Starting phenix.real_space_refine on Thu Mar 5 11:59:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xe9_22145/03_2026/6xe9_22145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xe9_22145/03_2026/6xe9_22145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xe9_22145/03_2026/6xe9_22145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xe9_22145/03_2026/6xe9_22145.map" model { file = "/net/cci-nas-00/data/ceres_data/6xe9_22145/03_2026/6xe9_22145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xe9_22145/03_2026/6xe9_22145.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 13855 2.51 5 N 3871 2.21 5 O 4241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22081 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 8719 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PTRANS': 26, 'TRANS': 1156} Chain breaks: 3 Unresolved non-hydrogen bonds: 934 Unresolved non-hydrogen angles: 1143 Unresolved non-hydrogen dihedrals: 748 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ARG:plan': 22, 'GLN:plan1': 26, 'GLU:plan': 49, 'PHE:plan': 4, 'TYR:plan': 3, 'ASP:plan': 23, 'ASN:plan1': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 566 Chain: "B" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain: "C" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1160 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "M" Number of atoms: 8724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 8724 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 26, 'TRANS': 1157} Chain breaks: 3 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1148 Unresolved non-hydrogen dihedrals: 751 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ARG:plan': 22, 'GLN:plan1': 26, 'GLU:plan': 50, 'PHE:plan': 4, 'TYR:plan': 3, 'ASP:plan': 23, 'ASN:plan1': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 570 Restraints were copied for chains: N, O Time building chain proxies: 5.54, per 1000 atoms: 0.25 Number of scatterers: 22081 At special positions: 0 Unit cell: (156.704, 130.144, 216.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4241 8.00 N 3871 7.00 C 13855 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: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5626 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 17 sheets defined 67.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 4.073A pdb=" N ALA A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.587A pdb=" N ARG A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 removed outlier: 3.571A pdb=" N LYS A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.994A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.294A pdb=" N TYR A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.987A pdb=" N MET A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.609A pdb=" N PHE A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 448 Processing helix chain 'A' and resid 476 through 508 removed outlier: 4.875A pdb=" N LEU A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU A 501 " --> pdb=" O MET A 497 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 removed outlier: 5.066A pdb=" N ILE A 528 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 575 through 578 Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.528A pdb=" N ALA A 622 " --> pdb=" O ASP A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 676 removed outlier: 3.809A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.631A pdb=" N CYS A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 735 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 779 through 836 removed outlier: 3.867A pdb=" N LYS A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL A 795 " --> pdb=" O LYS A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.866A pdb=" N LEU A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 953 Processing helix chain 'A' and resid 1398 through 1534 removed outlier: 3.917A pdb=" N LEU A1463 " --> pdb=" O PHE A1459 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A1466 " --> pdb=" O MET A1462 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A1534 " --> pdb=" O GLY A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1627 removed outlier: 3.961A pdb=" N SER A1539 " --> pdb=" O GLU A1535 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1627 " --> pdb=" O ALA A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1643 Processing helix chain 'A' and resid 1644 through 1675 removed outlier: 3.802A pdb=" N GLU A1648 " --> pdb=" O LYS A1644 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A1661 " --> pdb=" O GLN A1657 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A1666 " --> pdb=" O ASP A1662 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A1667 " --> pdb=" O TYR A1663 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 18 removed outlier: 3.551A pdb=" N PHE B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 84 through 96 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.670A pdb=" N VAL B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.700A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 49 through 61 removed outlier: 3.874A pdb=" N LEU C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 98 through 110 removed outlier: 3.757A pdb=" N CYS C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 134 through 144 removed outlier: 4.353A pdb=" N VAL C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 71 through 75 removed outlier: 3.676A pdb=" N ASP M 74 " --> pdb=" O SER M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 88 through 92 removed outlier: 3.637A pdb=" N GLU M 91 " --> pdb=" O ASP M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 110 Processing helix chain 'M' and resid 134 through 141 Processing helix chain 'M' and resid 152 through 168 Processing helix chain 'M' and resid 184 through 198 Processing helix chain 'M' and resid 218 through 234 removed outlier: 3.622A pdb=" N LYS M 222 " --> pdb=" O GLY M 218 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Proline residue: M 229 - end of helix Processing helix chain 'M' and resid 273 through 279 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.607A pdb=" N TYR M 291 " --> pdb=" O PHE M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 330 through 342 Processing helix chain 'M' and resid 345 through 358 Processing helix chain 'M' and resid 359 through 365 Processing helix chain 'M' and resid 386 through 391 Processing helix chain 'M' and resid 394 through 404 Processing helix chain 'M' and resid 420 through 451 Processing helix chain 'M' and resid 476 through 508 removed outlier: 5.681A pdb=" N GLU M 501 " --> pdb=" O MET M 497 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN M 506 " --> pdb=" O GLN M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 521 through 530 removed outlier: 3.596A pdb=" N ILE M 525 " --> pdb=" O LEU M 521 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE M 528 " --> pdb=" O CYS M 524 " (cutoff:3.500A) Processing helix chain 'M' and resid 536 through 546 Processing helix chain 'M' and resid 551 through 564 removed outlier: 3.829A pdb=" N PHE M 555 " --> pdb=" O THR M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 596 through 603 Processing helix chain 'M' and resid 611 through 615 Processing helix chain 'M' and resid 619 through 625 removed outlier: 3.533A pdb=" N ASP M 623 " --> pdb=" O LYS M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 658 through 676 Processing helix chain 'M' and resid 697 through 709 Processing helix chain 'M' and resid 710 through 720 Processing helix chain 'M' and resid 727 through 735 removed outlier: 3.767A pdb=" N ARG M 731 " --> pdb=" O PHE M 727 " (cutoff:3.500A) Processing helix chain 'M' and resid 748 through 761 Processing helix chain 'M' and resid 763 through 765 No H-bonds generated for 'chain 'M' and resid 763 through 765' Processing helix chain 'M' and resid 781 through 822 removed outlier: 3.696A pdb=" N GLU M 787 " --> pdb=" O HIS M 783 " (cutoff:3.500A) Processing helix chain 'M' and resid 824 through 837 removed outlier: 3.508A pdb=" N ASN M 828 " --> pdb=" O VAL M 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN M 837 " --> pdb=" O LEU M 833 " (cutoff:3.500A) Processing helix chain 'M' and resid 838 through 852 Proline residue: M 849 - end of helix Processing helix chain 'M' and resid 852 through 890 removed outlier: 4.316A pdb=" N GLN M 856 " --> pdb=" O GLN M 852 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU M 880 " --> pdb=" O LYS M 876 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU M 883 " --> pdb=" O ALA M 879 " (cutoff:3.500A) Processing helix chain 'M' and resid 892 through 954 Processing helix chain 'M' and resid 1398 through 1531 removed outlier: 3.568A pdb=" N PHE M1459 " --> pdb=" O LYS M1455 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER M1470 " --> pdb=" O GLU M1466 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP M1475 " --> pdb=" O SER M1471 " (cutoff:3.500A) Processing helix chain 'M' and resid 1535 through 1611 removed outlier: 3.973A pdb=" N ARG M1541 " --> pdb=" O GLU M1537 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL M1547 " --> pdb=" O LEU M1543 " (cutoff:3.500A) Processing helix chain 'M' and resid 1619 through 1676 removed outlier: 3.833A pdb=" N VAL M1632 " --> pdb=" O LEU M1628 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS M1633 " --> pdb=" O GLU M1629 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU M1653 " --> pdb=" O ALA M1649 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG M1654 " --> pdb=" O ILE M1650 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 18 removed outlier: 3.551A pdb=" N PHE N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 38 Processing helix chain 'N' and resid 43 through 51 Processing helix chain 'N' and resid 55 through 62 Processing helix chain 'N' and resid 68 through 78 Processing helix chain 'N' and resid 84 through 96 Processing helix chain 'N' and resid 105 through 114 Processing helix chain 'N' and resid 120 through 129 removed outlier: 3.670A pdb=" N VAL N 124 " --> pdb=" O THR N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 150 removed outlier: 3.700A pdb=" N LEU N 143 " --> pdb=" O ASN N 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 41 Processing helix chain 'O' and resid 49 through 61 removed outlier: 3.875A pdb=" N LEU O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 73 Processing helix chain 'O' and resid 81 through 94 Processing helix chain 'O' and resid 98 through 110 removed outlier: 3.757A pdb=" N CYS O 108 " --> pdb=" O ASN O 104 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP O 110 " --> pdb=" O PHE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 127 Processing helix chain 'O' and resid 134 through 144 removed outlier: 4.353A pdb=" N VAL O 138 " --> pdb=" O THR O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 163 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 5.022A pdb=" N ILE A 49 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 60 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU A 51 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.307A pdb=" N CYS A 121 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 682 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 174 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS A 684 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A 171 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU A 464 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 173 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 264 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 409 Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 570 removed outlier: 3.531A pdb=" N GLN A 570 " --> pdb=" O CYS A 582 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 582 " --> pdb=" O GLN A 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 725 through 726 Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA8, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AA9, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'M' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'M' and resid 121 through 123 removed outlier: 8.219A pdb=" N VAL M 682 " --> pdb=" O SER M 172 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU M 174 " --> pdb=" O VAL M 682 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS M 684 " --> pdb=" O LEU M 174 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR M 176 " --> pdb=" O CYS M 684 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE M 173 " --> pdb=" O LEU M 464 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY M 264 " --> pdb=" O ASN M 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'M' and resid 569 through 570 removed outlier: 3.648A pdb=" N GLN M 570 " --> pdb=" O CYS M 582 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS M 582 " --> pdb=" O GLN M 570 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 723 through 726 Processing sheet with id=AB6, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AB7, first strand: chain 'N' and resid 103 through 104 Processing sheet with id=AB8, first strand: chain 'O' and resid 116 through 118 1554 hydrogen bonds defined for protein. 4545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7619 1.34 - 1.46: 4305 1.46 - 1.58: 10299 1.58 - 1.69: 0 1.69 - 1.81: 190 Bond restraints: 22413 Sorted by residual: bond pdb=" CB ASN N 100 " pdb=" CG ASN N 100 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.28e+00 bond pdb=" CB ASN B 100 " pdb=" CG ASN B 100 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CA GLY M 462 " pdb=" C GLY M 462 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 8.22e-01 bond pdb=" CA ASN B 100 " pdb=" CB ASN B 100 " ideal model delta sigma weight residual 1.525 1.538 -0.013 1.43e-02 4.89e+03 7.74e-01 bond pdb=" CD GLN B 126 " pdb=" NE2 GLN B 126 " ideal model delta sigma weight residual 1.328 1.346 -0.018 2.10e-02 2.27e+03 7.17e-01 ... (remaining 22408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 29218 1.17 - 2.35: 869 2.35 - 3.52: 152 3.52 - 4.69: 41 4.69 - 5.87: 11 Bond angle restraints: 30291 Sorted by residual: angle pdb=" N VAL M 824 " pdb=" CA VAL M 824 " pdb=" C VAL M 824 " ideal model delta sigma weight residual 113.42 107.86 5.56 1.17e+00 7.31e-01 2.26e+01 angle pdb=" CA VAL M 824 " pdb=" C VAL M 824 " pdb=" N ILE M 825 " ideal model delta sigma weight residual 118.90 116.22 2.68 9.40e-01 1.13e+00 8.13e+00 angle pdb=" CA VAL M 824 " pdb=" C VAL M 824 " pdb=" O VAL M 824 " ideal model delta sigma weight residual 118.90 121.00 -2.10 8.80e-01 1.29e+00 5.68e+00 angle pdb=" C LYS A 578 " pdb=" N THR A 579 " pdb=" CA THR A 579 " ideal model delta sigma weight residual 121.54 126.01 -4.47 1.91e+00 2.74e-01 5.48e+00 angle pdb=" C LYS M 282 " pdb=" N ASP M 283 " pdb=" CA ASP M 283 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 ... (remaining 30286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12289 17.96 - 35.91: 1136 35.91 - 53.86: 190 53.86 - 71.82: 53 71.82 - 89.77: 25 Dihedral angle restraints: 13693 sinusoidal: 5068 harmonic: 8625 Sorted by residual: dihedral pdb=" CA LEU M1543 " pdb=" C LEU M1543 " pdb=" N GLU M1544 " pdb=" CA GLU M1544 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PRO M 534 " pdb=" C PRO M 534 " pdb=" N PRO M 535 " pdb=" CA PRO M 535 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N VAL A 35 " pdb=" CA VAL A 35 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 13690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2083 0.026 - 0.052: 846 0.052 - 0.078: 324 0.078 - 0.104: 126 0.104 - 0.130: 40 Chirality restraints: 3419 Sorted by residual: chirality pdb=" CA ILE A 471 " pdb=" N ILE A 471 " pdb=" C ILE A 471 " pdb=" CB ILE A 471 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE M 49 " pdb=" N ILE M 49 " pdb=" C ILE M 49 " pdb=" CB ILE M 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE M 774 " pdb=" N ILE M 774 " pdb=" C ILE M 774 " pdb=" CB ILE M 774 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 3416 not shown) Planarity restraints: 4025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN N 100 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ASN N 100 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN N 100 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY N 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 100 " -0.011 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C ASN B 100 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN B 100 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY B 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M 534 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO M 535 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO M 535 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO M 535 " 0.029 5.00e-02 4.00e+02 ... (remaining 4022 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 521 2.66 - 3.22: 24145 3.22 - 3.78: 39430 3.78 - 4.34: 49329 4.34 - 4.90: 74626 Nonbonded interactions: 188051 Sorted by model distance: nonbonded pdb=" NE2 GLN M 802 " pdb=" OH TYR N 88 " model vdw 2.096 3.120 nonbonded pdb=" OG SER A 39 " pdb=" OE1 GLU A 45 " model vdw 2.128 3.040 nonbonded pdb=" O ALA M 798 " pdb=" NE2 GLN M 802 " model vdw 2.175 3.120 nonbonded pdb=" OG1 THR A 485 " pdb=" OH TYR A 663 " model vdw 2.176 3.040 nonbonded pdb=" O ASP M 170 " pdb=" OG1 THR M 677 " model vdw 2.178 3.040 ... (remaining 188046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'M' and resid 24 through 1675) } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.003 0.035 22413 Z= 0.130 Angle : 0.501 5.869 30291 Z= 0.291 Chirality : 0.036 0.130 3419 Planarity : 0.003 0.051 4025 Dihedral : 14.921 89.775 8067 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.77 % Allowed : 4.75 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.14), residues: 2925 helix: -0.16 (0.11), residues: 1828 sheet: -3.15 (0.34), residues: 183 loop : -2.73 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 809 TYR 0.016 0.001 TYR M 270 PHE 0.020 0.001 PHE A 844 TRP 0.016 0.001 TRP A 841 HIS 0.006 0.001 HIS M 783 Details of bonding type rmsd covalent geometry : bond 0.00253 (22413) covalent geometry : angle 0.50083 (30291) hydrogen bonds : bond 0.12156 ( 1554) hydrogen bonds : angle 5.21660 ( 4545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 0.904 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.9688 (tt) cc_final: 0.9414 (pp) REVERT: A 391 MET cc_start: 0.9213 (tpp) cc_final: 0.8912 (tpp) REVERT: A 480 LEU cc_start: 0.9607 (tp) cc_final: 0.9400 (tp) REVERT: A 747 MET cc_start: 0.7071 (pmm) cc_final: 0.6659 (ptp) REVERT: B 18 PHE cc_start: 0.9180 (m-10) cc_final: 0.8925 (m-10) REVERT: B 35 MET cc_start: 0.8655 (mmm) cc_final: 0.8390 (tpp) REVERT: B 70 LEU cc_start: 0.9489 (mm) cc_final: 0.9265 (mm) REVERT: B 87 ASP cc_start: 0.9671 (OUTLIER) cc_final: 0.9454 (m-30) REVERT: B 104 MET cc_start: 0.9206 (mtt) cc_final: 0.9004 (mpp) REVERT: C 33 PHE cc_start: 0.8772 (m-80) cc_final: 0.8370 (m-80) REVERT: C 108 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7754 (m) REVERT: C 160 ARG cc_start: 0.8452 (tpp-160) cc_final: 0.8174 (ttp80) REVERT: M 140 MET cc_start: 0.9436 (tpt) cc_final: 0.9100 (tpp) REVERT: M 290 PHE cc_start: 0.8672 (m-10) cc_final: 0.8398 (m-80) REVERT: M 306 LEU cc_start: 0.8457 (mt) cc_final: 0.7770 (mp) REVERT: M 331 MET cc_start: 0.8450 (mmt) cc_final: 0.7808 (mmt) REVERT: M 340 ARG cc_start: 0.9645 (mtp180) cc_final: 0.9259 (ttm110) REVERT: M 378 MET cc_start: 0.8432 (tpt) cc_final: 0.8169 (tpp) REVERT: M 480 LEU cc_start: 0.9588 (mt) cc_final: 0.9372 (mt) REVERT: M 597 TRP cc_start: 0.8891 (m-10) cc_final: 0.8641 (m100) REVERT: N 30 GLN cc_start: 0.8669 (mt0) cc_final: 0.8442 (tm-30) REVERT: N 35 MET cc_start: 0.8804 (mmm) cc_final: 0.8532 (mmm) REVERT: N 104 MET cc_start: 0.9151 (mtt) cc_final: 0.8836 (mpp) REVERT: O 93 LEU cc_start: 0.9031 (tt) cc_final: 0.8819 (mm) outliers start: 16 outliers final: 3 residues processed: 268 average time/residue: 0.1669 time to fit residues: 67.4390 Evaluate side-chains 198 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 166 GLN A 186 ASN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 312 ASN A 364 ASN A 375 GLN A 422 GLN A 486 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 HIS A 732 GLN A 828 ASN A 839 GLN A 861 GLN A 948 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN C 94 ASN M 79 ASN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN M 288 HIS M 318 ASN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS M 719 GLN ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 856 GLN M 886 GLN ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN N 110 HIS O 94 ASN O 104 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.048362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035307 restraints weight = 232078.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036264 restraints weight = 154432.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036904 restraints weight = 115330.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.037383 restraints weight = 93702.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.037715 restraints weight = 80325.886| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22413 Z= 0.215 Angle : 0.593 10.111 30291 Z= 0.322 Chirality : 0.039 0.141 3419 Planarity : 0.004 0.057 4025 Dihedral : 4.391 29.719 3119 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.14 % Allowed : 6.72 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 2925 helix: 0.84 (0.12), residues: 1842 sheet: -2.81 (0.36), residues: 174 loop : -2.29 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 247 TYR 0.026 0.002 TYR O 68 PHE 0.035 0.002 PHE O 33 TRP 0.021 0.002 TRP A 841 HIS 0.008 0.002 HIS N 110 Details of bonding type rmsd covalent geometry : bond 0.00432 (22413) covalent geometry : angle 0.59291 (30291) hydrogen bonds : bond 0.04471 ( 1554) hydrogen bonds : angle 4.71033 ( 4545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 0.854 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: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8778 (mtp) cc_final: 0.8467 (mtm) REVERT: A 101 LEU cc_start: 0.9655 (tt) cc_final: 0.9414 (pp) REVERT: A 391 MET cc_start: 0.9246 (tpp) cc_final: 0.8866 (tpp) REVERT: A 480 LEU cc_start: 0.9631 (tp) cc_final: 0.9401 (tp) REVERT: A 487 GLU cc_start: 0.9414 (mt-10) cc_final: 0.9161 (mt-10) REVERT: A 747 MET cc_start: 0.6930 (pmm) cc_final: 0.6409 (ptp) REVERT: B 18 PHE cc_start: 0.9102 (m-10) cc_final: 0.8843 (m-10) REVERT: C 33 PHE cc_start: 0.8873 (m-80) cc_final: 0.8399 (m-80) REVERT: C 72 MET cc_start: 0.7682 (mpp) cc_final: 0.7317 (mmp) REVERT: C 160 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8390 (ttp80) REVERT: M 250 LYS cc_start: 0.8949 (mppt) cc_final: 0.8541 (mmtt) REVERT: M 290 PHE cc_start: 0.8630 (m-10) cc_final: 0.8343 (m-80) REVERT: M 331 MET cc_start: 0.8490 (mmt) cc_final: 0.7691 (mmt) REVERT: M 334 GLU cc_start: 0.9458 (pt0) cc_final: 0.9235 (pt0) REVERT: M 339 MET cc_start: 0.9708 (pmm) cc_final: 0.9425 (pmm) REVERT: M 340 ARG cc_start: 0.9634 (mtp180) cc_final: 0.9289 (mtm110) REVERT: M 378 MET cc_start: 0.8563 (tpt) cc_final: 0.8286 (tpp) REVERT: M 480 LEU cc_start: 0.9496 (mt) cc_final: 0.9194 (mt) REVERT: M 503 GLU cc_start: 0.9420 (pt0) cc_final: 0.9142 (pt0) REVERT: M 671 MET cc_start: 0.9007 (ptm) cc_final: 0.8768 (ptm) REVERT: M 756 MET cc_start: 0.9547 (ppp) cc_final: 0.9337 (ppp) REVERT: N 30 GLN cc_start: 0.8687 (mt0) cc_final: 0.8467 (mp10) REVERT: N 35 MET cc_start: 0.8883 (mmm) cc_final: 0.8538 (mmm) REVERT: N 73 MET cc_start: 0.8779 (ppp) cc_final: 0.8522 (ppp) REVERT: N 104 MET cc_start: 0.9128 (mtt) cc_final: 0.8728 (mpp) REVERT: N 146 MET cc_start: 0.9096 (ptt) cc_final: 0.8634 (ppp) REVERT: O 39 MET cc_start: 0.9186 (mmp) cc_final: 0.8972 (mmm) REVERT: O 68 TYR cc_start: 0.9622 (m-80) cc_final: 0.9287 (m-10) REVERT: O 141 MET cc_start: 0.9305 (tpt) cc_final: 0.9062 (mmm) outliers start: 3 outliers final: 0 residues processed: 217 average time/residue: 0.1698 time to fit residues: 56.8177 Evaluate side-chains 176 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 281 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 826 GLN A 828 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 ASN ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS M 802 GLN M 828 ASN M 875 GLN M 888 HIS ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.047296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.034226 restraints weight = 227406.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035115 restraints weight = 153614.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035724 restraints weight = 117053.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.036158 restraints weight = 96190.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.036463 restraints weight = 83384.069| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22413 Z= 0.236 Angle : 0.622 10.612 30291 Z= 0.337 Chirality : 0.041 0.169 3419 Planarity : 0.005 0.077 4025 Dihedral : 4.588 29.280 3119 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.14 % Allowed : 6.33 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2925 helix: 1.14 (0.12), residues: 1841 sheet: -2.87 (0.35), residues: 174 loop : -2.28 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 855 TYR 0.022 0.002 TYR M 270 PHE 0.041 0.002 PHE O 33 TRP 0.022 0.002 TRP A 841 HIS 0.007 0.002 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00471 (22413) covalent geometry : angle 0.62212 (30291) hydrogen bonds : bond 0.04427 ( 1554) hydrogen bonds : angle 4.71141 ( 4545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 0.900 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: symmetry clash REVERT: A 78 MET cc_start: 0.8775 (mtp) cc_final: 0.8460 (mtm) REVERT: A 101 LEU cc_start: 0.9614 (tt) cc_final: 0.9393 (pp) REVERT: A 342 MET cc_start: 0.9334 (mmp) cc_final: 0.9078 (mmm) REVERT: A 391 MET cc_start: 0.9289 (tpp) cc_final: 0.8886 (tpp) REVERT: A 480 LEU cc_start: 0.9658 (tp) cc_final: 0.9411 (tp) REVERT: A 497 MET cc_start: 0.9217 (tpt) cc_final: 0.8945 (tpt) REVERT: A 680 ASN cc_start: 0.9444 (t0) cc_final: 0.9182 (t0) REVERT: A 724 ARG cc_start: 0.9348 (mpp-170) cc_final: 0.8916 (mpp-170) REVERT: A 747 MET cc_start: 0.7030 (pmm) cc_final: 0.6784 (pmm) REVERT: A 776 PHE cc_start: 0.9175 (m-80) cc_final: 0.8871 (m-10) REVERT: B 18 PHE cc_start: 0.9075 (m-10) cc_final: 0.8737 (m-10) REVERT: B 30 GLN cc_start: 0.8960 (mt0) cc_final: 0.8645 (mp10) REVERT: C 72 MET cc_start: 0.8097 (mpp) cc_final: 0.7624 (mpp) REVERT: C 73 MET cc_start: 0.8726 (mtp) cc_final: 0.8348 (mpp) REVERT: C 123 ARG cc_start: 0.9228 (mpt-90) cc_final: 0.8912 (mmt90) REVERT: C 160 ARG cc_start: 0.8702 (tpp-160) cc_final: 0.8464 (ttp80) REVERT: M 149 MET cc_start: 0.8847 (mmp) cc_final: 0.8245 (mmm) REVERT: M 250 LYS cc_start: 0.9054 (mppt) cc_final: 0.8734 (mmtt) REVERT: M 331 MET cc_start: 0.8561 (mmt) cc_final: 0.7903 (mmt) REVERT: M 340 ARG cc_start: 0.9651 (mtp180) cc_final: 0.9270 (mtm110) REVERT: M 378 MET cc_start: 0.8287 (tpt) cc_final: 0.8001 (tpp) REVERT: M 503 GLU cc_start: 0.9444 (pt0) cc_final: 0.9090 (pt0) REVERT: M 671 MET cc_start: 0.9013 (ptm) cc_final: 0.8765 (ptm) REVERT: N 35 MET cc_start: 0.8910 (mmm) cc_final: 0.8487 (mmm) REVERT: N 87 ASP cc_start: 0.9313 (m-30) cc_final: 0.9086 (m-30) REVERT: N 104 MET cc_start: 0.9107 (mtt) cc_final: 0.8683 (mpp) REVERT: N 146 MET cc_start: 0.9136 (ptt) cc_final: 0.8672 (ppp) REVERT: O 68 TYR cc_start: 0.9617 (m-80) cc_final: 0.9253 (m-10) REVERT: O 141 MET cc_start: 0.9376 (tpt) cc_final: 0.9056 (mmm) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.1773 time to fit residues: 56.9946 Evaluate side-chains 174 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 37 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 123 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 168 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 394 ASN A 422 GLN A 490 GLN A 494 ASN A 723 ASN ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN A 856 GLN B 40 GLN C 104 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 GLN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS N 16 GLN O 29 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.050018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.036436 restraints weight = 214978.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.037414 restraints weight = 144073.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.038108 restraints weight = 108435.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.038593 restraints weight = 88120.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.038941 restraints weight = 75731.814| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22413 Z= 0.122 Angle : 0.562 14.061 30291 Z= 0.294 Chirality : 0.039 0.168 3419 Planarity : 0.004 0.057 4025 Dihedral : 4.423 29.962 3119 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.10 % Allowed : 4.22 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2925 helix: 1.39 (0.12), residues: 1863 sheet: -2.64 (0.38), residues: 161 loop : -2.26 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 507 TYR 0.018 0.002 TYR A 909 PHE 0.039 0.001 PHE O 33 TRP 0.015 0.001 TRP A 29 HIS 0.007 0.001 HIS O 164 Details of bonding type rmsd covalent geometry : bond 0.00248 (22413) covalent geometry : angle 0.56176 (30291) hydrogen bonds : bond 0.03944 ( 1554) hydrogen bonds : angle 4.44614 ( 4545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.871 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8513 (mtp) cc_final: 0.8175 (mtm) REVERT: A 101 LEU cc_start: 0.9555 (tt) cc_final: 0.9314 (pp) REVERT: A 139 ASP cc_start: 0.8958 (m-30) cc_final: 0.8709 (m-30) REVERT: A 173 ILE cc_start: 0.9714 (tt) cc_final: 0.9454 (tp) REVERT: A 353 LEU cc_start: 0.9389 (mm) cc_final: 0.9132 (mm) REVERT: A 368 LYS cc_start: 0.9722 (tptt) cc_final: 0.9507 (tppt) REVERT: A 480 LEU cc_start: 0.9635 (tp) cc_final: 0.9417 (tp) REVERT: A 497 MET cc_start: 0.9115 (tpt) cc_final: 0.8884 (tpp) REVERT: A 671 MET cc_start: 0.9415 (mtm) cc_final: 0.8929 (mpp) REVERT: A 680 ASN cc_start: 0.9416 (t0) cc_final: 0.8895 (t0) REVERT: A 747 MET cc_start: 0.6820 (pmm) cc_final: 0.6127 (ptp) REVERT: B 18 PHE cc_start: 0.8954 (m-10) cc_final: 0.8728 (m-10) REVERT: B 70 LEU cc_start: 0.9498 (mm) cc_final: 0.9244 (mm) REVERT: C 72 MET cc_start: 0.7880 (mpp) cc_final: 0.7367 (mmp) REVERT: C 73 MET cc_start: 0.8884 (mtp) cc_final: 0.8476 (mpp) REVERT: M 168 ARG cc_start: 0.8894 (tpm170) cc_final: 0.7750 (tpm170) REVERT: M 331 MET cc_start: 0.8534 (mmt) cc_final: 0.7769 (mmt) REVERT: M 340 ARG cc_start: 0.9631 (mtp180) cc_final: 0.9325 (mtm110) REVERT: M 378 MET cc_start: 0.8006 (tpt) cc_final: 0.7756 (tpp) REVERT: M 503 GLU cc_start: 0.9442 (pt0) cc_final: 0.9160 (pt0) REVERT: M 630 ARG cc_start: 0.8295 (mmt180) cc_final: 0.7813 (mmm160) REVERT: M 755 LEU cc_start: 0.9425 (mt) cc_final: 0.9212 (pp) REVERT: M 756 MET cc_start: 0.9393 (ppp) cc_final: 0.9021 (ppp) REVERT: N 30 GLN cc_start: 0.8677 (mt0) cc_final: 0.8390 (mp10) REVERT: N 35 MET cc_start: 0.8862 (mmm) cc_final: 0.8467 (mmm) REVERT: N 104 MET cc_start: 0.9069 (mtt) cc_final: 0.8649 (mpp) REVERT: N 146 MET cc_start: 0.9072 (ptt) cc_final: 0.8588 (ppp) REVERT: O 65 THR cc_start: 0.9422 (p) cc_final: 0.9043 (p) REVERT: O 68 TYR cc_start: 0.9598 (m-80) cc_final: 0.9277 (m-10) REVERT: O 141 MET cc_start: 0.9335 (tpt) cc_final: 0.9029 (mmm) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1682 time to fit residues: 60.5490 Evaluate side-chains 189 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 0.0370 chunk 290 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 130 optimal weight: 0.0070 chunk 203 optimal weight: 0.3980 chunk 165 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 828 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 ASN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS N 79 ASN O 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.050280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.036862 restraints weight = 216464.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.037848 restraints weight = 144754.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.038517 restraints weight = 108701.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.038990 restraints weight = 88534.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.039328 restraints weight = 76246.820| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22413 Z= 0.120 Angle : 0.555 12.409 30291 Z= 0.290 Chirality : 0.039 0.152 3419 Planarity : 0.004 0.056 4025 Dihedral : 4.342 29.854 3119 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2925 helix: 1.45 (0.12), residues: 1863 sheet: -2.66 (0.37), residues: 177 loop : -2.21 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 93 TYR 0.017 0.001 TYR M 270 PHE 0.039 0.001 PHE O 33 TRP 0.014 0.001 TRP A 29 HIS 0.009 0.001 HIS A 585 Details of bonding type rmsd covalent geometry : bond 0.00252 (22413) covalent geometry : angle 0.55518 (30291) hydrogen bonds : bond 0.03876 ( 1554) hydrogen bonds : angle 4.39652 ( 4545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.870 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8942 (m-30) cc_final: 0.8680 (m-30) REVERT: A 339 MET cc_start: 0.9708 (ptt) cc_final: 0.9359 (ptt) REVERT: A 342 MET cc_start: 0.9189 (mmm) cc_final: 0.8896 (mmm) REVERT: A 368 LYS cc_start: 0.9717 (tptt) cc_final: 0.9509 (tppt) REVERT: A 487 GLU cc_start: 0.9415 (mt-10) cc_final: 0.8966 (mp0) REVERT: A 747 MET cc_start: 0.6786 (pmm) cc_final: 0.6104 (ptp) REVERT: B 18 PHE cc_start: 0.8926 (m-10) cc_final: 0.8557 (m-10) REVERT: C 72 MET cc_start: 0.7761 (mpp) cc_final: 0.7256 (mpp) REVERT: C 73 MET cc_start: 0.8823 (mtp) cc_final: 0.8465 (mpp) REVERT: C 81 ASN cc_start: 0.9542 (t0) cc_final: 0.9250 (m-40) REVERT: C 88 MET cc_start: 0.9030 (ptp) cc_final: 0.8761 (ppp) REVERT: C 135 ASP cc_start: 0.9524 (p0) cc_final: 0.9257 (t0) REVERT: C 154 ASN cc_start: 0.9065 (p0) cc_final: 0.8847 (p0) REVERT: M 168 ARG cc_start: 0.8965 (tpm170) cc_final: 0.7849 (tpm170) REVERT: M 331 MET cc_start: 0.8571 (mmt) cc_final: 0.7932 (mmm) REVERT: M 340 ARG cc_start: 0.9630 (mtp180) cc_final: 0.9237 (mtm110) REVERT: M 378 MET cc_start: 0.8027 (tpt) cc_final: 0.7805 (tpp) REVERT: M 503 GLU cc_start: 0.9441 (pt0) cc_final: 0.9185 (pt0) REVERT: M 630 ARG cc_start: 0.8274 (mmt180) cc_final: 0.7783 (mmm160) REVERT: M 665 GLU cc_start: 0.9536 (mt-10) cc_final: 0.9227 (mt-10) REVERT: M 755 LEU cc_start: 0.9439 (mt) cc_final: 0.9224 (pp) REVERT: M 756 MET cc_start: 0.9422 (ppp) cc_final: 0.9145 (ppp) REVERT: N 104 MET cc_start: 0.9074 (mtt) cc_final: 0.8649 (mpp) REVERT: N 146 MET cc_start: 0.9051 (ptt) cc_final: 0.8563 (ppp) REVERT: O 65 THR cc_start: 0.9433 (p) cc_final: 0.9039 (p) REVERT: O 68 TYR cc_start: 0.9602 (m-80) cc_final: 0.9313 (m-10) REVERT: O 141 MET cc_start: 0.9336 (tpt) cc_final: 0.9023 (mmm) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1741 time to fit residues: 61.0431 Evaluate side-chains 188 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 267 optimal weight: 8.9990 chunk 143 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 286 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 236 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS O 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.050311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.036953 restraints weight = 218974.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.037951 restraints weight = 146819.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.038593 restraints weight = 110261.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.039074 restraints weight = 90147.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.039341 restraints weight = 77877.841| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22413 Z= 0.120 Angle : 0.540 7.140 30291 Z= 0.285 Chirality : 0.039 0.143 3419 Planarity : 0.004 0.061 4025 Dihedral : 4.278 29.786 3119 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2925 helix: 1.54 (0.12), residues: 1865 sheet: -2.57 (0.37), residues: 177 loop : -2.20 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 93 TYR 0.017 0.001 TYR M 270 PHE 0.040 0.001 PHE O 33 TRP 0.014 0.001 TRP A 29 HIS 0.006 0.001 HIS O 164 Details of bonding type rmsd covalent geometry : bond 0.00252 (22413) covalent geometry : angle 0.53998 (30291) hydrogen bonds : bond 0.03768 ( 1554) hydrogen bonds : angle 4.34984 ( 4545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.935 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: symmetry clash REVERT: A 139 ASP cc_start: 0.8918 (m-30) cc_final: 0.8655 (m-30) REVERT: A 331 MET cc_start: 0.8981 (mtm) cc_final: 0.8001 (mpp) REVERT: A 339 MET cc_start: 0.9689 (ptt) cc_final: 0.9346 (ptt) REVERT: A 368 LYS cc_start: 0.9726 (tptt) cc_final: 0.9510 (tppt) REVERT: A 747 MET cc_start: 0.6809 (pmm) cc_final: 0.6147 (ptp) REVERT: B 70 LEU cc_start: 0.9494 (mm) cc_final: 0.9242 (mm) REVERT: C 72 MET cc_start: 0.7877 (mpp) cc_final: 0.7431 (mmm) REVERT: C 73 MET cc_start: 0.8803 (mtp) cc_final: 0.8469 (mpp) REVERT: C 135 ASP cc_start: 0.9532 (p0) cc_final: 0.9262 (t70) REVERT: M 78 MET cc_start: 0.8255 (tpt) cc_final: 0.7723 (tpt) REVERT: M 149 MET cc_start: 0.8782 (mmp) cc_final: 0.8395 (mmm) REVERT: M 168 ARG cc_start: 0.8998 (tpm170) cc_final: 0.7936 (tpm170) REVERT: M 331 MET cc_start: 0.8594 (mmt) cc_final: 0.7971 (mmm) REVERT: M 340 ARG cc_start: 0.9631 (mtp180) cc_final: 0.9258 (ttm110) REVERT: M 378 MET cc_start: 0.8045 (tpt) cc_final: 0.7799 (tpp) REVERT: M 503 GLU cc_start: 0.9434 (pt0) cc_final: 0.9135 (pt0) REVERT: M 630 ARG cc_start: 0.8340 (mmt180) cc_final: 0.7878 (mmm160) REVERT: M 665 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9266 (mt-10) REVERT: M 755 LEU cc_start: 0.9442 (mt) cc_final: 0.9232 (pp) REVERT: M 756 MET cc_start: 0.9451 (ppp) cc_final: 0.9089 (ppp) REVERT: N 87 ASP cc_start: 0.9428 (m-30) cc_final: 0.9216 (m-30) REVERT: N 104 MET cc_start: 0.9089 (mtt) cc_final: 0.8662 (mpp) REVERT: N 146 MET cc_start: 0.9021 (ptt) cc_final: 0.8520 (ppp) REVERT: O 65 THR cc_start: 0.9446 (p) cc_final: 0.9053 (p) REVERT: O 68 TYR cc_start: 0.9592 (m-80) cc_final: 0.9335 (m-10) REVERT: O 141 MET cc_start: 0.9410 (tpt) cc_final: 0.8979 (mmp) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.1689 time to fit residues: 58.8410 Evaluate side-chains 186 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 80 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 561 GLN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS O 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036086 restraints weight = 229452.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.037035 restraints weight = 154156.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.037684 restraints weight = 115633.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.038144 restraints weight = 94123.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.038471 restraints weight = 80775.471| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22413 Z= 0.172 Angle : 0.570 7.694 30291 Z= 0.306 Chirality : 0.039 0.141 3419 Planarity : 0.004 0.058 4025 Dihedral : 4.349 29.395 3119 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.05 % Allowed : 2.02 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2925 helix: 1.58 (0.12), residues: 1860 sheet: -2.75 (0.35), residues: 183 loop : -2.14 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 93 TYR 0.023 0.002 TYR M 270 PHE 0.040 0.002 PHE O 33 TRP 0.015 0.002 TRP A 841 HIS 0.007 0.001 HIS A 585 Details of bonding type rmsd covalent geometry : bond 0.00353 (22413) covalent geometry : angle 0.56969 (30291) hydrogen bonds : bond 0.03899 ( 1554) hydrogen bonds : angle 4.40938 ( 4545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.629 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 139 ASP cc_start: 0.8982 (m-30) cc_final: 0.8744 (m-30) REVERT: A 339 MET cc_start: 0.9709 (ptt) cc_final: 0.9240 (ptt) REVERT: A 368 LYS cc_start: 0.9753 (tptt) cc_final: 0.9543 (tppt) REVERT: A 480 LEU cc_start: 0.9629 (tp) cc_final: 0.9383 (tp) REVERT: A 487 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8833 (mt-10) REVERT: A 680 ASN cc_start: 0.8689 (m-40) cc_final: 0.8464 (m-40) REVERT: B 30 GLN cc_start: 0.9146 (mt0) cc_final: 0.8715 (mp10) REVERT: C 72 MET cc_start: 0.7907 (mpp) cc_final: 0.7623 (mpp) REVERT: C 135 ASP cc_start: 0.9501 (p0) cc_final: 0.9214 (t0) REVERT: C 141 MET cc_start: 0.9325 (mpp) cc_final: 0.9056 (mpp) REVERT: C 154 ASN cc_start: 0.9148 (p0) cc_final: 0.8888 (p0) REVERT: M 149 MET cc_start: 0.8916 (mmp) cc_final: 0.8372 (mmm) REVERT: M 168 ARG cc_start: 0.9024 (tpm170) cc_final: 0.7975 (tpm170) REVERT: M 231 LEU cc_start: 0.9274 (mm) cc_final: 0.9068 (pp) REVERT: M 331 MET cc_start: 0.8529 (mmt) cc_final: 0.7856 (mmt) REVERT: M 340 ARG cc_start: 0.9636 (mtp180) cc_final: 0.9248 (mtm110) REVERT: M 378 MET cc_start: 0.8442 (tpt) cc_final: 0.8174 (tpp) REVERT: M 503 GLU cc_start: 0.9448 (pt0) cc_final: 0.9202 (pt0) REVERT: N 30 GLN cc_start: 0.8763 (mt0) cc_final: 0.8423 (mp10) REVERT: N 87 ASP cc_start: 0.9386 (m-30) cc_final: 0.9163 (m-30) REVERT: N 104 MET cc_start: 0.9026 (mtt) cc_final: 0.8520 (mpp) REVERT: N 146 MET cc_start: 0.9022 (ptt) cc_final: 0.8558 (ppp) REVERT: O 141 MET cc_start: 0.9443 (tpt) cc_final: 0.9095 (mmm) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1621 time to fit residues: 54.6952 Evaluate side-chains 176 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 154 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 chunk 216 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS O 29 GLN O 54 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.049072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036054 restraints weight = 228924.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036999 restraints weight = 152236.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.037652 restraints weight = 113959.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.038115 restraints weight = 92399.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.038440 restraints weight = 79215.020| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22413 Z= 0.168 Angle : 0.574 7.605 30291 Z= 0.307 Chirality : 0.040 0.185 3419 Planarity : 0.004 0.058 4025 Dihedral : 4.395 29.351 3119 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2925 helix: 1.58 (0.12), residues: 1855 sheet: -2.76 (0.35), residues: 181 loop : -2.10 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 918 TYR 0.022 0.002 TYR O 68 PHE 0.039 0.002 PHE O 33 TRP 0.015 0.002 TRP A 29 HIS 0.008 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00343 (22413) covalent geometry : angle 0.57361 (30291) hydrogen bonds : bond 0.03897 ( 1554) hydrogen bonds : angle 4.39561 ( 4545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.830 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 339 MET cc_start: 0.9681 (ptt) cc_final: 0.9282 (ptt) REVERT: A 342 MET cc_start: 0.9050 (mmm) cc_final: 0.8668 (mmm) REVERT: A 480 LEU cc_start: 0.9637 (tp) cc_final: 0.9359 (tp) REVERT: A 487 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8971 (mt-10) REVERT: A 497 MET cc_start: 0.9100 (tpt) cc_final: 0.8898 (tpp) REVERT: B 30 GLN cc_start: 0.9143 (mt0) cc_final: 0.8716 (mp10) REVERT: C 72 MET cc_start: 0.7726 (mpp) cc_final: 0.7440 (mpp) REVERT: C 84 MET cc_start: 0.9431 (ppp) cc_final: 0.9156 (ppp) REVERT: C 88 MET cc_start: 0.8714 (ppp) cc_final: 0.8489 (ppp) REVERT: C 135 ASP cc_start: 0.9508 (p0) cc_final: 0.9222 (t0) REVERT: C 141 MET cc_start: 0.9348 (mpp) cc_final: 0.9068 (mpp) REVERT: C 154 ASN cc_start: 0.9163 (p0) cc_final: 0.8904 (p0) REVERT: M 149 MET cc_start: 0.8939 (mmp) cc_final: 0.8418 (mmm) REVERT: M 168 ARG cc_start: 0.9042 (tpm170) cc_final: 0.8707 (tpm170) REVERT: M 331 MET cc_start: 0.8618 (mmt) cc_final: 0.7927 (mmt) REVERT: M 340 ARG cc_start: 0.9634 (mtp180) cc_final: 0.9239 (mtm110) REVERT: M 378 MET cc_start: 0.8295 (tpt) cc_final: 0.8030 (tpp) REVERT: M 501 GLU cc_start: 0.9012 (pp20) cc_final: 0.8769 (pp20) REVERT: M 503 GLU cc_start: 0.9408 (pt0) cc_final: 0.9117 (pt0) REVERT: M 671 MET cc_start: 0.9158 (ptm) cc_final: 0.8865 (ptm) REVERT: N 30 GLN cc_start: 0.8735 (mt0) cc_final: 0.8390 (mp10) REVERT: N 87 ASP cc_start: 0.9366 (m-30) cc_final: 0.9155 (m-30) REVERT: N 104 MET cc_start: 0.9023 (mtt) cc_final: 0.8540 (mpp) REVERT: N 146 MET cc_start: 0.9105 (ptt) cc_final: 0.8638 (ppp) REVERT: O 65 THR cc_start: 0.9362 (p) cc_final: 0.8735 (p) REVERT: O 68 TYR cc_start: 0.9642 (m-80) cc_final: 0.9309 (m-80) REVERT: O 141 MET cc_start: 0.9447 (tpt) cc_final: 0.9077 (mmm) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1609 time to fit residues: 54.4754 Evaluate side-chains 179 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 158 optimal weight: 0.3980 chunk 172 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 159 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 494 ASN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS O 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.049480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.036360 restraints weight = 227908.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.037318 restraints weight = 151784.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.037971 restraints weight = 113535.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.038451 restraints weight = 92085.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.038780 restraints weight = 78891.214| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22413 Z= 0.143 Angle : 0.573 8.751 30291 Z= 0.304 Chirality : 0.040 0.195 3419 Planarity : 0.004 0.059 4025 Dihedral : 4.405 29.487 3119 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.10 % Allowed : 0.67 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2925 helix: 1.58 (0.12), residues: 1867 sheet: -2.65 (0.37), residues: 177 loop : -2.08 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 93 TYR 0.019 0.002 TYR M 270 PHE 0.038 0.001 PHE O 33 TRP 0.081 0.002 TRP A 841 HIS 0.008 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00295 (22413) covalent geometry : angle 0.57310 (30291) hydrogen bonds : bond 0.03859 ( 1554) hydrogen bonds : angle 4.40206 ( 4545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.903 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 139 ASP cc_start: 0.9037 (m-30) cc_final: 0.8738 (m-30) REVERT: A 331 MET cc_start: 0.9041 (mtm) cc_final: 0.7959 (mpp) REVERT: A 339 MET cc_start: 0.9689 (ptt) cc_final: 0.9286 (ptt) REVERT: A 368 LYS cc_start: 0.9737 (tptt) cc_final: 0.9527 (tppt) REVERT: A 480 LEU cc_start: 0.9634 (tp) cc_final: 0.9352 (tp) REVERT: A 487 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8973 (mt-10) REVERT: A 497 MET cc_start: 0.9066 (tpt) cc_final: 0.8858 (tpp) REVERT: A 681 PHE cc_start: 0.8226 (m-10) cc_final: 0.7972 (m-10) REVERT: A 756 MET cc_start: 0.9172 (ppp) cc_final: 0.8960 (ppp) REVERT: C 72 MET cc_start: 0.7784 (mpp) cc_final: 0.7426 (mmm) REVERT: C 73 MET cc_start: 0.9095 (mmp) cc_final: 0.8511 (mmm) REVERT: C 84 MET cc_start: 0.9403 (ppp) cc_final: 0.9106 (ppp) REVERT: C 88 MET cc_start: 0.8721 (ppp) cc_final: 0.8495 (ppp) REVERT: C 135 ASP cc_start: 0.9526 (p0) cc_final: 0.9254 (t0) REVERT: C 154 ASN cc_start: 0.9147 (p0) cc_final: 0.8879 (p0) REVERT: M 149 MET cc_start: 0.8936 (mmp) cc_final: 0.8416 (mmm) REVERT: M 168 ARG cc_start: 0.9050 (tpm170) cc_final: 0.8729 (tpm170) REVERT: M 331 MET cc_start: 0.8637 (mmt) cc_final: 0.7981 (mmm) REVERT: M 340 ARG cc_start: 0.9621 (mtp180) cc_final: 0.9220 (mtm110) REVERT: M 378 MET cc_start: 0.8289 (tpt) cc_final: 0.8024 (tpp) REVERT: M 497 MET cc_start: 0.9078 (ppp) cc_final: 0.8742 (ppp) REVERT: M 501 GLU cc_start: 0.8972 (pp20) cc_final: 0.8748 (pp20) REVERT: M 503 GLU cc_start: 0.9423 (pt0) cc_final: 0.9137 (pt0) REVERT: M 671 MET cc_start: 0.9141 (ptm) cc_final: 0.8838 (ptm) REVERT: M 756 MET cc_start: 0.9450 (ppp) cc_final: 0.9028 (ppp) REVERT: N 30 GLN cc_start: 0.8745 (mt0) cc_final: 0.8393 (mp10) REVERT: N 36 ARG cc_start: 0.9143 (mtt90) cc_final: 0.8718 (mmt90) REVERT: N 104 MET cc_start: 0.8989 (mtt) cc_final: 0.8504 (mpp) REVERT: N 146 MET cc_start: 0.9132 (ptt) cc_final: 0.8672 (ppp) REVERT: O 65 THR cc_start: 0.9424 (p) cc_final: 0.9216 (p) REVERT: O 68 TYR cc_start: 0.9634 (m-80) cc_final: 0.9399 (m-80) REVERT: O 141 MET cc_start: 0.9440 (tpt) cc_final: 0.9066 (mmm) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.1658 time to fit residues: 56.2332 Evaluate side-chains 180 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 29 optimal weight: 0.0000 chunk 271 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 chunk 209 optimal weight: 9.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 HIS ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 GLN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 585 HIS ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS O 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.047675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034561 restraints weight = 225096.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035493 restraints weight = 150948.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036111 restraints weight = 113629.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.036556 restraints weight = 92936.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036790 restraints weight = 80435.180| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22413 Z= 0.229 Angle : 0.646 10.525 30291 Z= 0.346 Chirality : 0.042 0.220 3419 Planarity : 0.004 0.061 4025 Dihedral : 4.592 29.140 3119 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.10 % Allowed : 0.43 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 2925 helix: 1.48 (0.12), residues: 1860 sheet: -2.92 (0.35), residues: 181 loop : -2.16 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 93 TYR 0.025 0.002 TYR M 270 PHE 0.040 0.002 PHE O 33 TRP 0.068 0.003 TRP A 841 HIS 0.013 0.002 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00465 (22413) covalent geometry : angle 0.64578 (30291) hydrogen bonds : bond 0.04134 ( 1554) hydrogen bonds : angle 4.58166 ( 4545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.859 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 139 ASP cc_start: 0.9050 (m-30) cc_final: 0.8796 (m-30) REVERT: A 339 MET cc_start: 0.9705 (ptt) cc_final: 0.9203 (ptt) REVERT: A 342 MET cc_start: 0.9011 (mmm) cc_final: 0.8663 (mmm) REVERT: B 30 GLN cc_start: 0.9143 (mt0) cc_final: 0.8729 (mp10) REVERT: C 72 MET cc_start: 0.7871 (mpp) cc_final: 0.7455 (mpp) REVERT: C 73 MET cc_start: 0.9101 (mmp) cc_final: 0.8869 (mmm) REVERT: C 84 MET cc_start: 0.9463 (ppp) cc_final: 0.9137 (ppp) REVERT: C 88 MET cc_start: 0.8759 (ppp) cc_final: 0.8524 (ppp) REVERT: C 135 ASP cc_start: 0.9518 (p0) cc_final: 0.9252 (t0) REVERT: C 154 ASN cc_start: 0.9277 (p0) cc_final: 0.9002 (p0) REVERT: M 149 MET cc_start: 0.8923 (mmp) cc_final: 0.8360 (mmm) REVERT: M 168 ARG cc_start: 0.9023 (tpm170) cc_final: 0.8711 (tpm170) REVERT: M 339 MET cc_start: 0.9723 (pmm) cc_final: 0.9470 (pmm) REVERT: M 340 ARG cc_start: 0.9636 (mtp180) cc_final: 0.9253 (mtm110) REVERT: M 378 MET cc_start: 0.8314 (tpt) cc_final: 0.8034 (tpp) REVERT: M 497 MET cc_start: 0.9095 (ppp) cc_final: 0.8783 (ppp) REVERT: M 503 GLU cc_start: 0.9387 (pt0) cc_final: 0.9118 (pt0) REVERT: M 671 MET cc_start: 0.9172 (ptm) cc_final: 0.8809 (ptm) REVERT: N 30 GLN cc_start: 0.8758 (mt0) cc_final: 0.8428 (mp10) REVERT: N 35 MET cc_start: 0.8849 (mmm) cc_final: 0.8178 (mmm) REVERT: N 104 MET cc_start: 0.8988 (mtt) cc_final: 0.8517 (mpp) REVERT: N 146 MET cc_start: 0.9123 (ptt) cc_final: 0.8736 (ppp) REVERT: O 68 TYR cc_start: 0.9621 (m-80) cc_final: 0.9377 (m-80) REVERT: O 141 MET cc_start: 0.9422 (tpt) cc_final: 0.9005 (mmm) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.1591 time to fit residues: 52.2838 Evaluate side-chains 169 residues out of total 2591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 179 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 115 optimal weight: 50.0000 chunk 40 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 GLN ** M 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 689 HIS ** M 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.048113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.034998 restraints weight = 223734.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035939 restraints weight = 149113.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.036557 restraints weight = 112162.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.037002 restraints weight = 91776.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.037305 restraints weight = 79415.338| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22413 Z= 0.183 Angle : 0.608 10.079 30291 Z= 0.323 Chirality : 0.041 0.245 3419 Planarity : 0.004 0.059 4025 Dihedral : 4.604 29.464 3119 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.10 % Allowed : 0.53 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 2925 helix: 1.48 (0.12), residues: 1866 sheet: -2.89 (0.34), residues: 181 loop : -2.20 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 93 TYR 0.021 0.002 TYR M 270 PHE 0.040 0.002 PHE O 33 TRP 0.059 0.002 TRP A 841 HIS 0.006 0.001 HIS O 164 Details of bonding type rmsd covalent geometry : bond 0.00374 (22413) covalent geometry : angle 0.60816 (30291) hydrogen bonds : bond 0.03986 ( 1554) hydrogen bonds : angle 4.52577 ( 4545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.90 seconds wall clock time: 68 minutes 6.83 seconds (4086.83 seconds total)