Starting phenix.real_space_refine on Sun Aug 24 02:14:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e7i_31000/08_2025/7e7i_31000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e7i_31000/08_2025/7e7i_31000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e7i_31000/08_2025/7e7i_31000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e7i_31000/08_2025/7e7i_31000.map" model { file = "/net/cci-nas-00/data/ceres_data/7e7i_31000/08_2025/7e7i_31000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e7i_31000/08_2025/7e7i_31000_neut.cif" } resolution = 3.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 85 5.16 5 C 10136 2.51 5 N 2618 2.21 5 O 2883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15724 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2011, 15402 Classifications: {'peptide': 2011} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 98, 'TRANS': 1912} Chain breaks: 12 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 12, 'HIS:plan': 4, 'ARG:plan': 16, 'TRP:plan': 2, 'PHE:plan': 10, 'ASP:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 391 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 200 Unusual residues: {'3PE': 2, 'NAG': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.18, per 1000 atoms: 0.20 Number of scatterers: 15724 At special positions: 0 Unit cell: (100.44, 104.76, 241.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 2 15.00 O 2883 8.00 N 2618 7.00 C 10136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.04 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=1.92 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.15 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 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=1, symmetry=0 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " " BMA M 3 " - " BMA M 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " BETA1-6 " BMA D 3 " - " BMA D 5 " " BMA M 3 " - " BMA M 5 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 444 " " NAG A2303 " - " ASN A 504 " " NAG A2304 " - " ASN A1457 " " NAG A2305 " - " ASN A1469 " " NAG A2306 " - " ASN A1588 " " NAG A2307 " - " ASN A1662 " " NAG D 1 " - " ASN A 415 " " NAG M 1 " - " ASN A1529 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 510.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 50.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.677A pdb=" N GLN A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 37 removed outlier: 3.666A pdb=" N VAL A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.657A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.960A pdb=" N TYR A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.831A pdb=" N ILE A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 279 through 289 removed outlier: 4.657A pdb=" N ARG A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 284 " --> pdb=" O MET A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 385 through 395 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 415 through 430 removed outlier: 4.041A pdb=" N VAL A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.685A pdb=" N GLU A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.904A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.631A pdb=" N VAL A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 578 " --> pdb=" O ILE A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 578' Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 622 removed outlier: 3.579A pdb=" N LEU A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 663 removed outlier: 4.065A pdb=" N ILE A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Proline residue: A 656 - end of helix removed outlier: 3.940A pdb=" N TRP A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 680 removed outlier: 4.340A pdb=" N SER A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 689 removed outlier: 3.662A pdb=" N THR A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 722 removed outlier: 3.607A pdb=" N SER A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 753 removed outlier: 3.889A pdb=" N LEU A 733 " --> pdb=" O ASP A 729 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 734 " --> pdb=" O PRO A 730 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 772 removed outlier: 3.522A pdb=" N ALA A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.834A pdb=" N LEU A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.576A pdb=" N LYS A 791 " --> pdb=" O THR A 787 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 795 " --> pdb=" O LYS A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 815 removed outlier: 3.681A pdb=" N GLY A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 removed outlier: 3.706A pdb=" N MET A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 978 removed outlier: 3.644A pdb=" N THR A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1019 through 1033 removed outlier: 3.716A pdb=" N LYS A1031 " --> pdb=" O TYR A1027 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A1033 " --> pdb=" O GLN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1049 removed outlier: 3.512A pdb=" N GLU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1074 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1093 through 1107 removed outlier: 3.977A pdb=" N ARG A1098 " --> pdb=" O PRO A1094 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A1099 " --> pdb=" O TYR A1095 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1126 removed outlier: 3.552A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1152 removed outlier: 3.556A pdb=" N PHE A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1210 Processing helix chain 'A' and resid 1239 through 1253 removed outlier: 3.889A pdb=" N GLU A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1258 removed outlier: 3.942A pdb=" N LEU A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1278 removed outlier: 3.746A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1369 removed outlier: 3.852A pdb=" N GLN A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1376 removed outlier: 4.205A pdb=" N PHE A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A1375 " --> pdb=" O LYS A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1390 Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 3.821A pdb=" N TYR A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1467 through 1477 removed outlier: 3.758A pdb=" N GLN A1475 " --> pdb=" O THR A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1537 removed outlier: 3.504A pdb=" N PHE A1533 " --> pdb=" O ASN A1529 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A1535 " --> pdb=" O SER A1531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A1536 " --> pdb=" O ASP A1532 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A1537 " --> pdb=" O PHE A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1546 removed outlier: 4.391A pdb=" N SER A1544 " --> pdb=" O ALA A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1586 removed outlier: 3.606A pdb=" N VAL A1577 " --> pdb=" O GLY A1573 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A1579 " --> pdb=" O ALA A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1599 Processing helix chain 'A' and resid 1601 through 1606 removed outlier: 3.872A pdb=" N LEU A1606 " --> pdb=" O ILE A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1641 removed outlier: 3.877A pdb=" N PHE A1630 " --> pdb=" O ALA A1626 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A1632 " --> pdb=" O VAL A1628 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1639 " --> pdb=" O HIS A1635 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A1640 " --> pdb=" O ASN A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1652 removed outlier: 3.635A pdb=" N TYR A1652 " --> pdb=" O PRO A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1691 removed outlier: 3.715A pdb=" N ILE A1671 " --> pdb=" O GLN A1667 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL A1678 " --> pdb=" O LEU A1674 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A1679 " --> pdb=" O THR A1675 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A1684 " --> pdb=" O ALA A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1706 removed outlier: 3.776A pdb=" N VAL A1698 " --> pdb=" O PRO A1694 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A1699 " --> pdb=" O ALA A1695 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A1700 " --> pdb=" O SER A1696 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A1701 " --> pdb=" O PHE A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 removed outlier: 3.557A pdb=" N SER A1716 " --> pdb=" O LEU A1712 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A1718 " --> pdb=" O PHE A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1719 through 1750 removed outlier: 3.946A pdb=" N TYR A1723 " --> pdb=" O SER A1719 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A1733 " --> pdb=" O LEU A1729 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A1737 " --> pdb=" O MET A1733 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1779 removed outlier: 3.509A pdb=" N TYR A1770 " --> pdb=" O LEU A1766 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) Proline residue: A1776 - end of helix removed outlier: 3.635A pdb=" N TYR A1779 " --> pdb=" O ILE A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1784 removed outlier: 3.779A pdb=" N LEU A1784 " --> pdb=" O ALA A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1787 through 1815 removed outlier: 4.140A pdb=" N CYS A1797 " --> pdb=" O VAL A1793 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A1798 " --> pdb=" O ALA A1794 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A1800 " --> pdb=" O SER A1796 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A1803 " --> pdb=" O ASN A1799 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1805 " --> pdb=" O PHE A1801 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A1806 " --> pdb=" O ILE A1802 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1807 " --> pdb=" O GLY A1803 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE A1809 " --> pdb=" O ASN A1805 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A1811 " --> pdb=" O SER A1807 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A1815 " --> pdb=" O PHE A1811 " (cutoff:3.500A) Processing helix chain 'A' and resid 1821 through 1833 removed outlier: 3.593A pdb=" N VAL A1828 " --> pdb=" O ARG A1824 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A1831 " --> pdb=" O ALA A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1846 removed outlier: 3.801A pdb=" N CYS A1840 " --> pdb=" O PHE A1836 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A1844 " --> pdb=" O CYS A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1858 removed outlier: 3.993A pdb=" N GLN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A1858 " --> pdb=" O VAL A1854 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1861 No H-bonds generated for 'chain 'A' and resid 1859 through 1861' Processing helix chain 'A' and resid 1875 through 1894 removed outlier: 3.805A pdb=" N LEU A1879 " --> pdb=" O ILE A1875 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A1883 " --> pdb=" O LEU A1879 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1887 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A1889 " --> pdb=" O GLU A1885 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE A1890 " --> pdb=" O GLY A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1919 through 1927 removed outlier: 4.492A pdb=" N GLU A1923 " --> pdb=" O ASP A1919 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG A1927 " --> pdb=" O GLU A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1986 removed outlier: 3.813A pdb=" N PHE A1982 " --> pdb=" O LYS A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2006 through 2010 Processing helix chain 'A' and resid 2028 through 2039 removed outlier: 3.781A pdb=" N HIS A2032 " --> pdb=" O THR A2028 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A2033 " --> pdb=" O GLY A2029 " (cutoff:3.500A) Processing helix chain 'A' and resid 2046 through 2059 removed outlier: 3.565A pdb=" N LYS A2056 " --> pdb=" O ASN A2052 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A2058 " --> pdb=" O SER A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2074 through 2084 Processing helix chain 'A' and resid 2102 through 2118 removed outlier: 3.550A pdb=" N ARG A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A2107 " --> pdb=" O PRO A2103 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A2109 " --> pdb=" O ALA A2105 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A2112 " --> pdb=" O MET A2108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A2117 " --> pdb=" O ILE A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2136 Processing helix chain 'A' and resid 2153 through 2161 removed outlier: 3.571A pdb=" N SER A2159 " --> pdb=" O GLN A2155 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A2160 " --> pdb=" O HIS A2156 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2189 removed outlier: 4.225A pdb=" N GLU A2186 " --> pdb=" O LEU A2182 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A2187 " --> pdb=" O ASN A2183 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2193 removed outlier: 4.246A pdb=" N PHE A2193 " --> pdb=" O GLN A2190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2190 through 2193' Processing helix chain 'A' and resid 2241 through 2251 removed outlier: 3.587A pdb=" N PHE A2245 " --> pdb=" O LEU A2241 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN A2251 " --> pdb=" O ASN A2247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.575A pdb=" N PHE A 642 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.678A pdb=" N LYS A1616 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR A1414 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ILE A1560 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A1416 " --> pdb=" O ILE A1560 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A1415 " --> pdb=" O GLN A1523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 528 removed outlier: 6.296A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR A 528 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR A 400 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 399 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 952 through 953 removed outlier: 3.664A pdb=" N THR A 986 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1005 through 1008 removed outlier: 3.517A pdb=" N ILE A1084 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A1086 " --> pdb=" O CYS A1008 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A1083 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER A1116 " --> pdb=" O VAL A1083 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A1085 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN A 957 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N MET A1115 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR A 959 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A1130 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A1141 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A1132 " --> pdb=" O TYR A1139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1159 through 1161 removed outlier: 7.442A pdb=" N VAL A1160 " --> pdb=" O SER A1260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1967 through 1968 removed outlier: 6.414A pdb=" N VAL A2092 " --> pdb=" O VAL A2124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2208 through 2209 553 hydrogen bonds defined for protein. 1620 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: 2.67 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3303 1.33 - 1.45: 3881 1.45 - 1.58: 8753 1.58 - 1.70: 4 1.70 - 1.83: 137 Bond restraints: 16078 Sorted by residual: bond pdb=" C21 3PE A2309 " pdb=" O21 3PE A2309 " ideal model delta sigma weight residual 1.316 1.451 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C21 3PE A2308 " pdb=" O21 3PE A2308 " ideal model delta sigma weight residual 1.316 1.449 -0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C31 3PE A2308 " pdb=" O31 3PE A2308 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C31 3PE A2309 " pdb=" O31 3PE A2309 " ideal model delta sigma weight residual 1.331 1.444 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C1 NAG A2304 " pdb=" O5 NAG A2304 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 16073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.01: 21787 7.01 - 14.02: 46 14.02 - 21.03: 0 21.03 - 28.04: 1 28.04 - 35.05: 2 Bond angle restraints: 21836 Sorted by residual: angle pdb=" N ASN A1235 " pdb=" CA ASN A1235 " pdb=" C ASN A1235 " ideal model delta sigma weight residual 109.14 74.09 35.05 1.49e+00 4.50e-01 5.53e+02 angle pdb=" N LYS A1236 " pdb=" CA LYS A1236 " pdb=" CB LYS A1236 " ideal model delta sigma weight residual 110.49 140.50 -30.01 1.69e+00 3.50e-01 3.15e+02 angle pdb=" N LYS A1236 " pdb=" CA LYS A1236 " pdb=" C LYS A1236 " ideal model delta sigma weight residual 110.80 89.03 21.77 2.13e+00 2.20e-01 1.04e+02 angle pdb=" N CYS A1444 " pdb=" CA CYS A1444 " pdb=" C CYS A1444 " ideal model delta sigma weight residual 112.93 119.97 -7.04 1.12e+00 7.97e-01 3.95e+01 angle pdb=" N GLU A1666 " pdb=" CA GLU A1666 " pdb=" C GLU A1666 " ideal model delta sigma weight residual 114.04 107.03 7.01 1.24e+00 6.50e-01 3.20e+01 ... (remaining 21831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 9087 25.04 - 50.09: 540 50.09 - 75.13: 90 75.13 - 100.17: 51 100.17 - 125.22: 18 Dihedral angle restraints: 9786 sinusoidal: 3970 harmonic: 5816 Sorted by residual: dihedral pdb=" N LYS A1236 " pdb=" C LYS A1236 " pdb=" CA LYS A1236 " pdb=" CB LYS A1236 " ideal model delta harmonic sigma weight residual 122.80 144.55 -21.75 0 2.50e+00 1.60e-01 7.57e+01 dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1490 " pdb=" CB CYS A1490 " ideal model delta sinusoidal sigma weight residual -86.00 -156.07 70.07 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" N ASN A1235 " pdb=" C ASN A1235 " pdb=" CA ASN A1235 " pdb=" CB ASN A1235 " ideal model delta harmonic sigma weight residual 122.80 104.80 18.00 0 2.50e+00 1.60e-01 5.18e+01 ... (remaining 9783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2448 0.131 - 0.263: 78 0.263 - 0.394: 11 0.394 - 0.526: 1 0.526 - 0.657: 1 Chirality restraints: 2539 Sorted by residual: chirality pdb=" CA LYS A1236 " pdb=" N LYS A1236 " pdb=" C LYS A1236 " pdb=" CB LYS A1236 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG A2306 " pdb=" ND2 ASN A1588 " pdb=" C2 NAG A2306 " pdb=" O5 NAG A2306 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CB THR A2028 " pdb=" CA THR A2028 " pdb=" OG1 THR A2028 " pdb=" CG2 THR A2028 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2536 not shown) Planarity restraints: 2753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.063 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN A 98 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.058 2.00e-02 2.50e+03 pdb=" C1 NAG A2301 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" CG ASN A 98 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1746 " -0.024 2.00e-02 2.50e+03 2.13e-02 7.95e+00 pdb=" CG PHE A1746 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A1746 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A1746 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1746 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1746 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A1746 " -0.005 2.00e-02 2.50e+03 ... (remaining 2750 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 25 2.25 - 2.92: 6983 2.92 - 3.58: 20816 3.58 - 4.24: 33309 4.24 - 4.90: 57353 Nonbonded interactions: 118486 Sorted by model distance: nonbonded pdb=" SD MET A1163 " pdb=" N LEU A1201 " model vdw 1.593 3.480 nonbonded pdb=" CE MET A1163 " pdb=" O GLN A1199 " model vdw 1.614 3.460 nonbonded pdb=" SD MET A1163 " pdb=" CA LEU A1201 " model vdw 1.623 3.830 nonbonded pdb=" CE MET A1163 " pdb=" C VAL A1200 " model vdw 1.697 3.690 nonbonded pdb=" O LEU A1254 " pdb=" CD1 LEU A1257 " model vdw 1.722 3.460 ... (remaining 118481 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 'D' selection = chain 'M' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.850 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.135 16102 Z= 0.467 Angle : 1.253 41.897 21899 Z= 0.649 Chirality : 0.064 0.657 2539 Planarity : 0.006 0.064 2744 Dihedral : 18.445 125.216 6008 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.26 % Favored : 83.98 % Rotamer: Outliers : 1.82 % Allowed : 1.13 % Favored : 97.04 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: -4.06 (0.17), residues: 1985 helix: -1.84 (0.16), residues: 942 sheet: -2.59 (0.37), residues: 168 loop : -3.71 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1939 TYR 0.040 0.003 TYR A 400 PHE 0.049 0.003 PHE A1746 TRP 0.037 0.003 TRP A 697 HIS 0.013 0.002 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.01093 (16078) covalent geometry : angle 1.16417 (21836) SS BOND : bond 0.06906 ( 6) SS BOND : angle 16.23487 ( 12) hydrogen bonds : bond 0.17502 ( 553) hydrogen bonds : angle 6.77566 ( 1620) Misc. bond : bond 0.00249 ( 1) link_BETA1-3 : bond 0.00229 ( 2) link_BETA1-3 : angle 5.11370 ( 6) link_BETA1-4 : bond 0.01152 ( 4) link_BETA1-4 : angle 3.07924 ( 12) link_BETA1-6 : bond 0.00590 ( 2) link_BETA1-6 : angle 1.53994 ( 6) link_NAG-ASN : bond 0.01391 ( 9) link_NAG-ASN : angle 7.01698 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8738 (mmp) cc_final: 0.8344 (mmp) REVERT: A 1202 ASP cc_start: 0.5381 (OUTLIER) cc_final: 0.5007 (m-30) REVERT: A 1223 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: A 1241 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6887 (mtm-85) REVERT: A 1704 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 1939 ARG cc_start: 0.7582 (tmt170) cc_final: 0.6835 (tmt170) REVERT: A 2025 GLU cc_start: 0.8361 (pt0) cc_final: 0.7959 (pm20) outliers start: 29 outliers final: 20 residues processed: 208 average time/residue: 0.1097 time to fit residues: 34.3616 Evaluate side-chains 183 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1273 PHE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1492 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110287 restraints weight = 23480.228| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.38 r_work: 0.2964 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16102 Z= 0.160 Angle : 0.836 15.373 21899 Z= 0.405 Chirality : 0.049 0.407 2539 Planarity : 0.005 0.059 2744 Dihedral : 15.426 116.771 2627 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.74 % Favored : 87.91 % Rotamer: Outliers : 1.57 % Allowed : 8.49 % Favored : 89.94 % 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 aren not related in a simple way. whole: -3.45 (0.18), residues: 1985 helix: -1.29 (0.16), residues: 965 sheet: -1.92 (0.39), residues: 177 loop : -3.61 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2201 TYR 0.020 0.002 TYR A 400 PHE 0.026 0.002 PHE A1146 TRP 0.019 0.001 TRP A 605 HIS 0.006 0.001 HIS A1941 Details of bonding type rmsd covalent geometry : bond 0.00352 (16078) covalent geometry : angle 0.79933 (21836) SS BOND : bond 0.01108 ( 6) SS BOND : angle 1.97013 ( 12) hydrogen bonds : bond 0.05606 ( 553) hydrogen bonds : angle 5.07973 ( 1620) Misc. bond : bond 0.00111 ( 1) link_BETA1-3 : bond 0.00096 ( 2) link_BETA1-3 : angle 6.53725 ( 6) link_BETA1-4 : bond 0.00499 ( 4) link_BETA1-4 : angle 2.18314 ( 12) link_BETA1-6 : bond 0.00643 ( 2) link_BETA1-6 : angle 2.16544 ( 6) link_NAG-ASN : bond 0.01129 ( 9) link_NAG-ASN : angle 6.02472 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.8103 (t80) cc_final: 0.7864 (t80) REVERT: A 975 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8117 (mp) REVERT: A 992 ARG cc_start: 0.7768 (ptt180) cc_final: 0.7480 (ptt90) REVERT: A 1202 ASP cc_start: 0.5901 (OUTLIER) cc_final: 0.5529 (m-30) REVERT: A 1223 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: A 1241 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7031 (mtm-85) REVERT: A 2025 GLU cc_start: 0.8849 (pt0) cc_final: 0.8238 (pm20) outliers start: 25 outliers final: 16 residues processed: 200 average time/residue: 0.1158 time to fit residues: 34.6717 Evaluate side-chains 185 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2067 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 57 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 198 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1871 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111398 restraints weight = 23832.184| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.35 r_work: 0.3019 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16102 Z= 0.156 Angle : 0.777 15.030 21899 Z= 0.372 Chirality : 0.048 0.386 2539 Planarity : 0.004 0.058 2744 Dihedral : 13.178 116.107 2612 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.04 % Favored : 87.76 % Rotamer: Outliers : 2.96 % Allowed : 12.52 % Favored : 84.53 % 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 aren not related in a simple way. whole: -3.01 (0.18), residues: 1985 helix: -0.92 (0.17), residues: 967 sheet: -1.76 (0.40), residues: 172 loop : -3.38 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1161 TYR 0.021 0.001 TYR A 400 PHE 0.017 0.001 PHE A1247 TRP 0.017 0.001 TRP A 605 HIS 0.005 0.001 HIS A1941 Details of bonding type rmsd covalent geometry : bond 0.00363 (16078) covalent geometry : angle 0.74070 (21836) SS BOND : bond 0.00757 ( 6) SS BOND : angle 1.62040 ( 12) hydrogen bonds : bond 0.04812 ( 553) hydrogen bonds : angle 4.70954 ( 1620) Misc. bond : bond 0.00082 ( 1) link_BETA1-3 : bond 0.00152 ( 2) link_BETA1-3 : angle 6.80136 ( 6) link_BETA1-4 : bond 0.00408 ( 4) link_BETA1-4 : angle 2.17727 ( 12) link_BETA1-6 : bond 0.00864 ( 2) link_BETA1-6 : angle 2.02545 ( 6) link_NAG-ASN : bond 0.01044 ( 9) link_NAG-ASN : angle 5.60470 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8035 (tp40) REVERT: A 988 LEU cc_start: 0.7700 (mt) cc_final: 0.7450 (mt) REVERT: A 992 ARG cc_start: 0.7686 (ptt180) cc_final: 0.7359 (ptt90) REVERT: A 1223 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: A 1241 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6939 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8609 (t) cc_final: 0.8298 (t) REVERT: A 2025 GLU cc_start: 0.8777 (pt0) cc_final: 0.8277 (pm20) outliers start: 47 outliers final: 29 residues processed: 212 average time/residue: 0.1196 time to fit residues: 38.2466 Evaluate side-chains 193 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1933 ASN Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.146879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110297 restraints weight = 23555.591| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.14 r_work: 0.3041 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16102 Z= 0.154 Angle : 0.759 14.680 21899 Z= 0.361 Chirality : 0.048 0.380 2539 Planarity : 0.004 0.057 2744 Dihedral : 12.100 115.157 2608 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.84 % Favored : 88.06 % Rotamer: Outliers : 3.02 % Allowed : 13.96 % Favored : 83.02 % 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 aren not related in a simple way. whole: -2.70 (0.18), residues: 1985 helix: -0.66 (0.17), residues: 944 sheet: -1.41 (0.39), residues: 185 loop : -3.25 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1161 TYR 0.022 0.001 TYR A 400 PHE 0.033 0.001 PHE A1146 TRP 0.016 0.001 TRP A 605 HIS 0.005 0.001 HIS A1941 Details of bonding type rmsd covalent geometry : bond 0.00363 (16078) covalent geometry : angle 0.72526 (21836) SS BOND : bond 0.00508 ( 6) SS BOND : angle 1.47620 ( 12) hydrogen bonds : bond 0.04563 ( 553) hydrogen bonds : angle 4.51400 ( 1620) Misc. bond : bond 0.00062 ( 1) link_BETA1-3 : bond 0.00082 ( 2) link_BETA1-3 : angle 6.24105 ( 6) link_BETA1-4 : bond 0.00369 ( 4) link_BETA1-4 : angle 2.16620 ( 12) link_BETA1-6 : bond 0.00806 ( 2) link_BETA1-6 : angle 1.84875 ( 6) link_NAG-ASN : bond 0.00969 ( 9) link_NAG-ASN : angle 5.42509 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8042 (tp40) REVERT: A 603 TYR cc_start: 0.9462 (OUTLIER) cc_final: 0.9158 (m-80) REVERT: A 795 SER cc_start: 0.9226 (p) cc_final: 0.8962 (m) REVERT: A 992 ARG cc_start: 0.7676 (ptt180) cc_final: 0.7383 (ptt90) REVERT: A 1223 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: A 1241 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6998 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8594 (t) cc_final: 0.8307 (t) REVERT: A 1419 MET cc_start: 0.9056 (tpt) cc_final: 0.8682 (tpt) REVERT: A 2025 GLU cc_start: 0.8778 (pt0) cc_final: 0.8207 (pm20) outliers start: 48 outliers final: 26 residues processed: 221 average time/residue: 0.1212 time to fit residues: 40.8390 Evaluate side-chains 200 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 603 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1389 MET Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1933 ASN Chi-restraints excluded: chain A residue 2028 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1871 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110663 restraints weight = 23707.330| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.36 r_work: 0.3029 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16102 Z= 0.132 Angle : 0.723 14.271 21899 Z= 0.343 Chirality : 0.046 0.335 2539 Planarity : 0.004 0.057 2744 Dihedral : 11.359 114.387 2604 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.18 % Favored : 88.72 % Rotamer: Outliers : 3.46 % Allowed : 15.35 % Favored : 81.19 % 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 aren not related in a simple way. whole: -2.46 (0.19), residues: 1985 helix: -0.45 (0.17), residues: 945 sheet: -1.12 (0.39), residues: 184 loop : -3.19 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 948 TYR 0.017 0.001 TYR A 345 PHE 0.016 0.001 PHE A2161 TRP 0.018 0.001 TRP A 605 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00302 (16078) covalent geometry : angle 0.69104 (21836) SS BOND : bond 0.00462 ( 6) SS BOND : angle 1.24343 ( 12) hydrogen bonds : bond 0.04100 ( 553) hydrogen bonds : angle 4.32932 ( 1620) Misc. bond : bond 0.00069 ( 1) link_BETA1-3 : bond 0.00070 ( 2) link_BETA1-3 : angle 5.96297 ( 6) link_BETA1-4 : bond 0.00384 ( 4) link_BETA1-4 : angle 2.09191 ( 12) link_BETA1-6 : bond 0.00881 ( 2) link_BETA1-6 : angle 1.84018 ( 6) link_NAG-ASN : bond 0.00897 ( 9) link_NAG-ASN : angle 5.12194 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: A 603 TYR cc_start: 0.9427 (OUTLIER) cc_final: 0.9182 (m-80) REVERT: A 727 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7578 (p90) REVERT: A 795 SER cc_start: 0.9204 (p) cc_final: 0.8828 (m) REVERT: A 992 ARG cc_start: 0.7638 (ptt180) cc_final: 0.7381 (ptt90) REVERT: A 1147 LEU cc_start: 0.9337 (mm) cc_final: 0.9109 (mm) REVERT: A 1241 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6933 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8296 (t) REVERT: A 1419 MET cc_start: 0.9101 (tpt) cc_final: 0.8756 (tpt) REVERT: A 1491 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (p) REVERT: A 1648 SER cc_start: 0.8832 (t) cc_final: 0.8618 (p) REVERT: A 1893 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8766 (t) REVERT: A 2025 GLU cc_start: 0.8795 (pt0) cc_final: 0.8210 (pm20) REVERT: A 2209 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7221 (tm-30) outliers start: 55 outliers final: 30 residues processed: 224 average time/residue: 0.1188 time to fit residues: 40.2674 Evaluate side-chains 206 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 603 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1389 MET Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 176 optimal weight: 0.0470 chunk 129 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 160 optimal weight: 0.0970 chunk 198 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN A1933 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109998 restraints weight = 23650.799| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.30 r_work: 0.3027 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16102 Z= 0.152 Angle : 0.767 19.097 21899 Z= 0.360 Chirality : 0.047 0.350 2539 Planarity : 0.004 0.056 2744 Dihedral : 11.055 113.879 2599 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.23 % Favored : 88.66 % Rotamer: Outliers : 3.14 % Allowed : 16.67 % Favored : 80.19 % 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 aren not related in a simple way. whole: -2.36 (0.19), residues: 1985 helix: -0.41 (0.17), residues: 945 sheet: -1.04 (0.40), residues: 183 loop : -3.09 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1161 TYR 0.022 0.001 TYR A 400 PHE 0.023 0.001 PHE A1146 TRP 0.014 0.001 TRP A 605 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00354 (16078) covalent geometry : angle 0.71892 (21836) SS BOND : bond 0.00522 ( 6) SS BOND : angle 1.22407 ( 12) hydrogen bonds : bond 0.04273 ( 553) hydrogen bonds : angle 4.35717 ( 1620) Misc. bond : bond 0.00049 ( 1) link_BETA1-3 : bond 0.00092 ( 2) link_BETA1-3 : angle 5.68253 ( 6) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 2.21762 ( 12) link_BETA1-6 : bond 0.00746 ( 2) link_BETA1-6 : angle 1.86240 ( 6) link_NAG-ASN : bond 0.01168 ( 9) link_NAG-ASN : angle 6.92078 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8044 (tp40) REVERT: A 304 MET cc_start: 0.5391 (ppp) cc_final: 0.5081 (ppp) REVERT: A 508 ARG cc_start: 0.7771 (ttt180) cc_final: 0.7494 (tpt-90) REVERT: A 603 TYR cc_start: 0.9453 (OUTLIER) cc_final: 0.9152 (m-80) REVERT: A 727 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7512 (p90) REVERT: A 795 SER cc_start: 0.9280 (p) cc_final: 0.8927 (m) REVERT: A 1147 LEU cc_start: 0.9331 (mm) cc_final: 0.9093 (mm) REVERT: A 1241 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6865 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8303 (t) REVERT: A 1419 MET cc_start: 0.9091 (tpt) cc_final: 0.8722 (tpt) REVERT: A 1491 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 1871 HIS cc_start: 0.7645 (t-90) cc_final: 0.7376 (t-90) REVERT: A 2025 GLU cc_start: 0.8773 (pt0) cc_final: 0.8198 (pm20) REVERT: A 2189 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6514 (m-10) REVERT: A 2209 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7318 (tm-30) outliers start: 50 outliers final: 35 residues processed: 216 average time/residue: 0.1130 time to fit residues: 37.3377 Evaluate side-chains 212 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 603 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1389 MET Chi-restraints excluded: chain A residue 1491 SER Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 171 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 129 optimal weight: 0.0040 chunk 75 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113173 restraints weight = 23447.865| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.37 r_work: 0.3067 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16102 Z= 0.120 Angle : 0.721 19.017 21899 Z= 0.339 Chirality : 0.045 0.348 2539 Planarity : 0.004 0.057 2744 Dihedral : 10.709 113.126 2599 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 3.02 % Allowed : 17.42 % Favored : 79.56 % 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 aren not related in a simple way. whole: -2.19 (0.19), residues: 1985 helix: -0.24 (0.18), residues: 946 sheet: -0.83 (0.40), residues: 183 loop : -3.08 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 602 TYR 0.016 0.001 TYR A 345 PHE 0.025 0.001 PHE A1373 TRP 0.018 0.001 TRP A 605 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00260 (16078) covalent geometry : angle 0.67993 (21836) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.09009 ( 12) hydrogen bonds : bond 0.03760 ( 553) hydrogen bonds : angle 4.20392 ( 1620) Misc. bond : bond 0.00067 ( 1) link_BETA1-3 : bond 0.00080 ( 2) link_BETA1-3 : angle 5.49062 ( 6) link_BETA1-4 : bond 0.00386 ( 4) link_BETA1-4 : angle 2.02857 ( 12) link_BETA1-6 : bond 0.00853 ( 2) link_BETA1-6 : angle 1.73396 ( 6) link_NAG-ASN : bond 0.00967 ( 9) link_NAG-ASN : angle 6.18675 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7967 (tp40) REVERT: A 304 MET cc_start: 0.5438 (ppp) cc_final: 0.5055 (ppp) REVERT: A 603 TYR cc_start: 0.9418 (OUTLIER) cc_final: 0.9174 (m-80) REVERT: A 727 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7448 (p90) REVERT: A 795 SER cc_start: 0.9241 (p) cc_final: 0.8880 (m) REVERT: A 1276 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8287 (t) REVERT: A 1419 MET cc_start: 0.9074 (tpt) cc_final: 0.8761 (tpt) REVERT: A 1899 HIS cc_start: 0.7606 (m-70) cc_final: 0.7041 (t-90) REVERT: A 2025 GLU cc_start: 0.8735 (pt0) cc_final: 0.8150 (pm20) REVERT: A 2102 ASP cc_start: 0.7432 (m-30) cc_final: 0.6852 (p0) REVERT: A 2161 PHE cc_start: 0.8326 (m-80) cc_final: 0.7965 (m-10) REVERT: A 2189 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6420 (m-10) REVERT: A 2209 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 2222 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7794 (pp) outliers start: 48 outliers final: 33 residues processed: 215 average time/residue: 0.1233 time to fit residues: 40.7895 Evaluate side-chains 211 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 603 TYR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1389 MET Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2099 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 chunk 157 optimal weight: 0.3980 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN A1871 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.150200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113481 restraints weight = 23841.587| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.43 r_work: 0.3073 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16102 Z= 0.118 Angle : 0.712 16.154 21899 Z= 0.334 Chirality : 0.045 0.351 2539 Planarity : 0.004 0.055 2744 Dihedral : 10.325 112.495 2595 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 2.77 % Allowed : 17.61 % Favored : 79.62 % 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 aren not related in a simple way. whole: -2.03 (0.19), residues: 1985 helix: -0.12 (0.18), residues: 951 sheet: -0.71 (0.41), residues: 177 loop : -2.99 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.017 0.001 TYR A 345 PHE 0.041 0.001 PHE A1146 TRP 0.018 0.001 TRP A 605 HIS 0.006 0.001 HIS A1871 Details of bonding type rmsd covalent geometry : bond 0.00259 (16078) covalent geometry : angle 0.67786 (21836) SS BOND : bond 0.00536 ( 6) SS BOND : angle 1.07544 ( 12) hydrogen bonds : bond 0.03715 ( 553) hydrogen bonds : angle 4.17748 ( 1620) Misc. bond : bond 0.00061 ( 1) link_BETA1-3 : bond 0.00091 ( 2) link_BETA1-3 : angle 5.24814 ( 6) link_BETA1-4 : bond 0.00384 ( 4) link_BETA1-4 : angle 2.04181 ( 12) link_BETA1-6 : bond 0.00776 ( 2) link_BETA1-6 : angle 1.71559 ( 6) link_NAG-ASN : bond 0.01029 ( 9) link_NAG-ASN : angle 5.55995 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7944 (tp40) REVERT: A 304 MET cc_start: 0.5659 (ppp) cc_final: 0.5267 (ppp) REVERT: A 603 TYR cc_start: 0.9412 (OUTLIER) cc_final: 0.9158 (m-80) REVERT: A 677 GLU cc_start: 0.8652 (pp20) cc_final: 0.8228 (tt0) REVERT: A 727 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7448 (p90) REVERT: A 795 SER cc_start: 0.9169 (p) cc_final: 0.8895 (m) REVERT: A 1276 VAL cc_start: 0.8523 (t) cc_final: 0.8257 (t) REVERT: A 1414 TYR cc_start: 0.8363 (m-80) cc_final: 0.8087 (m-80) REVERT: A 1419 MET cc_start: 0.9103 (tpt) cc_final: 0.8777 (tpt) REVERT: A 1899 HIS cc_start: 0.7589 (m-70) cc_final: 0.7021 (t-90) REVERT: A 1966 GLU cc_start: 0.7662 (pt0) cc_final: 0.7322 (pt0) REVERT: A 2025 GLU cc_start: 0.8681 (pt0) cc_final: 0.8129 (pm20) REVERT: A 2102 ASP cc_start: 0.7335 (m-30) cc_final: 0.6779 (p0) REVERT: A 2161 PHE cc_start: 0.8270 (m-80) cc_final: 0.7929 (m-10) REVERT: A 2189 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6358 (m-10) REVERT: A 2209 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 2222 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7843 (pp) outliers start: 44 outliers final: 35 residues processed: 214 average time/residue: 0.1186 time to fit residues: 39.3788 Evaluate side-chains 213 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 603 TYR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1389 MET Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2099 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 184 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 chunk 48 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 192 optimal weight: 0.4980 chunk 113 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 179 optimal weight: 0.0050 chunk 27 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112349 restraints weight = 23869.625| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.41 r_work: 0.3081 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16102 Z= 0.124 Angle : 0.720 16.209 21899 Z= 0.337 Chirality : 0.046 0.353 2539 Planarity : 0.004 0.055 2744 Dihedral : 10.195 112.034 2595 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 2.64 % Allowed : 18.11 % Favored : 79.25 % 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 aren not related in a simple way. whole: -1.97 (0.19), residues: 1985 helix: -0.04 (0.18), residues: 951 sheet: -0.61 (0.43), residues: 165 loop : -3.00 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1528 TYR 0.018 0.001 TYR A 345 PHE 0.031 0.001 PHE A1146 TRP 0.017 0.001 TRP A 605 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00278 (16078) covalent geometry : angle 0.68680 (21836) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.24923 ( 12) hydrogen bonds : bond 0.03772 ( 553) hydrogen bonds : angle 4.20113 ( 1620) Misc. bond : bond 0.00056 ( 1) link_BETA1-3 : bond 0.00089 ( 2) link_BETA1-3 : angle 5.10281 ( 6) link_BETA1-4 : bond 0.00375 ( 4) link_BETA1-4 : angle 2.07118 ( 12) link_BETA1-6 : bond 0.00782 ( 2) link_BETA1-6 : angle 1.73854 ( 6) link_NAG-ASN : bond 0.00965 ( 9) link_NAG-ASN : angle 5.47759 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7932 (tp40) REVERT: A 304 MET cc_start: 0.5488 (ppp) cc_final: 0.5103 (ppp) REVERT: A 603 TYR cc_start: 0.9420 (OUTLIER) cc_final: 0.9166 (m-80) REVERT: A 677 GLU cc_start: 0.8610 (pp20) cc_final: 0.8186 (tt0) REVERT: A 727 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7379 (p90) REVERT: A 795 SER cc_start: 0.9167 (p) cc_final: 0.8903 (m) REVERT: A 1030 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8947 (tt) REVERT: A 1276 VAL cc_start: 0.8473 (t) cc_final: 0.8202 (t) REVERT: A 1414 TYR cc_start: 0.8372 (m-80) cc_final: 0.8111 (m-80) REVERT: A 1419 MET cc_start: 0.9144 (tpt) cc_final: 0.8837 (tpt) REVERT: A 1493 ARG cc_start: 0.6955 (tpt90) cc_final: 0.6527 (tpt90) REVERT: A 1601 GLU cc_start: 0.7410 (pp20) cc_final: 0.6451 (pp20) REVERT: A 1899 HIS cc_start: 0.7568 (m-70) cc_final: 0.6997 (t-90) REVERT: A 1966 GLU cc_start: 0.7643 (pt0) cc_final: 0.7195 (pt0) REVERT: A 2025 GLU cc_start: 0.8721 (pt0) cc_final: 0.8154 (pm20) REVERT: A 2102 ASP cc_start: 0.7296 (m-30) cc_final: 0.6763 (p0) REVERT: A 2108 MET cc_start: 0.8587 (mmm) cc_final: 0.8282 (mmp) REVERT: A 2161 PHE cc_start: 0.8220 (m-80) cc_final: 0.7873 (m-10) REVERT: A 2189 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6350 (m-10) REVERT: A 2209 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7595 (tm-30) REVERT: A 2222 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7774 (pp) outliers start: 42 outliers final: 35 residues processed: 209 average time/residue: 0.1188 time to fit residues: 38.4236 Evaluate side-chains 218 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 603 TYR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1389 MET Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1836 PHE Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2099 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 63 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 89 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112803 restraints weight = 23625.364| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.34 r_work: 0.3067 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16102 Z= 0.131 Angle : 0.723 15.531 21899 Z= 0.340 Chirality : 0.047 0.436 2539 Planarity : 0.004 0.054 2744 Dihedral : 10.077 111.599 2595 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 2.77 % Allowed : 18.24 % Favored : 78.99 % 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 aren not related in a simple way. whole: -1.94 (0.19), residues: 1985 helix: -0.03 (0.18), residues: 952 sheet: -0.63 (0.41), residues: 178 loop : -2.97 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.020 0.001 TYR A 400 PHE 0.029 0.001 PHE A1146 TRP 0.016 0.001 TRP A 605 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00300 (16078) covalent geometry : angle 0.69122 (21836) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.23922 ( 12) hydrogen bonds : bond 0.03942 ( 553) hydrogen bonds : angle 4.22058 ( 1620) Misc. bond : bond 0.00055 ( 1) link_BETA1-3 : bond 0.00099 ( 2) link_BETA1-3 : angle 4.96922 ( 6) link_BETA1-4 : bond 0.00389 ( 4) link_BETA1-4 : angle 2.11556 ( 12) link_BETA1-6 : bond 0.00695 ( 2) link_BETA1-6 : angle 1.71277 ( 6) link_NAG-ASN : bond 0.00968 ( 9) link_NAG-ASN : angle 5.34207 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: A 304 MET cc_start: 0.5556 (ppp) cc_final: 0.5162 (ppp) REVERT: A 603 TYR cc_start: 0.9414 (OUTLIER) cc_final: 0.9178 (m-80) REVERT: A 727 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7441 (p90) REVERT: A 795 SER cc_start: 0.9168 (p) cc_final: 0.8903 (m) REVERT: A 1030 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8928 (tt) REVERT: A 1241 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6678 (mtm-85) REVERT: A 1276 VAL cc_start: 0.8509 (t) cc_final: 0.8248 (t) REVERT: A 1414 TYR cc_start: 0.8428 (m-80) cc_final: 0.8161 (m-80) REVERT: A 1419 MET cc_start: 0.9150 (tpt) cc_final: 0.8850 (tpt) REVERT: A 1493 ARG cc_start: 0.7155 (tpt90) cc_final: 0.6742 (tpt90) REVERT: A 1601 GLU cc_start: 0.7355 (pp20) cc_final: 0.6396 (pp20) REVERT: A 1899 HIS cc_start: 0.7658 (m-70) cc_final: 0.6943 (t-90) REVERT: A 1966 GLU cc_start: 0.7645 (pt0) cc_final: 0.7249 (pt0) REVERT: A 2025 GLU cc_start: 0.8780 (pt0) cc_final: 0.8206 (pm20) REVERT: A 2102 ASP cc_start: 0.7352 (m-30) cc_final: 0.6786 (p0) REVERT: A 2108 MET cc_start: 0.8636 (mmm) cc_final: 0.8376 (mmp) REVERT: A 2161 PHE cc_start: 0.8180 (m-80) cc_final: 0.7853 (m-10) REVERT: A 2189 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6404 (m-10) REVERT: A 2209 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 2222 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7799 (pp) outliers start: 44 outliers final: 33 residues processed: 210 average time/residue: 0.1261 time to fit residues: 40.6633 Evaluate side-chains 213 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 603 TYR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1215 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1241 ARG Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1389 MET Chi-restraints excluded: chain A residue 1523 GLN Chi-restraints excluded: chain A residue 1793 VAL Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2099 THR Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 141 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113184 restraints weight = 23387.515| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.35 r_work: 0.3070 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16102 Z= 0.145 Angle : 0.734 14.819 21899 Z= 0.346 Chirality : 0.047 0.473 2539 Planarity : 0.004 0.054 2744 Dihedral : 10.033 111.573 2595 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 2.64 % Allowed : 18.11 % Favored : 79.25 % 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 aren not related in a simple way. whole: -1.96 (0.19), residues: 1985 helix: -0.04 (0.18), residues: 949 sheet: -0.68 (0.41), residues: 180 loop : -2.99 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 920 TYR 0.020 0.001 TYR A 345 PHE 0.025 0.001 PHE A1146 TRP 0.013 0.001 TRP A 298 HIS 0.003 0.001 HIS A1941 Details of bonding type rmsd covalent geometry : bond 0.00343 (16078) covalent geometry : angle 0.70430 (21836) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.30940 ( 12) hydrogen bonds : bond 0.04132 ( 553) hydrogen bonds : angle 4.27805 ( 1620) Misc. bond : bond 0.00052 ( 1) link_BETA1-3 : bond 0.00076 ( 2) link_BETA1-3 : angle 4.86847 ( 6) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 2.17098 ( 12) link_BETA1-6 : bond 0.00672 ( 2) link_BETA1-6 : angle 1.74963 ( 6) link_NAG-ASN : bond 0.00955 ( 9) link_NAG-ASN : angle 5.23535 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3579.12 seconds wall clock time: 62 minutes 10.61 seconds (3730.61 seconds total)