final: 0.8712 (ppp) REVERT: B 1120 CYS cc_start: 0.8563 (p) cc_final: 0.8076 (p) REVERT: B 1237 LYS cc_start: 0.9124 (mttt) cc_final: 0.8907 (mtpt) REVERT: B 1238 LEU cc_start: 0.9036 (tp) cc_final: 0.8759 (tp) REVERT: B 1298 MET cc_start: 0.9497 (mtm) cc_final: 0.9066 (mtt) REVERT: B 1303 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8712 (mt-10) REVERT: B 1307 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8858 (mt-10) REVERT: B 1325 ILE cc_start: 0.8974 (pt) cc_final: 0.8737 (pt) REVERT: B 1391 ASN cc_start: 0.9217 (p0) cc_final: 0.8122 (t0) REVERT: B 1410 TYR cc_start: 0.8924 (p90) cc_final: 0.8535 (p90) REVERT: B 1541 PHE cc_start: 0.8416 (t80) cc_final: 0.8185 (t80) REVERT: B 1611 MET cc_start: 0.3964 (mmp) cc_final: 0.3509 (mmm) REVERT: B 1655 PHE cc_start: 0.7043 (m-10) cc_final: 0.6365 (m-80) REVERT: B 1739 VAL cc_start: 0.8778 (t) cc_final: 0.8313 (p) REVERT: B 1775 TYR cc_start: 0.9532 (t80) cc_final: 0.9175 (t80) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.1095 time to fit residues: 51.6157 Evaluate side-chains 252 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 278 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 334 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN B1378 HIS ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.087116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.065328 restraints weight = 62563.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067806 restraints weight = 39732.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069621 restraints weight = 28679.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070815 restraints weight = 22394.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071765 restraints weight = 18804.250| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28332 Z= 0.166 Angle : 0.603 11.275 38434 Z= 0.309 Chirality : 0.043 0.279 4344 Planarity : 0.004 0.056 4922 Dihedral : 4.337 24.265 3790 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.07 % Allowed : 1.57 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.50 (0.14), residues: 3462 helix: 0.30 (0.15), residues: 1142 sheet: -1.07 (0.19), residues: 646 loop : -0.32 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1261 TYR 0.020 0.002 TYR A1376 PHE 0.043 0.002 PHE B1132 TRP 0.060 0.002 TRP B1503 HIS 0.006 0.001 HIS B1136 Details of bonding type rmsd covalent geometry : bond 0.00350 (28332) covalent geometry : angle 0.60255 (38434) hydrogen bonds : bond 0.03817 ( 1146) hydrogen bonds : angle 5.55831 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8572 (mmt) cc_final: 0.8367 (mmt) REVERT: B 143 LEU cc_start: 0.8012 (mt) cc_final: 0.7753 (mp) REVERT: B 196 LEU cc_start: 0.9431 (tt) cc_final: 0.8972 (mt) REVERT: B 209 ILE cc_start: 0.8271 (mt) cc_final: 0.7859 (mt) REVERT: B 215 ARG cc_start: 0.8968 (mtm180) cc_final: 0.8485 (mtm-85) REVERT: B 219 TYR cc_start: 0.8253 (m-80) cc_final: 0.7801 (m-80) REVERT: B 334 ILE cc_start: 0.9420 (tp) cc_final: 0.9180 (tp) REVERT: B 386 ASP cc_start: 0.7912 (t0) cc_final: 0.7377 (t0) REVERT: B 410 ASN cc_start: 0.8158 (t0) cc_final: 0.7781 (t0) REVERT: B 444 MET cc_start: 0.8937 (mmp) cc_final: 0.8031 (mmm) REVERT: B 469 LEU cc_start: 0.9039 (tp) cc_final: 0.8652 (tp) REVERT: B 470 PHE cc_start: 0.9362 (m-10) cc_final: 0.8645 (m-10) REVERT: B 472 LEU cc_start: 0.9193 (mt) cc_final: 0.8887 (mt) REVERT: B 496 CYS cc_start: 0.8907 (p) cc_final: 0.8608 (p) REVERT: B 551 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8125 (mt-10) REVERT: B 556 ASN cc_start: 0.9395 (p0) cc_final: 0.9124 (p0) REVERT: B 557 ASP cc_start: 0.8552 (t0) cc_final: 0.8272 (t70) REVERT: B 601 ASP cc_start: 0.8727 (t0) cc_final: 0.8079 (t0) REVERT: B 658 LEU cc_start: 0.8537 (mt) cc_final: 0.8322 (mt) REVERT: B 793 PHE cc_start: 0.8553 (m-10) cc_final: 0.7875 (m-10) REVERT: B 876 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8772 (mt-10) REVERT: B 891 GLU cc_start: 0.8970 (pm20) cc_final: 0.8702 (pm20) REVERT: B 929 GLU cc_start: 0.9288 (tt0) cc_final: 0.8913 (tm-30) REVERT: B 979 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8888 (mt-10) REVERT: B 1042 MET cc_start: 0.8932 (tpt) cc_final: 0.8623 (tpt) REVERT: B 1227 PHE cc_start: 0.8016 (m-80) cc_final: 0.7632 (m-80) REVERT: B 1237 LYS cc_start: 0.8970 (mttt) cc_final: 0.8651 (mtpt) REVERT: B 1303 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8788 (mt-10) REVERT: B 1377 LEU cc_start: 0.9462 (mp) cc_final: 0.9119 (tp) REVERT: B 1391 ASN cc_start: 0.9205 (p0) cc_final: 0.8019 (t0) REVERT: B 1410 TYR cc_start: 0.9083 (p90) cc_final: 0.8522 (p90) REVERT: B 1541 PHE cc_start: 0.8482 (t80) cc_final: 0.8258 (t80) REVERT: B 1611 MET cc_start: 0.4274 (mmp) cc_final: 0.3609 (tpt) REVERT: B 1655 PHE cc_start: 0.7257 (m-10) cc_final: 0.6731 (m-80) REVERT: B 1706 TRP cc_start: 0.8759 (m100) cc_final: 0.7483 (m100) outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.1084 time to fit residues: 47.4292 Evaluate side-chains 221 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 11 optimal weight: 0.0770 chunk 208 optimal weight: 5.9990 chunk 244 optimal weight: 0.0030 chunk 278 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 286 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 HIS ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.090120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068169 restraints weight = 60500.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070769 restraints weight = 38302.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072655 restraints weight = 27542.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073970 restraints weight = 21415.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074936 restraints weight = 17725.935| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28332 Z= 0.101 Angle : 0.568 8.432 38434 Z= 0.287 Chirality : 0.043 0.161 4344 Planarity : 0.004 0.050 4922 Dihedral : 4.177 22.129 3790 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.07 % Allowed : 1.11 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.60 (0.14), residues: 3462 helix: 0.23 (0.15), residues: 1124 sheet: -1.06 (0.19), residues: 648 loop : -0.42 (0.16), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1462 TYR 0.025 0.001 TYR A1376 PHE 0.030 0.002 PHE A1492 TRP 0.049 0.002 TRP B1503 HIS 0.007 0.001 HIS A1312 Details of bonding type rmsd covalent geometry : bond 0.00218 (28332) covalent geometry : angle 0.56768 (38434) hydrogen bonds : bond 0.03527 ( 1146) hydrogen bonds : angle 5.35218 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8500 (mmt) cc_final: 0.8260 (mmt) REVERT: B 143 LEU cc_start: 0.7914 (mt) cc_final: 0.7659 (mp) REVERT: B 157 LEU cc_start: 0.9797 (tp) cc_final: 0.9592 (tp) REVERT: B 196 LEU cc_start: 0.9411 (tt) cc_final: 0.8979 (mt) REVERT: B 209 ILE cc_start: 0.8168 (mt) cc_final: 0.7807 (mt) REVERT: B 215 ARG cc_start: 0.8968 (mtm180) cc_final: 0.8598 (mtm-85) REVERT: B 219 TYR cc_start: 0.8169 (m-80) cc_final: 0.7639 (m-80) REVERT: B 334 ILE cc_start: 0.9361 (tp) cc_final: 0.9143 (tp) REVERT: B 386 ASP cc_start: 0.7816 (t0) cc_final: 0.7282 (t0) REVERT: B 410 ASN cc_start: 0.8021 (t0) cc_final: 0.7783 (t0) REVERT: B 444 MET cc_start: 0.8830 (mmp) cc_final: 0.8362 (mmm) REVERT: B 469 LEU cc_start: 0.9048 (tp) cc_final: 0.8674 (tp) REVERT: B 470 PHE cc_start: 0.9311 (m-10) cc_final: 0.8807 (m-80) REVERT: B 472 LEU cc_start: 0.9111 (mt) cc_final: 0.8816 (mt) REVERT: B 496 CYS cc_start: 0.8847 (p) cc_final: 0.8607 (p) REVERT: B 556 ASN cc_start: 0.9377 (p0) cc_final: 0.9139 (p0) REVERT: B 557 ASP cc_start: 0.8439 (t0) cc_final: 0.8140 (t70) REVERT: B 569 LEU cc_start: 0.8798 (mm) cc_final: 0.8314 (tt) REVERT: B 601 ASP cc_start: 0.8647 (t0) cc_final: 0.7988 (t0) REVERT: B 622 MET cc_start: 0.9097 (mmm) cc_final: 0.8565 (mmm) REVERT: B 640 LYS cc_start: 0.6971 (mmtt) cc_final: 0.6621 (mmtt) REVERT: B 793 PHE cc_start: 0.8330 (m-10) cc_final: 0.7634 (m-10) REVERT: B 891 GLU cc_start: 0.8945 (pm20) cc_final: 0.8642 (pm20) REVERT: B 902 GLU cc_start: 0.9295 (pt0) cc_final: 0.9009 (pp20) REVERT: B 929 GLU cc_start: 0.9324 (tt0) cc_final: 0.8892 (tm-30) REVERT: B 969 GLU cc_start: 0.9179 (mp0) cc_final: 0.8753 (pp20) REVERT: B 979 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8919 (mt-10) REVERT: B 1027 PHE cc_start: 0.8734 (t80) cc_final: 0.8195 (t80) REVERT: B 1086 TRP cc_start: 0.8400 (p90) cc_final: 0.8086 (p90) REVERT: B 1116 MET cc_start: 0.9222 (ppp) cc_final: 0.8687 (ppp) REVERT: B 1188 PHE cc_start: 0.9137 (m-10) cc_final: 0.8928 (m-10) REVERT: B 1237 LYS cc_start: 0.8994 (mttt) cc_final: 0.8689 (mtmm) REVERT: B 1303 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8780 (mt-10) REVERT: B 1377 LEU cc_start: 0.9376 (mp) cc_final: 0.9120 (tp) REVERT: B 1391 ASN cc_start: 0.9204 (p0) cc_final: 0.7834 (t0) REVERT: B 1410 TYR cc_start: 0.9121 (p90) cc_final: 0.8656 (p90) REVERT: B 1611 MET cc_start: 0.4246 (mmp) cc_final: 0.3577 (tpt) REVERT: B 1655 PHE cc_start: 0.7102 (m-10) cc_final: 0.6591 (m-80) REVERT: B 1706 TRP cc_start: 0.8655 (m100) cc_final: 0.7482 (m100) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.1051 time to fit residues: 46.6039 Evaluate side-chains 234 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 168 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 244 optimal weight: 0.0060 chunk 228 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 0.0070 chunk 254 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN B 383 GLN B 407 ASN B 993 HIS B1263 GLN ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.090873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068739 restraints weight = 60463.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071348 restraints weight = 38652.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073178 restraints weight = 27834.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074476 restraints weight = 21740.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075509 restraints weight = 18059.354| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28332 Z= 0.099 Angle : 0.570 9.627 38434 Z= 0.286 Chirality : 0.043 0.169 4344 Planarity : 0.004 0.051 4922 Dihedral : 4.078 22.106 3790 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.07 % Allowed : 0.98 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.82 (0.14), residues: 3462 helix: 0.15 (0.15), residues: 1126 sheet: -1.30 (0.19), residues: 654 loop : -0.58 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1462 TYR 0.024 0.001 TYR A1376 PHE 0.023 0.002 PHE A1492 TRP 0.047 0.002 TRP A1503 HIS 0.003 0.001 HIS B 800 Details of bonding type rmsd covalent geometry : bond 0.00213 (28332) covalent geometry : angle 0.57002 (38434) hydrogen bonds : bond 0.03430 ( 1146) hydrogen bonds : angle 5.26782 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8494 (ttp80) REVERT: B 122 ASN cc_start: 0.9315 (t0) cc_final: 0.9087 (t0) REVERT: B 196 LEU cc_start: 0.9353 (tt) cc_final: 0.8848 (mt) REVERT: B 209 ILE cc_start: 0.8253 (mt) cc_final: 0.7764 (mt) REVERT: B 215 ARG cc_start: 0.8994 (mtm180) cc_final: 0.8559 (mtm-85) REVERT: B 219 TYR cc_start: 0.8088 (m-80) cc_final: 0.7749 (m-80) REVERT: B 367 LEU cc_start: 0.9018 (tp) cc_final: 0.8812 (tp) REVERT: B 386 ASP cc_start: 0.7703 (t0) cc_final: 0.7437 (t0) REVERT: B 401 HIS cc_start: 0.9263 (m170) cc_final: 0.9057 (m-70) REVERT: B 444 MET cc_start: 0.8736 (mmp) cc_final: 0.8169 (mmm) REVERT: B 469 LEU cc_start: 0.9024 (tp) cc_final: 0.8687 (tp) REVERT: B 470 PHE cc_start: 0.9262 (m-10) cc_final: 0.8712 (m-80) REVERT: B 472 LEU cc_start: 0.9087 (mt) cc_final: 0.8824 (mt) REVERT: B 476 MET cc_start: 0.6646 (pmm) cc_final: 0.6277 (pmm) REVERT: B 496 CYS cc_start: 0.8698 (p) cc_final: 0.8451 (p) REVERT: B 557 ASP cc_start: 0.8354 (t0) cc_final: 0.8068 (t0) REVERT: B 560 LEU cc_start: 0.6860 (tt) cc_final: 0.6400 (mm) REVERT: B 569 LEU cc_start: 0.8797 (mm) cc_final: 0.8518 (tp) REVERT: B 601 ASP cc_start: 0.8678 (t0) cc_final: 0.7984 (t0) REVERT: B 622 MET cc_start: 0.9107 (mmm) cc_final: 0.8560 (mmm) REVERT: B 640 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6542 (mmtt) REVERT: B 793 PHE cc_start: 0.8288 (m-10) cc_final: 0.7772 (m-80) REVERT: B 850 LEU cc_start: 0.9410 (tt) cc_final: 0.9140 (mm) REVERT: B 891 GLU cc_start: 0.8902 (pm20) cc_final: 0.8578 (pm20) REVERT: B 902 GLU cc_start: 0.9302 (pt0) cc_final: 0.9000 (pp20) REVERT: B 929 GLU cc_start: 0.9344 (tt0) cc_final: 0.8894 (tm-30) REVERT: B 979 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8909 (mt-10) REVERT: B 1027 PHE cc_start: 0.8600 (t80) cc_final: 0.7968 (t80) REVERT: B 1106 VAL cc_start: 0.8605 (t) cc_final: 0.8197 (p) REVERT: B 1116 MET cc_start: 0.9241 (ppp) cc_final: 0.8760 (ppp) REVERT: B 1188 PHE cc_start: 0.9151 (m-10) cc_final: 0.8935 (m-10) REVERT: B 1237 LYS cc_start: 0.8965 (mttt) cc_final: 0.8663 (mtpt) REVERT: B 1303 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8792 (mt-10) REVERT: B 1377 LEU cc_start: 0.9378 (mp) cc_final: 0.9015 (tp) REVERT: B 1388 LYS cc_start: 0.9388 (tptp) cc_final: 0.9079 (tptp) REVERT: B 1391 ASN cc_start: 0.9184 (p0) cc_final: 0.7820 (t0) REVERT: B 1410 TYR cc_start: 0.9131 (p90) cc_final: 0.8747 (p90) REVERT: B 1611 MET cc_start: 0.4298 (mmp) cc_final: 0.3606 (tpt) REVERT: B 1655 PHE cc_start: 0.7118 (m-10) cc_final: 0.6623 (m-80) REVERT: B 1706 TRP cc_start: 0.8547 (m100) cc_final: 0.7484 (m100) REVERT: B 1775 TYR cc_start: 0.9275 (t80) cc_final: 0.8735 (t80) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.1042 time to fit residues: 46.9964 Evaluate side-chains 237 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 62 optimal weight: 0.0870 chunk 156 optimal weight: 0.3980 chunk 227 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 113 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 chunk 205 optimal weight: 0.0170 chunk 63 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A 383 GLN A 659 GLN A 851 GLN A1291 HIS ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1908 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.090884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069112 restraints weight = 59961.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071690 restraints weight = 38010.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073583 restraints weight = 27386.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074921 restraints weight = 21258.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075940 restraints weight = 17501.110| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28332 Z= 0.097 Angle : 0.565 7.920 38434 Z= 0.284 Chirality : 0.043 0.165 4344 Planarity : 0.004 0.050 4922 Dihedral : 4.001 21.872 3790 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 0.07 % Allowed : 0.39 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.90 (0.14), residues: 3462 helix: 0.06 (0.15), residues: 1128 sheet: -1.27 (0.19), residues: 650 loop : -0.65 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1462 TYR 0.021 0.001 TYR A1376 PHE 0.023 0.002 PHE A1630 TRP 0.085 0.002 TRP A1503 HIS 0.003 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00206 (28332) covalent geometry : angle 0.56495 (38434) hydrogen bonds : bond 0.03400 ( 1146) hydrogen bonds : angle 5.25086 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8934 (ttm170) cc_final: 0.8517 (ttp80) REVERT: A 196 LEU cc_start: 0.9298 (tt) cc_final: 0.8795 (mt) REVERT: A 209 ILE cc_start: 0.8154 (mt) cc_final: 0.7790 (mt) REVERT: A 219 TYR cc_start: 0.8086 (m-80) cc_final: 0.7720 (m-80) REVERT: A 334 ILE cc_start: 0.9332 (tp) cc_final: 0.9055 (tp) REVERT: A 428 LYS cc_start: 0.9340 (ptpp) cc_final: 0.8983 (mmmt) REVERT: A 444 MET cc_start: 0.8808 (mmp) cc_final: 0.8315 (mmm) REVERT: A 469 LEU cc_start: 0.9031 (tp) cc_final: 0.8712 (tp) REVERT: A 470 PHE cc_start: 0.9254 (m-10) cc_final: 0.8691 (m-80) REVERT: A 472 LEU cc_start: 0.9037 (mt) cc_final: 0.8762 (mt) REVERT: A 556 ASN cc_start: 0.9369 (p0) cc_final: 0.9142 (p0) REVERT: A 557 ASP cc_start: 0.8339 (t0) cc_final: 0.8002 (t70) REVERT: A 569 LEU cc_start: 0.8849 (mm) cc_final: 0.8558 (tp) REVERT: A 601 ASP cc_start: 0.8654 (t0) cc_final: 0.7962 (t0) REVERT: A 622 MET cc_start: 0.9089 (mmm) cc_final: 0.8529 (mmm) REVERT: A 782 CYS cc_start: 0.9249 (t) cc_final: 0.9005 (t) REVERT: A 793 PHE cc_start: 0.8382 (m-10) cc_final: 0.7797 (m-80) REVERT: A 850 LEU cc_start: 0.9412 (tt) cc_final: 0.9117 (mm) REVERT: A 891 GLU cc_start: 0.8944 (pm20) cc_final: 0.8668 (pm20) REVERT: A 894 GLN cc_start: 0.9530 (tp40) cc_final: 0.9294 (mm-40) REVERT: A 929 GLU cc_start: 0.9339 (tt0) cc_final: 0.8819 (tm-30) REVERT: A 936 ASN cc_start: 0.8729 (t0) cc_final: 0.8261 (p0) REVERT: A 956 MET cc_start: 0.9187 (tmm) cc_final: 0.8745 (ptp) REVERT: A 979 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8900 (mt-10) REVERT: A 1006 MET cc_start: 0.7297 (mmp) cc_final: 0.6311 (ppp) REVERT: A 1086 TRP cc_start: 0.8397 (p90) cc_final: 0.8022 (p90) REVERT: A 1106 VAL cc_start: 0.8639 (t) cc_final: 0.8230 (p) REVERT: A 1116 MET cc_start: 0.9203 (ppp) cc_final: 0.8794 (ppp) REVERT: A 1130 MET cc_start: 0.8277 (ppp) cc_final: 0.8064 (ppp) REVERT: A 1188 PHE cc_start: 0.9165 (m-10) cc_final: 0.8948 (m-10) REVERT: A 1190 MET cc_start: 0.9290 (pmm) cc_final: 0.9035 (pmm) REVERT: A 1237 LYS cc_start: 0.8984 (mttt) cc_final: 0.8709 (mttm) REVERT: A 1299 LYS cc_start: 0.9196 (mmtt) cc_final: 0.8570 (mmtt) REVERT: A 1303 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8815 (mt-10) REVERT: A 1377 LEU cc_start: 0.9374 (mp) cc_final: 0.9044 (tp) REVERT: A 1388 LYS cc_start: 0.9339 (tptp) cc_final: 0.9090 (tptp) REVERT: A 1391 ASN cc_start: 0.9195 (p0) cc_final: 0.8005 (t0) REVERT: A 1410 TYR cc_start: 0.9109 (p90) cc_final: 0.8799 (p90) REVERT: A 1611 MET cc_start: 0.3991 (mmp) cc_final: 0.3333 (tpt) REVERT: A 1655 PHE cc_start: 0.7029 (m-10) cc_final: 0.6593 (m-80) REVERT: A 1706 TRP cc_start: 0.8369 (m100) cc_final: 0.7029 (m100) REVERT: A 1775 TYR cc_start: 0.9272 (t80) cc_final: 0.8727 (t80) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.1051 time to fit residues: 48.1118 Evaluate side-chains 246 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 22 optimal weight: 1.9990 chunk 188 optimal weight: 0.0870 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 0.0870 chunk 292 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 267 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 851 GLN ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.091011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069007 restraints weight = 61364.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071559 restraints weight = 39379.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073390 restraints weight = 28490.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074716 restraints weight = 22307.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075714 restraints weight = 18446.103| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28332 Z= 0.101 Angle : 0.580 10.731 38434 Z= 0.292 Chirality : 0.043 0.232 4344 Planarity : 0.004 0.067 4922 Dihedral : 4.070 22.464 3790 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -0.96 (0.14), residues: 3462 helix: 0.02 (0.15), residues: 1130 sheet: -1.31 (0.19), residues: 656 loop : -0.68 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 64 TYR 0.018 0.001 TYR A1769 PHE 0.022 0.002 PHE A1630 TRP 0.058 0.002 TRP A1503 HIS 0.023 0.001 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00219 (28332) covalent geometry : angle 0.58023 (38434) hydrogen bonds : bond 0.03372 ( 1146) hydrogen bonds : angle 5.23834 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 LEU cc_start: 0.9807 (tp) cc_final: 0.9604 (tp) REVERT: B 196 LEU cc_start: 0.9283 (tt) cc_final: 0.8883 (mt) REVERT: B 209 ILE cc_start: 0.8129 (mt) cc_final: 0.7745 (mt) REVERT: B 215 ARG cc_start: 0.8960 (mtm180) cc_final: 0.8563 (mtm-85) REVERT: B 219 TYR cc_start: 0.8060 (m-80) cc_final: 0.7696 (m-80) REVERT: B 235 LEU cc_start: 0.9389 (mm) cc_final: 0.8708 (mm) REVERT: B 367 LEU cc_start: 0.9079 (tp) cc_final: 0.8872 (tp) REVERT: B 428 LYS cc_start: 0.9396 (ptpp) cc_final: 0.9081 (mmmt) REVERT: B 444 MET cc_start: 0.8826 (mmp) cc_final: 0.8325 (mmm) REVERT: B 469 LEU cc_start: 0.9058 (tp) cc_final: 0.8720 (tp) REVERT: B 470 PHE cc_start: 0.9261 (m-10) cc_final: 0.8786 (m-80) REVERT: B 472 LEU cc_start: 0.9058 (mt) cc_final: 0.8802 (mt) REVERT: B 476 MET cc_start: 0.6609 (pmm) cc_final: 0.6302 (pmm) REVERT: B 499 LEU cc_start: 0.8853 (tt) cc_final: 0.8487 (tt) REVERT: B 556 ASN cc_start: 0.9339 (p0) cc_final: 0.9101 (p0) REVERT: B 557 ASP cc_start: 0.8353 (t0) cc_final: 0.8096 (t70) REVERT: B 569 LEU cc_start: 0.8815 (mm) cc_final: 0.8524 (tp) REVERT: B 601 ASP cc_start: 0.8710 (t0) cc_final: 0.8008 (t0) REVERT: B 622 MET cc_start: 0.9124 (mmm) cc_final: 0.8578 (mmm) REVERT: B 793 PHE cc_start: 0.8365 (m-10) cc_final: 0.7762 (m-80) REVERT: B 891 GLU cc_start: 0.8898 (pm20) cc_final: 0.8630 (pm20) REVERT: B 894 GLN cc_start: 0.9513 (tp40) cc_final: 0.9297 (mm-40) REVERT: B 902 GLU cc_start: 0.9333 (pt0) cc_final: 0.8976 (pp20) REVERT: B 929 GLU cc_start: 0.9313 (tt0) cc_final: 0.8806 (tm-30) REVERT: B 956 MET cc_start: 0.9186 (tmm) cc_final: 0.8765 (ptp) REVERT: B 969 GLU cc_start: 0.9132 (mp0) cc_final: 0.8741 (pp20) REVERT: B 979 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8883 (mt-10) REVERT: B 1006 MET cc_start: 0.7278 (mmp) cc_final: 0.6305 (ppp) REVERT: B 1027 PHE cc_start: 0.8388 (t80) cc_final: 0.8087 (t80) REVERT: B 1086 TRP cc_start: 0.8408 (p90) cc_final: 0.8010 (p90) REVERT: B 1106 VAL cc_start: 0.8641 (t) cc_final: 0.8220 (p) REVERT: B 1116 MET cc_start: 0.9168 (ppp) cc_final: 0.8788 (ppp) REVERT: B 1188 PHE cc_start: 0.9170 (m-10) cc_final: 0.8910 (m-10) REVERT: B 1190 MET cc_start: 0.9286 (pmm) cc_final: 0.9052 (pmm) REVERT: B 1237 LYS cc_start: 0.8979 (mttt) cc_final: 0.8697 (mttm) REVERT: B 1275 LYS cc_start: 0.8904 (pptt) cc_final: 0.8662 (tmmt) REVERT: B 1299 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8528 (mmtt) REVERT: B 1303 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8792 (mt-10) REVERT: B 1377 LEU cc_start: 0.9448 (mp) cc_final: 0.9158 (tp) REVERT: B 1388 LYS cc_start: 0.9388 (tptp) cc_final: 0.9098 (tptp) REVERT: B 1391 ASN cc_start: 0.9193 (p0) cc_final: 0.7885 (t0) REVERT: B 1410 TYR cc_start: 0.9131 (p90) cc_final: 0.8812 (p90) REVERT: B 1541 PHE cc_start: 0.8508 (t80) cc_final: 0.8282 (t80) REVERT: B 1611 MET cc_start: 0.4410 (mmp) cc_final: 0.3700 (tpt) REVERT: B 1655 PHE cc_start: 0.7168 (m-10) cc_final: 0.6725 (m-80) REVERT: B 1706 TRP cc_start: 0.8789 (m100) cc_final: 0.7813 (m100) REVERT: B 1775 TYR cc_start: 0.9258 (t80) cc_final: 0.8702 (t80) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1055 time to fit residues: 46.0734 Evaluate side-chains 240 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 154 optimal weight: 0.3980 chunk 335 optimal weight: 0.0370 chunk 289 optimal weight: 0.0970 chunk 180 optimal weight: 3.9990 chunk 323 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 328 optimal weight: 0.3980 chunk 220 optimal weight: 10.0000 chunk 3 optimal weight: 0.0370 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN A1136 HIS A1291 HIS ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.091460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069695 restraints weight = 59961.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.072260 restraints weight = 38355.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074125 restraints weight = 27651.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075504 restraints weight = 21487.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.076452 restraints weight = 17656.520| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28332 Z= 0.101 Angle : 0.602 11.298 38434 Z= 0.300 Chirality : 0.044 0.273 4344 Planarity : 0.004 0.055 4922 Dihedral : 4.100 22.291 3790 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -1.01 (0.14), residues: 3462 helix: -0.04 (0.15), residues: 1124 sheet: -1.28 (0.19), residues: 656 loop : -0.73 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.014 0.001 TYR B1775 PHE 0.023 0.002 PHE B1997 TRP 0.063 0.002 TRP A1503 HIS 0.017 0.001 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00215 (28332) covalent geometry : angle 0.60221 (38434) hydrogen bonds : bond 0.03350 ( 1146) hydrogen bonds : angle 5.20406 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8876 (ttm170) cc_final: 0.8577 (tmm160) REVERT: A 196 LEU cc_start: 0.9258 (tt) cc_final: 0.8849 (mt) REVERT: A 198 LEU cc_start: 0.9212 (tp) cc_final: 0.8976 (tp) REVERT: A 209 ILE cc_start: 0.8146 (mt) cc_final: 0.7766 (mt) REVERT: A 215 ARG cc_start: 0.8916 (mtm180) cc_final: 0.8527 (mtm110) REVERT: A 219 TYR cc_start: 0.7983 (m-80) cc_final: 0.7728 (m-80) REVERT: A 235 LEU cc_start: 0.9392 (mm) cc_final: 0.8950 (mm) REVERT: A 239 TYR cc_start: 0.7961 (m-80) cc_final: 0.7707 (m-80) REVERT: A 428 LYS cc_start: 0.9346 (ptpp) cc_final: 0.9006 (mmpt) REVERT: A 444 MET cc_start: 0.8834 (mmp) cc_final: 0.8296 (mmm) REVERT: A 469 LEU cc_start: 0.9012 (tp) cc_final: 0.8700 (tp) REVERT: A 470 PHE cc_start: 0.9252 (m-10) cc_final: 0.8748 (m-80) REVERT: A 472 LEU cc_start: 0.9072 (mt) cc_final: 0.8840 (mt) REVERT: A 485 LEU cc_start: 0.8707 (mm) cc_final: 0.8391 (mm) REVERT: A 556 ASN cc_start: 0.9359 (p0) cc_final: 0.9132 (p0) REVERT: A 557 ASP cc_start: 0.8456 (t0) cc_final: 0.8203 (t70) REVERT: A 569 LEU cc_start: 0.8795 (mm) cc_final: 0.8473 (tp) REVERT: A 601 ASP cc_start: 0.8699 (t0) cc_final: 0.7960 (t0) REVERT: A 622 MET cc_start: 0.9081 (mmm) cc_final: 0.8522 (mmm) REVERT: A 640 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6843 (tptt) REVERT: A 793 PHE cc_start: 0.8318 (m-10) cc_final: 0.7681 (m-80) REVERT: A 891 GLU cc_start: 0.8929 (pm20) cc_final: 0.8665 (pm20) REVERT: A 894 GLN cc_start: 0.9540 (tp40) cc_final: 0.9324 (mm-40) REVERT: A 900 LEU cc_start: 0.8540 (mt) cc_final: 0.8311 (mt) REVERT: A 902 GLU cc_start: 0.9350 (pt0) cc_final: 0.9010 (pp20) REVERT: A 929 GLU cc_start: 0.9347 (tt0) cc_final: 0.8813 (tm-30) REVERT: A 936 ASN cc_start: 0.8715 (t0) cc_final: 0.8230 (p0) REVERT: A 969 GLU cc_start: 0.9121 (mp0) cc_final: 0.8724 (pp20) REVERT: A 979 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8895 (mt-10) REVERT: A 1006 MET cc_start: 0.7326 (mmp) cc_final: 0.6318 (ppp) REVERT: A 1027 PHE cc_start: 0.8440 (t80) cc_final: 0.8181 (t80) REVERT: A 1086 TRP cc_start: 0.8379 (p90) cc_final: 0.7983 (p90) REVERT: A 1106 VAL cc_start: 0.8652 (t) cc_final: 0.8215 (p) REVERT: A 1116 MET cc_start: 0.9177 (ppp) cc_final: 0.8797 (ppp) REVERT: A 1188 PHE cc_start: 0.9117 (m-10) cc_final: 0.8832 (m-10) REVERT: A 1190 MET cc_start: 0.9306 (pmm) cc_final: 0.9028 (pmm) REVERT: A 1237 LYS cc_start: 0.8947 (mttt) cc_final: 0.8669 (mttm) REVERT: A 1275 LYS cc_start: 0.8860 (pptt) cc_final: 0.8623 (tmmt) REVERT: A 1299 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8530 (mmtt) REVERT: A 1303 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8775 (mt-10) REVERT: A 1377 LEU cc_start: 0.9415 (mp) cc_final: 0.9153 (tp) REVERT: A 1541 PHE cc_start: 0.8558 (t80) cc_final: 0.8296 (t80) REVERT: A 1611 MET cc_start: 0.4294 (mmp) cc_final: 0.3603 (tpt) REVERT: A 1655 PHE cc_start: 0.7039 (m-10) cc_final: 0.6603 (m-80) REVERT: A 1706 TRP cc_start: 0.8709 (m100) cc_final: 0.7638 (m100) REVERT: A 1775 TYR cc_start: 0.9306 (t80) cc_final: 0.8803 (t80) outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.1057 time to fit residues: 47.1304 Evaluate side-chains 238 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 102 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 343 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 52 optimal weight: 0.0270 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 287 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN B 383 GLN B 710 ASN ** B1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.091304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069520 restraints weight = 61222.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072115 restraints weight = 39272.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074001 restraints weight = 28318.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075379 restraints weight = 22118.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076333 restraints weight = 18245.378| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28332 Z= 0.097 Angle : 0.588 11.970 38434 Z= 0.293 Chirality : 0.043 0.281 4344 Planarity : 0.004 0.055 4922 Dihedral : 4.069 21.861 3790 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 aren not related in a simple way. whole: -1.02 (0.14), residues: 3462 helix: -0.02 (0.15), residues: 1126 sheet: -1.34 (0.18), residues: 660 loop : -0.73 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1462 TYR 0.013 0.001 TYR B1775 PHE 0.019 0.002 PHE A1630 TRP 0.055 0.002 TRP A1503 HIS 0.016 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00208 (28332) covalent geometry : angle 0.58781 (38434) hydrogen bonds : bond 0.03227 ( 1146) hydrogen bonds : angle 5.14561 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3108.54 seconds wall clock time: 55 minutes 22.30 seconds (3322.30 seconds total)