Starting phenix.real_space_refine on Sun Jun 15 19:19:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y69_38982/06_2025/8y69_38982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y69_38982/06_2025/8y69_38982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y69_38982/06_2025/8y69_38982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y69_38982/06_2025/8y69_38982.map" model { file = "/net/cci-nas-00/data/ceres_data/8y69_38982/06_2025/8y69_38982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y69_38982/06_2025/8y69_38982.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 11320 2.51 5 N 2934 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17577 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5697 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 36, 'TRANS': 693} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1409 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5733 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 698} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1362 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.99, per 1000 atoms: 0.68 Number of scatterers: 17577 At special positions: 0 Unit cell: (148.869, 126.378, 159.579, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3207 8.00 N 2934 7.00 C 11320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS E 447 " - pdb=" SG CYS E 520 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 52 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 78 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 110 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 124 " distance=2.03 Simple disulfide: pdb=" SG CYS G 128 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 364 " distance=2.03 Simple disulfide: pdb=" SG CYS D 618 " - pdb=" SG CYS D 693 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 136 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 52 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 78 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 110 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 124 " distance=2.03 Simple disulfide: pdb=" SG CYS J 128 " - pdb=" SG CYS J 141 " 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=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 2.0 seconds 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4226 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 28.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.571A pdb=" N ILE A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.743A pdb=" N ASN A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.743A pdb=" N ILE A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.783A pdb=" N THR A 384 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 386 " --> pdb=" O GLY A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 466 through 473 removed outlier: 4.428A pdb=" N CYS A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 555 removed outlier: 3.565A pdb=" N ARG A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.625A pdb=" N LEU A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.753A pdb=" N PHE A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 4.077A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 649 removed outlier: 3.756A pdb=" N GLY A 622 " --> pdb=" O CYS A 618 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 641 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 683 removed outlier: 3.594A pdb=" N ALA A 665 " --> pdb=" O GLN A 661 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N THR A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 680 - end of helix removed outlier: 3.847A pdb=" N HIS A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 732 removed outlier: 3.878A pdb=" N VAL A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 718 " --> pdb=" O ASN A 714 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS A 730 " --> pdb=" O THR A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 760 removed outlier: 3.815A pdb=" N ILE A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 758 " --> pdb=" O PHE A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 768 removed outlier: 3.762A pdb=" N ALA A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE A 765 " --> pdb=" O CYS A 761 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 767 " --> pdb=" O VAL A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.708A pdb=" N MET A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 783 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 removed outlier: 3.542A pdb=" N VAL A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 818 removed outlier: 3.984A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 816 " --> pdb=" O TRP A 812 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.501A pdb=" N LYS C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 186 through 198 removed outlier: 3.937A pdb=" N LYS C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.807A pdb=" N PHE C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU C 223 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 229 " --> pdb=" O PHE C 225 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS C 233 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 243 removed outlier: 3.804A pdb=" N LEU C 237 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 533 through 537 removed outlier: 4.022A pdb=" N ILE E 536 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE E 537 " --> pdb=" O TRP E 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 533 through 537' Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 241 through 247 removed outlier: 4.180A pdb=" N ILE D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.907A pdb=" N CYS D 470 " --> pdb=" O TYR D 466 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 466 through 471' Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 538 through 552 removed outlier: 3.959A pdb=" N LEU D 543 " --> pdb=" O TRP D 539 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 544 " --> pdb=" O MET D 540 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 545 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 564 removed outlier: 3.804A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 558 " --> pdb=" O PHE D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 601 removed outlier: 3.914A pdb=" N PHE D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 581 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 582 " --> pdb=" O GLY D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 615 removed outlier: 3.870A pdb=" N ILE D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 614 " --> pdb=" O ILE D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 648 removed outlier: 3.630A pdb=" N GLY D 622 " --> pdb=" O CYS D 618 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 623 " --> pdb=" O LYS D 619 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 641 " --> pdb=" O MET D 637 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 683 removed outlier: 3.734A pdb=" N LEU D 668 " --> pdb=" O VAL D 664 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Proline residue: D 680 - end of helix removed outlier: 4.456A pdb=" N HIS D 683 " --> pdb=" O PHE D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 727 removed outlier: 3.709A pdb=" N VAL D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR D 709 " --> pdb=" O GLY D 705 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 714 " --> pdb=" O LEU D 710 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 717 " --> pdb=" O LEU D 713 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 718 " --> pdb=" O ASN D 714 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 719 " --> pdb=" O SER D 715 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 724 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR D 725 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 732 removed outlier: 4.121A pdb=" N ASN D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 766 removed outlier: 4.188A pdb=" N LYS D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS D 748 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 760 " --> pdb=" O ASN D 756 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS D 761 " --> pdb=" O CYS D 757 " (cutoff:3.500A) Proline residue: D 762 - end of helix removed outlier: 3.832A pdb=" N PHE D 766 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.570A pdb=" N MET D 782 " --> pdb=" O SER D 778 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 783 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 784 " --> pdb=" O GLU D 780 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 804 removed outlier: 4.593A pdb=" N VAL D 799 " --> pdb=" O CYS D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 820 removed outlier: 3.712A pdb=" N ASP D 811 " --> pdb=" O LYS D 807 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 813 " --> pdb=" O LYS D 809 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 814 " --> pdb=" O GLU D 810 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 816 " --> pdb=" O TRP D 812 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 819 " --> pdb=" O LEU D 815 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 106 removed outlier: 3.566A pdb=" N LEU H 106 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 163 through 171 removed outlier: 3.905A pdb=" N GLY H 171 " --> pdb=" O GLN H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 198 removed outlier: 3.645A pdb=" N LYS H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 197 " --> pdb=" O ASN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 243 removed outlier: 4.395A pdb=" N ILE H 221 " --> pdb=" O PHE H 217 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE H 222 " --> pdb=" O ASP H 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE H 226 " --> pdb=" O PHE H 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS H 233 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 243 " --> pdb=" O LYS H 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 7.003A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 86 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N HIS A 157 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N LEU A 184 " --> pdb=" O HIS A 157 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N TRP A 159 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N LEU A 186 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASP A 161 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.876A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 removed outlier: 7.157A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 303 removed outlier: 6.317A pdb=" N LEU A 324 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 348 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 395 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 394 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.652A pdb=" N ILE A 380 " --> pdb=" O GLU A 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 65 removed outlier: 7.691A pdb=" N ILE C 155 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY C 122 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP C 157 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 124 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.502A pdb=" N VAL E 24 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 497 " --> pdb=" O THR E 502 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN E 506 " --> pdb=" O THR E 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.637A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS E 458 " --> pdb=" O ARG E 523 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG E 523 " --> pdb=" O CYS E 458 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.637A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS E 458 " --> pdb=" O ARG E 523 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG E 523 " --> pdb=" O CYS E 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 70 through 75 removed outlier: 3.595A pdb=" N GLU G 73 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE G 62 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE G 61 " --> pdb=" O CYS G 93 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ARG G 95 " --> pdb=" O PHE G 61 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N LEU G 63 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 101 through 104 Processing sheet with id=AB4, first strand: chain 'D' and resid 34 through 35 removed outlier: 6.647A pdb=" N LEU D 62 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU D 86 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'D' and resid 191 through 192 removed outlier: 4.448A pdb=" N ILE D 192 " --> pdb=" O SER D 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 252 through 254 removed outlier: 7.190A pdb=" N LEU D 253 " --> pdb=" O HIS D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 301 through 303 removed outlier: 6.281A pdb=" N LEU D 301 " --> pdb=" O THR D 325 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU D 324 " --> pdb=" O ASP D 349 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 370 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU D 394 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 440 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 439 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 58 through 65 removed outlier: 3.741A pdb=" N TYR H 77 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP H 120 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE H 155 " --> pdb=" O TRP H 120 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY H 122 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP H 157 " --> pdb=" O GLY H 122 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL H 124 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 23 through 26 removed outlier: 3.704A pdb=" N VAL I 24 " --> pdb=" O ALA I 448 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER I 446 " --> pdb=" O SER I 26 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU I 443 " --> pdb=" O MET I 507 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP I 497 " --> pdb=" O THR I 502 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 482 through 484 removed outlier: 6.086A pdb=" N GLY I 472 " --> pdb=" O ARG I 463 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG I 463 " --> pdb=" O GLY I 472 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA I 474 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N CYS I 458 " --> pdb=" O ARG I 523 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG I 523 " --> pdb=" O CYS I 458 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 482 through 484 removed outlier: 6.086A pdb=" N GLY I 472 " --> pdb=" O ARG I 463 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG I 463 " --> pdb=" O GLY I 472 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA I 474 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N CYS I 458 " --> pdb=" O ARG I 523 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG I 523 " --> pdb=" O CYS I 458 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 60 through 65 Processing sheet with id=AC6, first strand: chain 'J' and resid 82 through 85 Processing sheet with id=AC7, first strand: chain 'J' and resid 101 through 106 removed outlier: 6.209A pdb=" N CYS J 101 " --> pdb=" O CYS J 113 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS J 113 " --> pdb=" O CYS J 101 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER J 103 " --> pdb=" O THR J 111 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE J 109 " --> pdb=" O PHE J 105 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1383 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: 6.07 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5631 1.34 - 1.46: 4230 1.46 - 1.59: 7960 1.59 - 1.71: 0 1.71 - 1.83: 151 Bond restraints: 17972 Sorted by residual: bond pdb=" C THR A 701 " pdb=" N PRO A 702 " ideal model delta sigma weight residual 1.335 1.354 -0.019 8.70e-03 1.32e+04 4.73e+00 bond pdb=" CA GLY A 537 " pdb=" C GLY A 537 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.53e+00 bond pdb=" N GLY A 537 " pdb=" CA GLY A 537 " ideal model delta sigma weight residual 1.464 1.449 0.016 1.12e-02 7.97e+03 1.94e+00 bond pdb=" CA CYS J 43 " pdb=" CB CYS J 43 " ideal model delta sigma weight residual 1.539 1.520 0.019 1.36e-02 5.41e+03 1.87e+00 bond pdb=" C PHE A 268 " pdb=" N ASP A 269 " ideal model delta sigma weight residual 1.332 1.316 0.015 1.29e-02 6.01e+03 1.42e+00 ... (remaining 17967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 23553 1.61 - 3.22: 735 3.22 - 4.83: 94 4.83 - 6.44: 13 6.44 - 8.05: 1 Bond angle restraints: 24396 Sorted by residual: angle pdb=" N LYS D 46 " pdb=" CA LYS D 46 " pdb=" C LYS D 46 " ideal model delta sigma weight residual 112.72 107.50 5.22 1.28e+00 6.10e-01 1.66e+01 angle pdb=" N ILE A 788 " pdb=" CA ILE A 788 " pdb=" C ILE A 788 " ideal model delta sigma weight residual 113.53 110.02 3.51 9.80e-01 1.04e+00 1.28e+01 angle pdb=" N ILE A 758 " pdb=" CA ILE A 758 " pdb=" C ILE A 758 " ideal model delta sigma weight residual 112.35 107.61 4.74 1.41e+00 5.03e-01 1.13e+01 angle pdb=" N LYS A 46 " pdb=" CA LYS A 46 " pdb=" C LYS A 46 " ideal model delta sigma weight residual 114.04 110.24 3.80 1.24e+00 6.50e-01 9.38e+00 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 113.12 109.34 3.78 1.25e+00 6.40e-01 9.17e+00 ... (remaining 24391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.44: 9868 12.44 - 24.87: 732 24.87 - 37.31: 184 37.31 - 49.75: 46 49.75 - 62.18: 16 Dihedral angle restraints: 10846 sinusoidal: 4329 harmonic: 6517 Sorted by residual: dihedral pdb=" CB CYS G 78 " pdb=" SG CYS G 78 " pdb=" SG CYS G 93 " pdb=" CB CYS G 93 " ideal model delta sinusoidal sigma weight residual 93.00 142.98 -49.98 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS J 78 " pdb=" SG CYS J 78 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 142.33 -49.33 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CA LEU D 208 " pdb=" C LEU D 208 " pdb=" N HIS D 209 " pdb=" CA HIS D 209 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 10843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1696 0.032 - 0.064: 820 0.064 - 0.096: 180 0.096 - 0.128: 106 0.128 - 0.160: 10 Chirality restraints: 2812 Sorted by residual: chirality pdb=" CA ASN D 210 " pdb=" N ASN D 210 " pdb=" C ASN D 210 " pdb=" CB ASN D 210 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CG LEU D 441 " pdb=" CB LEU D 441 " pdb=" CD1 LEU D 441 " pdb=" CD2 LEU D 441 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE A 263 " pdb=" N ILE A 263 " pdb=" C ILE A 263 " pdb=" CB ILE A 263 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2809 not shown) Planarity restraints: 3097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 209 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO C 210 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 373 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C GLN A 373 " -0.021 2.00e-02 2.50e+03 pdb=" O GLN A 373 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 374 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 351 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C SER D 351 " 0.021 2.00e-02 2.50e+03 pdb=" O SER D 351 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR D 352 " -0.007 2.00e-02 2.50e+03 ... (remaining 3094 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1207 2.73 - 3.28: 18029 3.28 - 3.82: 28388 3.82 - 4.36: 33352 4.36 - 4.90: 57001 Nonbonded interactions: 137977 Sorted by model distance: nonbonded pdb=" OG1 THR A 526 " pdb=" O LYS A 530 " model vdw 2.194 3.040 nonbonded pdb=" N ASP D 161 " pdb=" OD1 ASP D 161 " model vdw 2.212 3.120 nonbonded pdb=" NE2 GLN D 113 " pdb=" O HIS J 76 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR A 468 " pdb=" OE2 GLU A 613 " model vdw 2.233 3.040 nonbonded pdb=" O ILE D 541 " pdb=" OG1 THR D 544 " model vdw 2.245 3.040 ... (remaining 137972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 744 or (resid 745 and (name N or name CA or nam \ e C or name O or name CB )) or resid 746 through 820)) selection = (chain 'D' and (resid 33 through 564 or resid 570 through 724 or (resid 725 and \ (name N or name CA or name C or name O or name CB )) or resid 726 through 727 or \ (resid 728 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 9 through 820)) } ncs_group { reference = (chain 'C' and (resid 56 through 86 or (resid 87 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 207 or (resid 208 and ( \ name N or name CA or name C or name O or name CB )) or resid 209 through 210 or \ (resid 211 through 212 and (name N or name CA or name C or name O or name CB )) \ or (resid 215 through 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 243)) selection = (chain 'H' and resid 56 through 243) } ncs_group { reference = chain 'E' selection = (chain 'I' and (resid 21 through 499 or (resid 500 and (name N or name CA or nam \ e C or name O or name CB )) or resid 501 through 549)) } ncs_group { reference = chain 'G' selection = chain 'J' } 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: 8.200 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.160 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17994 Z= 0.176 Angle : 0.662 8.045 24440 Z= 0.395 Chirality : 0.041 0.160 2812 Planarity : 0.003 0.039 3097 Dihedral : 9.883 62.183 6554 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.56 % Allowed : 8.31 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.18), residues: 2215 helix: -0.10 (0.24), residues: 521 sheet: -2.15 (0.26), residues: 368 loop : -1.82 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 159 HIS 0.005 0.001 HIS A 209 PHE 0.014 0.001 PHE D 696 TYR 0.010 0.001 TYR J 83 ARG 0.002 0.000 ARG I 470 Details of bonding type rmsd hydrogen bonds : bond 0.26016 ( 466) hydrogen bonds : angle 7.85096 ( 1383) SS BOND : bond 0.00260 ( 22) SS BOND : angle 0.77855 ( 44) covalent geometry : bond 0.00334 (17972) covalent geometry : angle 0.66198 (24396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.7671 (ptp) cc_final: 0.7380 (ptp) REVERT: A 638 LEU cc_start: 0.8863 (mm) cc_final: 0.8657 (mt) REVERT: A 782 MET cc_start: 0.8096 (ttm) cc_final: 0.7753 (ttt) REVERT: C 221 ILE cc_start: 0.8333 (mt) cc_final: 0.7686 (mm) REVERT: E 22 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 24 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (m) REVERT: E 459 MET cc_start: 0.8431 (mmm) cc_final: 0.7849 (mmt) REVERT: E 475 THR cc_start: 0.8641 (m) cc_final: 0.8369 (p) REVERT: E 484 TYR cc_start: 0.8709 (m-80) cc_final: 0.7925 (m-80) REVERT: E 504 TYR cc_start: 0.8551 (m-80) cc_final: 0.8286 (m-80) REVERT: E 510 LEU cc_start: 0.7359 (mp) cc_final: 0.6834 (pp) REVERT: E 519 TYR cc_start: 0.8427 (m-80) cc_final: 0.8196 (m-80) REVERT: E 532 LEU cc_start: 0.8233 (mt) cc_final: 0.8016 (mp) REVERT: G 139 MET cc_start: 0.7471 (tpp) cc_final: 0.6802 (tpp) REVERT: D 80 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7371 (p90) REVERT: D 211 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8060 (p0) REVERT: D 546 TRP cc_start: 0.7473 (m100) cc_final: 0.7099 (m100) REVERT: D 549 PHE cc_start: 0.8841 (t80) cc_final: 0.8569 (t80) REVERT: H 108 ASN cc_start: 0.8371 (t0) cc_final: 0.8118 (t0) REVERT: I 464 GLN cc_start: 0.7563 (tt0) cc_final: 0.7299 (tt0) REVERT: I 475 THR cc_start: 0.7571 (m) cc_final: 0.7308 (p) REVERT: I 486 ASP cc_start: 0.8033 (p0) cc_final: 0.7780 (p0) REVERT: I 517 MET cc_start: 0.8271 (tpp) cc_final: 0.8028 (tpt) REVERT: I 519 TYR cc_start: 0.8344 (m-80) cc_final: 0.8127 (m-80) REVERT: J 64 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7843 (ttm-80) REVERT: J 71 TYR cc_start: 0.8479 (p90) cc_final: 0.8092 (p90) REVERT: J 112 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8641 (ttpp) outliers start: 69 outliers final: 33 residues processed: 357 average time/residue: 0.2966 time to fit residues: 158.5527 Evaluate side-chains 225 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 114 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 202 optimal weight: 0.0770 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 140 HIS A 157 HIS A 187 ASN A 199 ASN A 282 ASN A 293 HIS A 354 ASN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN C 169 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN D 67 ASN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 180 GLN D 402 HIS D 444 ASN H 100 GLN I 506 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.098973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068924 restraints weight = 53297.843| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.49 r_work: 0.3157 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17994 Z= 0.131 Angle : 0.624 10.826 24440 Z= 0.308 Chirality : 0.043 0.194 2812 Planarity : 0.004 0.045 3097 Dihedral : 6.094 58.792 2575 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 3.10 % Allowed : 12.80 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.18), residues: 2215 helix: 0.16 (0.23), residues: 549 sheet: -1.78 (0.27), residues: 367 loop : -1.85 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 474 HIS 0.004 0.001 HIS A 209 PHE 0.025 0.001 PHE A 547 TYR 0.012 0.001 TYR H 182 ARG 0.009 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 466) hydrogen bonds : angle 5.34416 ( 1383) SS BOND : bond 0.00260 ( 22) SS BOND : angle 0.87653 ( 44) covalent geometry : bond 0.00286 (17972) covalent geometry : angle 0.62388 (24396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8528 (pt) REVERT: A 308 MET cc_start: 0.8576 (tmm) cc_final: 0.8294 (tmm) REVERT: A 344 MET cc_start: 0.8311 (ptp) cc_final: 0.7736 (ptp) REVERT: A 540 MET cc_start: 0.8760 (mtm) cc_final: 0.8460 (mtm) REVERT: A 638 LEU cc_start: 0.8863 (mm) cc_final: 0.8577 (mt) REVERT: A 782 MET cc_start: 0.8493 (ttm) cc_final: 0.8110 (ttt) REVERT: A 801 TYR cc_start: 0.7819 (t80) cc_final: 0.7532 (t80) REVERT: C 128 GLN cc_start: 0.8372 (mp10) cc_final: 0.8132 (mp10) REVERT: C 190 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8686 (ptmt) REVERT: C 221 ILE cc_start: 0.8035 (mt) cc_final: 0.7823 (mm) REVERT: E 22 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7967 (tm-30) REVERT: E 459 MET cc_start: 0.8962 (mmm) cc_final: 0.8361 (mmt) REVERT: E 475 THR cc_start: 0.8931 (m) cc_final: 0.8725 (p) REVERT: E 477 ASP cc_start: 0.7522 (t0) cc_final: 0.7261 (t70) REVERT: E 484 TYR cc_start: 0.8856 (m-80) cc_final: 0.8594 (m-80) REVERT: E 491 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.6104 (ttt-90) REVERT: E 492 PHE cc_start: 0.6684 (m-10) cc_final: 0.6236 (m-10) REVERT: E 504 TYR cc_start: 0.8798 (m-80) cc_final: 0.8567 (m-80) REVERT: E 510 LEU cc_start: 0.7676 (mp) cc_final: 0.7429 (pp) REVERT: E 519 TYR cc_start: 0.8129 (m-80) cc_final: 0.7803 (m-80) REVERT: E 532 LEU cc_start: 0.7866 (mt) cc_final: 0.7628 (mp) REVERT: G 66 GLU cc_start: 0.8812 (pm20) cc_final: 0.8501 (pm20) REVERT: G 68 MET cc_start: 0.8568 (mtm) cc_final: 0.8328 (mtp) REVERT: G 114 LYS cc_start: 0.9130 (ttpp) cc_final: 0.8657 (mmtm) REVERT: G 139 MET cc_start: 0.7183 (tpp) cc_final: 0.6938 (tpp) REVERT: D 80 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7624 (p90) REVERT: D 137 ASP cc_start: 0.8464 (m-30) cc_final: 0.7951 (m-30) REVERT: D 308 MET cc_start: 0.9031 (ttt) cc_final: 0.8744 (tmm) REVERT: D 549 PHE cc_start: 0.8857 (t80) cc_final: 0.8457 (t80) REVERT: D 754 PHE cc_start: 0.9092 (m-80) cc_final: 0.8618 (m-80) REVERT: H 101 MET cc_start: 0.8704 (mmm) cc_final: 0.8483 (mtp) REVERT: I 486 ASP cc_start: 0.8811 (p0) cc_final: 0.8537 (p0) REVERT: I 497 ASP cc_start: 0.8322 (t0) cc_final: 0.8026 (t0) REVERT: I 519 TYR cc_start: 0.8447 (m-80) cc_final: 0.8059 (m-80) REVERT: I 539 TYR cc_start: 0.8464 (m-80) cc_final: 0.8025 (m-80) REVERT: J 64 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8059 (ttm-80) REVERT: J 66 GLU cc_start: 0.8569 (pm20) cc_final: 0.8106 (pm20) REVERT: J 71 TYR cc_start: 0.8403 (p90) cc_final: 0.8117 (p90) REVERT: J 99 GLU cc_start: 0.8787 (pp20) cc_final: 0.8447 (pp20) REVERT: J 102 ASP cc_start: 0.8682 (m-30) cc_final: 0.8385 (m-30) outliers start: 60 outliers final: 31 residues processed: 275 average time/residue: 0.2845 time to fit residues: 119.7980 Evaluate side-chains 219 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 379 GLN A 756 ASN D 209 HIS D 556 ASN ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.097859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067587 restraints weight = 53717.533| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.47 r_work: 0.3123 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17994 Z= 0.165 Angle : 0.627 12.054 24440 Z= 0.308 Chirality : 0.043 0.150 2812 Planarity : 0.004 0.047 3097 Dihedral : 5.668 54.449 2553 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.13 % Favored : 92.78 % Rotamer: Outliers : 3.56 % Allowed : 12.75 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), residues: 2215 helix: 0.42 (0.24), residues: 537 sheet: -1.47 (0.29), residues: 340 loop : -1.84 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 474 HIS 0.006 0.001 HIS A 209 PHE 0.024 0.001 PHE A 547 TYR 0.013 0.001 TYR J 83 ARG 0.007 0.000 ARG I 525 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 466) hydrogen bonds : angle 5.00649 ( 1383) SS BOND : bond 0.00250 ( 22) SS BOND : angle 0.72177 ( 44) covalent geometry : bond 0.00373 (17972) covalent geometry : angle 0.62676 (24396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 308 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8416 (tmm) REVERT: A 344 MET cc_start: 0.8300 (ptp) cc_final: 0.7750 (ptp) REVERT: A 597 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8158 (tp) REVERT: A 623 PHE cc_start: 0.8357 (t80) cc_final: 0.8067 (t80) REVERT: A 638 LEU cc_start: 0.8808 (mm) cc_final: 0.8508 (mt) REVERT: A 782 MET cc_start: 0.8433 (ttm) cc_final: 0.8116 (ttt) REVERT: A 801 TYR cc_start: 0.7867 (t80) cc_final: 0.7555 (t80) REVERT: C 128 GLN cc_start: 0.8518 (mp10) cc_final: 0.8296 (mp10) REVERT: C 190 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8653 (ttmt) REVERT: C 197 LYS cc_start: 0.9484 (mmmt) cc_final: 0.8911 (mppt) REVERT: E 459 MET cc_start: 0.8981 (mmm) cc_final: 0.8227 (mmp) REVERT: E 463 ARG cc_start: 0.8207 (ptt90) cc_final: 0.7974 (ptt90) REVERT: E 464 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7413 (tm-30) REVERT: E 477 ASP cc_start: 0.7550 (t0) cc_final: 0.7206 (t70) REVERT: E 484 TYR cc_start: 0.8868 (m-80) cc_final: 0.8171 (m-80) REVERT: E 489 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8777 (mmmt) REVERT: E 504 TYR cc_start: 0.8547 (m-80) cc_final: 0.8321 (m-80) REVERT: E 510 LEU cc_start: 0.7743 (mp) cc_final: 0.7125 (pp) REVERT: E 519 TYR cc_start: 0.8035 (m-80) cc_final: 0.7825 (m-80) REVERT: E 532 LEU cc_start: 0.7931 (mt) cc_final: 0.7568 (mt) REVERT: G 66 GLU cc_start: 0.8789 (pm20) cc_final: 0.8433 (pm20) REVERT: G 68 MET cc_start: 0.8701 (mtm) cc_final: 0.8390 (mtp) REVERT: G 114 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8815 (mmtm) REVERT: D 80 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7753 (p90) REVERT: D 137 ASP cc_start: 0.8390 (m-30) cc_final: 0.7842 (m-30) REVERT: D 308 MET cc_start: 0.9107 (ttt) cc_final: 0.8779 (tmm) REVERT: D 721 MET cc_start: 0.8249 (tmm) cc_final: 0.7855 (tmm) REVERT: D 754 PHE cc_start: 0.9091 (m-80) cc_final: 0.8620 (m-80) REVERT: H 100 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6024 (tm-30) REVERT: H 134 LYS cc_start: 0.9226 (tptp) cc_final: 0.8991 (tptp) REVERT: H 144 LYS cc_start: 0.9255 (tmmt) cc_final: 0.8998 (tptt) REVERT: H 239 LYS cc_start: 0.9078 (tptt) cc_final: 0.8756 (tttt) REVERT: I 22 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6616 (tm-30) REVERT: I 497 ASP cc_start: 0.8388 (t0) cc_final: 0.7928 (t0) REVERT: I 519 TYR cc_start: 0.8386 (m-80) cc_final: 0.8154 (m-80) REVERT: I 539 TYR cc_start: 0.8376 (m-80) cc_final: 0.7860 (m-80) REVERT: J 64 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8042 (ttm-80) REVERT: J 66 GLU cc_start: 0.8579 (pm20) cc_final: 0.8013 (pm20) REVERT: J 71 TYR cc_start: 0.8362 (p90) cc_final: 0.8011 (p90) REVERT: J 99 GLU cc_start: 0.8863 (pp20) cc_final: 0.8603 (pp20) REVERT: J 102 ASP cc_start: 0.8720 (m-30) cc_final: 0.7768 (m-30) REVERT: J 112 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8255 (ttpp) outliers start: 69 outliers final: 38 residues processed: 270 average time/residue: 0.3109 time to fit residues: 129.1433 Evaluate side-chains 218 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 209 optimal weight: 0.2980 chunk 197 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN D 714 ASN I 464 GLN ** I 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.095849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.065248 restraints weight = 53817.977| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.43 r_work: 0.3075 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17994 Z= 0.247 Angle : 0.678 8.324 24440 Z= 0.338 Chirality : 0.045 0.235 2812 Planarity : 0.004 0.050 3097 Dihedral : 5.841 55.221 2549 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.24 % Rotamer: Outliers : 4.28 % Allowed : 13.47 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.18), residues: 2215 helix: 0.52 (0.24), residues: 541 sheet: -1.55 (0.29), residues: 323 loop : -1.91 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 474 HIS 0.008 0.001 HIS A 209 PHE 0.041 0.002 PHE D 634 TYR 0.019 0.002 TYR J 83 ARG 0.010 0.001 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 466) hydrogen bonds : angle 4.97589 ( 1383) SS BOND : bond 0.00493 ( 22) SS BOND : angle 0.86399 ( 44) covalent geometry : bond 0.00561 (17972) covalent geometry : angle 0.67716 (24396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 193 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 308 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8352 (tmm) REVERT: A 344 MET cc_start: 0.8480 (ptp) cc_final: 0.7921 (ptp) REVERT: A 638 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8522 (mt) REVERT: A 782 MET cc_start: 0.8481 (ttm) cc_final: 0.8166 (ttt) REVERT: C 128 GLN cc_start: 0.8530 (mp10) cc_final: 0.8257 (mp10) REVERT: C 190 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8757 (ttmt) REVERT: E 459 MET cc_start: 0.9023 (mmm) cc_final: 0.8291 (mmp) REVERT: E 464 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7222 (tp-100) REVERT: E 468 LYS cc_start: 0.8764 (mppt) cc_final: 0.8508 (mppt) REVERT: E 477 ASP cc_start: 0.7688 (t0) cc_final: 0.7290 (t70) REVERT: E 492 PHE cc_start: 0.8014 (m-10) cc_final: 0.7736 (m-10) REVERT: E 539 TYR cc_start: 0.8335 (m-80) cc_final: 0.7753 (m-80) REVERT: G 66 GLU cc_start: 0.8781 (pm20) cc_final: 0.8415 (pm20) REVERT: G 68 MET cc_start: 0.8827 (mtm) cc_final: 0.8459 (mtp) REVERT: G 114 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8712 (mmtm) REVERT: D 80 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7948 (p90) REVERT: D 308 MET cc_start: 0.9165 (ttt) cc_final: 0.8965 (ttt) REVERT: D 754 PHE cc_start: 0.9088 (m-80) cc_final: 0.8625 (m-80) REVERT: H 100 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.6371 (tm-30) REVERT: I 479 ASP cc_start: 0.9629 (m-30) cc_final: 0.9340 (p0) REVERT: I 497 ASP cc_start: 0.8279 (t0) cc_final: 0.7947 (t0) REVERT: I 519 TYR cc_start: 0.8434 (m-80) cc_final: 0.8181 (m-80) REVERT: I 539 TYR cc_start: 0.8379 (m-80) cc_final: 0.7833 (m-80) REVERT: J 64 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8040 (ttm-80) REVERT: J 66 GLU cc_start: 0.8510 (pm20) cc_final: 0.8163 (pm20) REVERT: J 71 TYR cc_start: 0.8383 (p90) cc_final: 0.8150 (p90) REVERT: J 99 GLU cc_start: 0.8956 (pp20) cc_final: 0.8377 (pp20) REVERT: J 100 ASN cc_start: 0.9523 (m-40) cc_final: 0.9212 (m-40) REVERT: J 102 ASP cc_start: 0.8638 (m-30) cc_final: 0.8397 (m-30) outliers start: 83 outliers final: 50 residues processed: 258 average time/residue: 0.3550 time to fit residues: 145.4597 Evaluate side-chains 225 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 477 ASP Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 189 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN C 206 GLN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN ** I 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.098060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067680 restraints weight = 53909.345| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.49 r_work: 0.3130 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17994 Z= 0.124 Angle : 0.605 15.716 24440 Z= 0.295 Chirality : 0.042 0.170 2812 Planarity : 0.003 0.043 3097 Dihedral : 5.493 56.817 2549 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.23 % Favored : 93.68 % Rotamer: Outliers : 3.51 % Allowed : 15.07 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2215 helix: 0.68 (0.24), residues: 530 sheet: -1.32 (0.30), residues: 319 loop : -1.83 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 474 HIS 0.005 0.000 HIS A 209 PHE 0.023 0.001 PHE D 547 TYR 0.023 0.001 TYR E 484 ARG 0.004 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 466) hydrogen bonds : angle 4.68448 ( 1383) SS BOND : bond 0.00427 ( 22) SS BOND : angle 0.95880 ( 44) covalent geometry : bond 0.00281 (17972) covalent geometry : angle 0.60443 (24396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 201 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.8876 (mp10) cc_final: 0.8580 (mp10) REVERT: A 111 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 308 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8354 (tmm) REVERT: A 344 MET cc_start: 0.8375 (ptp) cc_final: 0.7816 (ptp) REVERT: A 623 PHE cc_start: 0.8385 (t80) cc_final: 0.8065 (t80) REVERT: A 638 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8509 (mt) REVERT: A 782 MET cc_start: 0.8408 (ttm) cc_final: 0.8087 (ttt) REVERT: C 128 GLN cc_start: 0.8494 (mp10) cc_final: 0.8207 (mp10) REVERT: E 459 MET cc_start: 0.8832 (mmm) cc_final: 0.8222 (mmp) REVERT: E 477 ASP cc_start: 0.7789 (t0) cc_final: 0.7545 (t70) REVERT: E 484 TYR cc_start: 0.8711 (m-80) cc_final: 0.7443 (m-80) REVERT: E 514 ASP cc_start: 0.8668 (t0) cc_final: 0.7957 (m-30) REVERT: E 539 TYR cc_start: 0.8302 (m-80) cc_final: 0.7692 (m-80) REVERT: G 66 GLU cc_start: 0.8884 (pm20) cc_final: 0.8559 (pm20) REVERT: G 68 MET cc_start: 0.8631 (mtm) cc_final: 0.8406 (mtp) REVERT: G 112 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8150 (ttpp) REVERT: G 114 LYS cc_start: 0.9214 (ttpp) cc_final: 0.8842 (mmtm) REVERT: G 139 MET cc_start: 0.6780 (tpt) cc_final: 0.6146 (tpp) REVERT: D 80 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7932 (p90) REVERT: D 137 ASP cc_start: 0.8284 (m-30) cc_final: 0.7880 (m-30) REVERT: D 308 MET cc_start: 0.9134 (ttt) cc_final: 0.8911 (ttt) REVERT: D 591 THR cc_start: 0.8867 (m) cc_final: 0.8662 (t) REVERT: D 721 MET cc_start: 0.8146 (tmm) cc_final: 0.7883 (tmm) REVERT: D 754 PHE cc_start: 0.9087 (m-80) cc_final: 0.8586 (m-80) REVERT: H 134 LYS cc_start: 0.9185 (tptp) cc_final: 0.8952 (tptp) REVERT: H 144 LYS cc_start: 0.9280 (tmmt) cc_final: 0.9016 (tptp) REVERT: I 22 GLN cc_start: 0.8673 (mp10) cc_final: 0.8378 (tm-30) REVERT: I 475 THR cc_start: 0.7870 (m) cc_final: 0.7466 (p) REVERT: I 479 ASP cc_start: 0.9608 (m-30) cc_final: 0.9353 (p0) REVERT: I 497 ASP cc_start: 0.8404 (t0) cc_final: 0.8001 (t0) REVERT: I 519 TYR cc_start: 0.8380 (m-80) cc_final: 0.8109 (m-80) REVERT: I 539 TYR cc_start: 0.8375 (m-80) cc_final: 0.7950 (m-80) REVERT: J 64 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8006 (ttm-80) REVERT: J 66 GLU cc_start: 0.8584 (pm20) cc_final: 0.8297 (pm20) REVERT: J 99 GLU cc_start: 0.9040 (pp20) cc_final: 0.8402 (pp20) REVERT: J 100 ASN cc_start: 0.9569 (m-40) cc_final: 0.9151 (m-40) REVERT: J 102 ASP cc_start: 0.8667 (m-30) cc_final: 0.8379 (m-30) REVERT: J 118 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: J 126 ASP cc_start: 0.8229 (p0) cc_final: 0.7314 (p0) outliers start: 68 outliers final: 43 residues processed: 252 average time/residue: 0.2888 time to fit residues: 114.0188 Evaluate side-chains 223 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 477 ASP Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 137 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 162 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN I 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.097525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067015 restraints weight = 54048.590| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.48 r_work: 0.3107 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17994 Z= 0.148 Angle : 0.620 15.262 24440 Z= 0.303 Chirality : 0.042 0.179 2812 Planarity : 0.003 0.039 3097 Dihedral : 5.447 47.247 2549 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.51 % Rotamer: Outliers : 3.61 % Allowed : 15.64 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.18), residues: 2215 helix: 0.66 (0.24), residues: 537 sheet: -1.23 (0.31), residues: 319 loop : -1.81 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 474 HIS 0.006 0.001 HIS A 209 PHE 0.026 0.001 PHE A 547 TYR 0.018 0.001 TYR D 729 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 466) hydrogen bonds : angle 4.59552 ( 1383) SS BOND : bond 0.00518 ( 22) SS BOND : angle 0.85549 ( 44) covalent geometry : bond 0.00339 (17972) covalent geometry : angle 0.61931 (24396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 188 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7915 (p90) REVERT: A 87 GLN cc_start: 0.8869 (mp10) cc_final: 0.8537 (mp10) REVERT: A 111 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 308 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: A 344 MET cc_start: 0.8419 (ptp) cc_final: 0.7857 (ptp) REVERT: A 623 PHE cc_start: 0.8349 (t80) cc_final: 0.8023 (t80) REVERT: A 634 PHE cc_start: 0.7434 (m-10) cc_final: 0.7209 (m-80) REVERT: A 638 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8465 (mt) REVERT: A 782 MET cc_start: 0.8430 (ttm) cc_final: 0.8117 (ttt) REVERT: C 128 GLN cc_start: 0.8519 (mp10) cc_final: 0.8227 (mp10) REVERT: E 22 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 484 TYR cc_start: 0.8734 (m-80) cc_final: 0.7499 (m-80) REVERT: E 514 ASP cc_start: 0.8640 (t0) cc_final: 0.7875 (m-30) REVERT: E 539 TYR cc_start: 0.8314 (m-80) cc_final: 0.7665 (m-80) REVERT: G 66 GLU cc_start: 0.8875 (pm20) cc_final: 0.8541 (pm20) REVERT: G 68 MET cc_start: 0.8736 (mtm) cc_final: 0.8459 (mtp) REVERT: G 112 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8108 (ttpp) REVERT: G 114 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8832 (mmtm) REVERT: G 139 MET cc_start: 0.6728 (tpt) cc_final: 0.5959 (tpp) REVERT: D 80 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7957 (p90) REVERT: D 137 ASP cc_start: 0.8432 (m-30) cc_final: 0.7875 (m-30) REVERT: D 308 MET cc_start: 0.9118 (ttt) cc_final: 0.8890 (ttt) REVERT: D 637 MET cc_start: 0.5205 (tpt) cc_final: 0.4920 (tpp) REVERT: D 721 MET cc_start: 0.8034 (tmm) cc_final: 0.7696 (tmm) REVERT: D 754 PHE cc_start: 0.9079 (m-80) cc_final: 0.8609 (m-80) REVERT: H 100 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.5915 (tm-30) REVERT: I 22 GLN cc_start: 0.8686 (mp10) cc_final: 0.8409 (tm-30) REVERT: I 479 ASP cc_start: 0.9599 (m-30) cc_final: 0.9354 (p0) REVERT: I 486 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8748 (p0) REVERT: I 496 GLN cc_start: 0.8481 (tp40) cc_final: 0.8240 (tp40) REVERT: I 497 ASP cc_start: 0.8283 (t0) cc_final: 0.7722 (t0) REVERT: I 539 TYR cc_start: 0.8385 (m-80) cc_final: 0.7913 (m-80) REVERT: J 66 GLU cc_start: 0.8645 (pm20) cc_final: 0.8441 (pm20) REVERT: J 99 GLU cc_start: 0.9085 (pp20) cc_final: 0.8482 (pp20) REVERT: J 100 ASN cc_start: 0.9611 (m-40) cc_final: 0.9125 (m-40) REVERT: J 102 ASP cc_start: 0.8622 (m-30) cc_final: 0.7923 (m-30) REVERT: J 112 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8338 (ttpp) REVERT: J 118 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: J 126 ASP cc_start: 0.8180 (p0) cc_final: 0.7257 (p0) outliers start: 70 outliers final: 52 residues processed: 241 average time/residue: 0.3342 time to fit residues: 133.2480 Evaluate side-chains 237 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain I residue 458 CYS Chi-restraints excluded: chain I residue 477 ASP Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 87 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** I 506 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 = 0.3946 r_free = 0.3946 target = 0.097685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.067344 restraints weight = 53194.839| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.42 r_work: 0.3124 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17994 Z= 0.137 Angle : 0.609 15.561 24440 Z= 0.296 Chirality : 0.042 0.173 2812 Planarity : 0.003 0.041 3097 Dihedral : 5.222 48.159 2543 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.82 % Favored : 93.09 % Rotamer: Outliers : 3.46 % Allowed : 16.21 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 2215 helix: 0.73 (0.24), residues: 538 sheet: -0.99 (0.32), residues: 311 loop : -1.77 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 751 HIS 0.006 0.001 HIS A 209 PHE 0.025 0.001 PHE D 547 TYR 0.018 0.001 TYR E 484 ARG 0.005 0.000 ARG J 64 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 466) hydrogen bonds : angle 4.55602 ( 1383) SS BOND : bond 0.00335 ( 22) SS BOND : angle 0.87302 ( 44) covalent geometry : bond 0.00316 (17972) covalent geometry : angle 0.60863 (24396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.7884 (p90) REVERT: A 87 GLN cc_start: 0.8916 (mp10) cc_final: 0.8596 (mp10) REVERT: A 111 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 308 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8383 (tmm) REVERT: A 344 MET cc_start: 0.8394 (ptp) cc_final: 0.7838 (ptp) REVERT: A 623 PHE cc_start: 0.8364 (t80) cc_final: 0.8014 (t80) REVERT: A 634 PHE cc_start: 0.7559 (m-10) cc_final: 0.7327 (m-80) REVERT: A 638 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8488 (mt) REVERT: A 782 MET cc_start: 0.8426 (ttm) cc_final: 0.8114 (ttt) REVERT: C 128 GLN cc_start: 0.8540 (mp10) cc_final: 0.8237 (mp10) REVERT: E 464 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7490 (tm-30) REVERT: E 484 TYR cc_start: 0.8751 (m-80) cc_final: 0.8546 (m-80) REVERT: E 514 ASP cc_start: 0.8815 (t0) cc_final: 0.8043 (m-30) REVERT: E 539 TYR cc_start: 0.8332 (m-80) cc_final: 0.7675 (m-80) REVERT: G 66 GLU cc_start: 0.8885 (pm20) cc_final: 0.8547 (pm20) REVERT: G 114 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8840 (mmtm) REVERT: G 139 MET cc_start: 0.6766 (tpt) cc_final: 0.6236 (tpp) REVERT: D 66 MET cc_start: 0.7758 (ppp) cc_final: 0.7546 (ppp) REVERT: D 80 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7976 (p90) REVERT: D 137 ASP cc_start: 0.8352 (m-30) cc_final: 0.7874 (m-30) REVERT: D 308 MET cc_start: 0.9124 (ttt) cc_final: 0.8883 (ttt) REVERT: D 344 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8166 (ptt) REVERT: D 637 MET cc_start: 0.5214 (tpt) cc_final: 0.4903 (tpp) REVERT: D 721 MET cc_start: 0.8019 (tmm) cc_final: 0.7668 (tmm) REVERT: D 754 PHE cc_start: 0.9059 (m-80) cc_final: 0.8585 (m-80) REVERT: H 100 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.6018 (tm-30) REVERT: I 444 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7583 (mmm-85) REVERT: I 479 ASP cc_start: 0.9603 (m-30) cc_final: 0.9337 (p0) REVERT: I 486 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8769 (p0) REVERT: I 497 ASP cc_start: 0.8236 (t0) cc_final: 0.7812 (t0) REVERT: I 539 TYR cc_start: 0.8396 (m-80) cc_final: 0.7932 (m-80) REVERT: J 102 ASP cc_start: 0.8627 (m-30) cc_final: 0.8357 (m-30) REVERT: J 107 LYS cc_start: 0.9555 (ttpp) cc_final: 0.9205 (ttmm) REVERT: J 118 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: J 126 ASP cc_start: 0.8204 (p0) cc_final: 0.7289 (p0) outliers start: 67 outliers final: 48 residues processed: 236 average time/residue: 0.3508 time to fit residues: 137.8137 Evaluate side-chains 232 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 155 optimal weight: 0.0570 chunk 106 optimal weight: 0.7980 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.096516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065983 restraints weight = 53687.748| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 4.42 r_work: 0.3090 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17994 Z= 0.186 Angle : 0.641 15.709 24440 Z= 0.316 Chirality : 0.044 0.172 2812 Planarity : 0.003 0.039 3097 Dihedral : 5.416 50.165 2543 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.74 % Rotamer: Outliers : 3.77 % Allowed : 16.06 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 2215 helix: 0.67 (0.24), residues: 545 sheet: -1.00 (0.31), residues: 318 loop : -1.76 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 751 HIS 0.007 0.001 HIS A 209 PHE 0.024 0.001 PHE A 547 TYR 0.017 0.001 TYR E 484 ARG 0.003 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 466) hydrogen bonds : angle 4.55637 ( 1383) SS BOND : bond 0.00379 ( 22) SS BOND : angle 0.77822 ( 44) covalent geometry : bond 0.00423 (17972) covalent geometry : angle 0.64040 (24396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 179 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7893 (p90) REVERT: A 87 GLN cc_start: 0.8875 (mp10) cc_final: 0.8547 (mp10) REVERT: A 111 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 308 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8429 (tmm) REVERT: A 344 MET cc_start: 0.8418 (ptp) cc_final: 0.7901 (ptp) REVERT: A 623 PHE cc_start: 0.8450 (t80) cc_final: 0.8132 (t80) REVERT: A 634 PHE cc_start: 0.7702 (m-10) cc_final: 0.7474 (m-80) REVERT: A 638 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 782 MET cc_start: 0.8426 (ttm) cc_final: 0.8127 (ttt) REVERT: C 97 GLU cc_start: 0.8693 (pm20) cc_final: 0.8419 (pm20) REVERT: C 128 GLN cc_start: 0.8514 (mp10) cc_final: 0.8205 (mp10) REVERT: C 219 MET cc_start: 0.6997 (mtt) cc_final: 0.6728 (mtp) REVERT: E 459 MET cc_start: 0.8976 (mtp) cc_final: 0.8711 (ttt) REVERT: E 464 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 484 TYR cc_start: 0.8824 (m-80) cc_final: 0.7705 (m-80) REVERT: E 514 ASP cc_start: 0.8925 (t0) cc_final: 0.8278 (m-30) REVERT: E 539 TYR cc_start: 0.8401 (m-80) cc_final: 0.7734 (m-80) REVERT: G 66 GLU cc_start: 0.8813 (pm20) cc_final: 0.8432 (pm20) REVERT: G 114 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8848 (mmtm) REVERT: G 139 MET cc_start: 0.6801 (tpt) cc_final: 0.6178 (tpp) REVERT: D 80 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8073 (p90) REVERT: D 137 ASP cc_start: 0.8427 (m-30) cc_final: 0.8093 (m-30) REVERT: D 308 MET cc_start: 0.9115 (ttt) cc_final: 0.8877 (ttt) REVERT: D 637 MET cc_start: 0.5411 (tpt) cc_final: 0.5080 (tpp) REVERT: D 721 MET cc_start: 0.8061 (tmm) cc_final: 0.7697 (tmm) REVERT: D 754 PHE cc_start: 0.9056 (m-80) cc_final: 0.8590 (m-80) REVERT: H 100 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.6140 (tm-30) REVERT: I 444 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7688 (mmm160) REVERT: I 475 THR cc_start: 0.7971 (m) cc_final: 0.7454 (p) REVERT: I 479 ASP cc_start: 0.9624 (m-30) cc_final: 0.9408 (p0) REVERT: I 486 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8781 (p0) REVERT: I 497 ASP cc_start: 0.7985 (t0) cc_final: 0.7685 (t0) REVERT: I 519 TYR cc_start: 0.8425 (m-80) cc_final: 0.8041 (m-80) REVERT: I 539 TYR cc_start: 0.8413 (m-80) cc_final: 0.7944 (m-80) REVERT: J 102 ASP cc_start: 0.8608 (m-30) cc_final: 0.7945 (m-30) REVERT: J 107 LYS cc_start: 0.9568 (ttpp) cc_final: 0.9203 (ttmm) REVERT: J 112 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8325 (ttpp) outliers start: 73 outliers final: 57 residues processed: 238 average time/residue: 0.3365 time to fit residues: 128.7825 Evaluate side-chains 238 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 142 optimal weight: 0.5980 chunk 80 optimal weight: 0.0980 chunk 92 optimal weight: 0.0050 chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 756 ASN D 584 ASN ** I 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.098209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067830 restraints weight = 53966.265| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.51 r_work: 0.3135 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17994 Z= 0.117 Angle : 0.630 15.903 24440 Z= 0.306 Chirality : 0.043 0.154 2812 Planarity : 0.003 0.059 3097 Dihedral : 5.174 51.359 2543 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.81 % Rotamer: Outliers : 3.20 % Allowed : 17.04 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2215 helix: 0.70 (0.24), residues: 546 sheet: -0.95 (0.31), residues: 320 loop : -1.69 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 474 HIS 0.005 0.000 HIS A 209 PHE 0.027 0.001 PHE D 547 TYR 0.018 0.001 TYR E 484 ARG 0.003 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 466) hydrogen bonds : angle 4.46554 ( 1383) SS BOND : bond 0.00406 ( 22) SS BOND : angle 1.08967 ( 44) covalent geometry : bond 0.00270 (17972) covalent geometry : angle 0.62877 (24396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.7878 (p90) REVERT: A 87 GLN cc_start: 0.8904 (mp10) cc_final: 0.8576 (mp10) REVERT: A 111 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 308 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8374 (tmm) REVERT: A 344 MET cc_start: 0.8353 (ptp) cc_final: 0.7844 (ptp) REVERT: A 623 PHE cc_start: 0.8454 (t80) cc_final: 0.8092 (t80) REVERT: A 634 PHE cc_start: 0.7625 (m-10) cc_final: 0.7395 (m-80) REVERT: A 638 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 721 MET cc_start: 0.6982 (ptp) cc_final: 0.6660 (ttp) REVERT: A 782 MET cc_start: 0.8383 (ttm) cc_final: 0.8060 (ttt) REVERT: C 97 GLU cc_start: 0.8617 (pm20) cc_final: 0.8352 (pm20) REVERT: C 128 GLN cc_start: 0.8476 (mp10) cc_final: 0.8158 (mp10) REVERT: C 219 MET cc_start: 0.6859 (mtt) cc_final: 0.6585 (mtp) REVERT: E 459 MET cc_start: 0.8943 (mtp) cc_final: 0.8678 (ttm) REVERT: E 464 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7404 (tm-30) REVERT: E 484 TYR cc_start: 0.8790 (m-80) cc_final: 0.8407 (m-80) REVERT: E 514 ASP cc_start: 0.8934 (t0) cc_final: 0.8192 (m-30) REVERT: E 539 TYR cc_start: 0.8440 (m-80) cc_final: 0.7769 (m-80) REVERT: G 66 GLU cc_start: 0.8855 (pm20) cc_final: 0.8524 (pm20) REVERT: G 114 LYS cc_start: 0.9186 (ttpp) cc_final: 0.8835 (mmtm) REVERT: G 139 MET cc_start: 0.6768 (tpt) cc_final: 0.6188 (tpp) REVERT: D 80 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8002 (p90) REVERT: D 137 ASP cc_start: 0.8303 (m-30) cc_final: 0.7848 (m-30) REVERT: D 308 MET cc_start: 0.9115 (ttt) cc_final: 0.8859 (ttt) REVERT: D 344 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8168 (ptt) REVERT: D 419 ASP cc_start: 0.8607 (t0) cc_final: 0.8326 (t0) REVERT: D 519 ILE cc_start: 0.7015 (mm) cc_final: 0.6359 (tt) REVERT: D 637 MET cc_start: 0.5483 (tpt) cc_final: 0.5174 (tpp) REVERT: D 721 MET cc_start: 0.8002 (tmm) cc_final: 0.7632 (tmm) REVERT: D 754 PHE cc_start: 0.9048 (m-80) cc_final: 0.8574 (m-80) REVERT: I 444 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7613 (mmm160) REVERT: I 475 THR cc_start: 0.7892 (m) cc_final: 0.7496 (p) REVERT: I 486 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8728 (p0) REVERT: I 539 TYR cc_start: 0.8372 (m-80) cc_final: 0.7952 (m-80) REVERT: J 102 ASP cc_start: 0.8659 (m-30) cc_final: 0.7993 (m-30) REVERT: J 112 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8362 (ttpp) outliers start: 62 outliers final: 52 residues processed: 233 average time/residue: 0.2939 time to fit residues: 109.6308 Evaluate side-chains 233 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 84 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN ** I 508 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.097574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.067275 restraints weight = 53374.454| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.40 r_work: 0.3122 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17994 Z= 0.145 Angle : 0.653 15.828 24440 Z= 0.314 Chirality : 0.043 0.225 2812 Planarity : 0.004 0.056 3097 Dihedral : 5.212 51.538 2543 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.49 % Favored : 92.42 % Rotamer: Outliers : 3.46 % Allowed : 16.83 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2215 helix: 0.74 (0.24), residues: 546 sheet: -0.86 (0.32), residues: 311 loop : -1.74 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 751 HIS 0.006 0.001 HIS A 209 PHE 0.029 0.001 PHE A 718 TYR 0.018 0.001 TYR E 484 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 466) hydrogen bonds : angle 4.47607 ( 1383) SS BOND : bond 0.00379 ( 22) SS BOND : angle 0.85674 ( 44) covalent geometry : bond 0.00337 (17972) covalent geometry : angle 0.65250 (24396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4430 Ramachandran restraints generated. 2215 Oldfield, 0 Emsley, 2215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8525 (m-30) cc_final: 0.8218 (t0) REVERT: A 80 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7879 (p90) REVERT: A 87 GLN cc_start: 0.8868 (mp10) cc_final: 0.8501 (mp10) REVERT: A 111 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 308 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8402 (tmm) REVERT: A 344 MET cc_start: 0.8353 (ptp) cc_final: 0.7844 (ptp) REVERT: A 354 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8439 (p0) REVERT: A 623 PHE cc_start: 0.8461 (t80) cc_final: 0.8059 (t80) REVERT: A 634 PHE cc_start: 0.7672 (m-10) cc_final: 0.7448 (m-80) REVERT: A 638 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 721 MET cc_start: 0.7142 (ptp) cc_final: 0.6801 (ttp) REVERT: A 782 MET cc_start: 0.8416 (ttm) cc_final: 0.8094 (ttt) REVERT: C 97 GLU cc_start: 0.8675 (pm20) cc_final: 0.8412 (pm20) REVERT: C 128 GLN cc_start: 0.8495 (mp10) cc_final: 0.8183 (mp10) REVERT: E 464 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7436 (tm-30) REVERT: E 484 TYR cc_start: 0.8828 (m-80) cc_final: 0.8460 (m-80) REVERT: E 486 ASP cc_start: 0.9229 (p0) cc_final: 0.8994 (p0) REVERT: E 514 ASP cc_start: 0.9022 (t0) cc_final: 0.8295 (m-30) REVERT: E 539 TYR cc_start: 0.8435 (m-80) cc_final: 0.7761 (m-80) REVERT: G 66 GLU cc_start: 0.8845 (pm20) cc_final: 0.8520 (pm20) REVERT: G 114 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8843 (mmtm) REVERT: G 139 MET cc_start: 0.6760 (tpt) cc_final: 0.6184 (tpp) REVERT: D 80 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8043 (p90) REVERT: D 137 ASP cc_start: 0.8375 (m-30) cc_final: 0.8093 (m-30) REVERT: D 308 MET cc_start: 0.9114 (ttt) cc_final: 0.8858 (ttt) REVERT: D 344 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8122 (ptp) REVERT: D 519 ILE cc_start: 0.7010 (mm) cc_final: 0.6377 (tt) REVERT: D 637 MET cc_start: 0.5557 (tpt) cc_final: 0.5252 (tpp) REVERT: D 721 MET cc_start: 0.8017 (tmm) cc_final: 0.7642 (tmm) REVERT: D 754 PHE cc_start: 0.9047 (m-80) cc_final: 0.8569 (m-80) REVERT: I 475 THR cc_start: 0.8069 (m) cc_final: 0.7587 (p) REVERT: I 486 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8736 (p0) REVERT: I 539 TYR cc_start: 0.8412 (m-80) cc_final: 0.7996 (m-80) REVERT: J 102 ASP cc_start: 0.8659 (m-30) cc_final: 0.7979 (m-30) REVERT: J 112 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8352 (ttpp) outliers start: 67 outliers final: 54 residues processed: 229 average time/residue: 0.2491 time to fit residues: 92.6177 Evaluate side-chains 232 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 486 ASP Chi-restraints excluded: chain I residue 510 LEU Chi-restraints excluded: chain I residue 520 CYS Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 130 optimal weight: 0.0870 chunk 134 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** I 508 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.098558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068375 restraints weight = 53150.650| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.46 r_work: 0.3148 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17994 Z= 0.117 Angle : 0.652 15.860 24440 Z= 0.311 Chirality : 0.043 0.419 2812 Planarity : 0.003 0.054 3097 Dihedral : 5.088 52.092 2541 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 3.25 % Allowed : 17.45 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2215 helix: 0.72 (0.23), residues: 549 sheet: -0.88 (0.32), residues: 320 loop : -1.68 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 751 HIS 0.005 0.000 HIS A 209 PHE 0.030 0.001 PHE A 760 TYR 0.019 0.001 TYR E 484 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 466) hydrogen bonds : angle 4.46529 ( 1383) SS BOND : bond 0.00492 ( 22) SS BOND : angle 0.99150 ( 44) covalent geometry : bond 0.00273 (17972) covalent geometry : angle 0.65172 (24396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12464.19 seconds wall clock time: 223 minutes 13.38 seconds (13393.38 seconds total)