Starting phenix.real_space_refine (version: dev) on Mon Feb 20 18:58:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2023/7uob_26645_neut_updated.pdb" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.038 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 Process input model Symmetric amino acids flipped Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12718 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7478 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1420 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 697 Classifications: {'RNA': 33} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 32} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 69 Unusual residues: {' MG': 3, ' ZN': 2, 'GTP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'L2B': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "T" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2462 SG CYS A 301 57.554 99.369 56.439 1.00 6.51 S ATOM 2503 SG CYS A 306 56.004 102.601 55.673 1.00 6.95 S ATOM 2535 SG CYS A 310 55.728 99.686 52.918 1.00 6.84 S ATOM 3943 SG CYS A 487 57.356 96.727 77.177 1.00 5.28 S ATOM 5196 SG CYS A 645 56.187 100.394 76.846 1.00 7.74 S ATOM 5202 SG CYS A 646 58.444 98.558 74.213 1.00 6.47 S Time building chain proxies: 7.70, per 1000 atoms: 0.61 Number of scatterers: 12718 At special positions: 0 Unit cell: (92.88, 129.6, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 76 15.00 Mg 3 11.99 O 2859 8.00 N 2104 7.00 C 7592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 9 sheets defined 50.4% alpha, 11.4% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.539A pdb=" N PHE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.558A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.740A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.654A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.084A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.248A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.829A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.473A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.593A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.664A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.801A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 3.601A pdb=" N ARG A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 removed outlier: 3.584A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 693 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 856 through 871 removed outlier: 3.695A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.780A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.234A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.748A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 4.052A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 33 through 95 removed outlier: 3.515A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.713A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.513A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.679A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.884A pdb=" N THR D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 removed outlier: 3.852A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 removed outlier: 3.517A pdb=" N MET D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.569A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.521A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.560A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.647A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 799 through 802 removed outlier: 3.658A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 816 through 822 removed outlier: 4.084A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.351A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.568A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 6.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3819 1.34 - 1.48: 3591 1.48 - 1.61: 5279 1.61 - 1.74: 12 1.74 - 1.87: 129 Bond restraints: 12830 Sorted by residual: bond pdb=" C2' L2B P 101 " pdb=" C3' L2B P 101 " ideal model delta sigma weight residual 1.281 1.523 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" O5' L2B P 101 " pdb=" P L2B P 101 " ideal model delta sigma weight residual 1.648 1.874 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C4' L2B P 101 " pdb=" C5' L2B P 101 " ideal model delta sigma weight residual 1.418 1.633 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C1' L2B P 101 " pdb=" N1 L2B P 101 " ideal model delta sigma weight residual 1.463 1.624 -0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" C5 L2B P 101 " pdb=" C6 L2B P 101 " ideal model delta sigma weight residual 1.493 1.357 0.136 2.00e-02 2.50e+03 4.64e+01 ... (remaining 12825 not shown) Histogram of bond angle deviations from ideal: 92.95 - 102.00: 125 102.00 - 111.04: 5221 111.04 - 120.09: 6892 120.09 - 129.14: 5389 129.14 - 138.18: 115 Bond angle restraints: 17742 Sorted by residual: angle pdb=" O2A GTP A1006 " pdb=" PA GTP A1006 " pdb=" O3A GTP A1006 " ideal model delta sigma weight residual 109.50 92.95 16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" OP1 L2B P 101 " pdb=" P L2B P 101 " pdb=" OP2 L2B P 101 " ideal model delta sigma weight residual 109.47 123.64 -14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" PA GTP A1006 " pdb=" O3A GTP A1006 " pdb=" PB GTP A1006 " ideal model delta sigma weight residual 120.50 133.49 -12.99 3.00e+00 1.11e-01 1.88e+01 angle pdb=" O1A GTP A1006 " pdb=" PA GTP A1006 " pdb=" O3A GTP A1006 " ideal model delta sigma weight residual 108.20 118.57 -10.37 3.00e+00 1.11e-01 1.19e+01 angle pdb=" O1A GTP A1007 " pdb=" PA GTP A1007 " pdb=" O2A GTP A1007 " ideal model delta sigma weight residual 109.50 119.09 -9.59 3.00e+00 1.11e-01 1.02e+01 ... (remaining 17737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 7396 35.03 - 70.05: 111 70.05 - 105.08: 9 105.08 - 140.11: 2 140.11 - 175.13: 5 Dihedral angle restraints: 7523 sinusoidal: 3436 harmonic: 4087 Sorted by residual: dihedral pdb=" O2G GTP A1006 " pdb=" O3B GTP A1006 " pdb=" PG GTP A1006 " pdb=" PB GTP A1006 " ideal model delta sinusoidal sigma weight residual 177.30 2.17 175.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP A1007 " pdb=" C5' GTP A1007 " pdb=" O5' GTP A1007 " pdb=" PA GTP A1007 " ideal model delta sinusoidal sigma weight residual 260.87 86.66 174.22 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3B GTP A1006 " pdb=" O3A GTP A1006 " pdb=" PB GTP A1006 " pdb=" PA GTP A1006 " ideal model delta sinusoidal sigma weight residual -68.92 101.54 -170.46 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 7520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1658 0.045 - 0.090: 305 0.090 - 0.134: 87 0.134 - 0.179: 4 0.179 - 0.224: 1 Chirality restraints: 2055 Sorted by residual: chirality pdb=" C1' L2B P 101 " pdb=" C2' L2B P 101 " pdb=" N1 L2B P 101 " pdb=" O4' L2B P 101 " both_signs ideal model delta sigma weight residual False 2.38 2.60 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2' L2B P 101 " pdb=" C1' L2B P 101 " pdb=" C3' L2B P 101 " pdb=" O2' L2B P 101 " both_signs ideal model delta sigma weight residual False -2.42 -2.58 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB ILE A 696 " pdb=" CA ILE A 696 " pdb=" CG1 ILE A 696 " pdb=" CG2 ILE A 696 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 2052 not shown) Planarity restraints: 2001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP A1007 " -0.031 2.00e-02 2.50e+03 1.24e-02 4.62e+00 pdb=" C2 GTP A1007 " 0.000 2.00e-02 2.50e+03 pdb=" C4 GTP A1007 " 0.006 2.00e-02 2.50e+03 pdb=" C5 GTP A1007 " -0.003 2.00e-02 2.50e+03 pdb=" C6 GTP A1007 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP A1007 " 0.011 2.00e-02 2.50e+03 pdb=" N1 GTP A1007 " -0.009 2.00e-02 2.50e+03 pdb=" N2 GTP A1007 " 0.002 2.00e-02 2.50e+03 pdb=" N3 GTP A1007 " 0.010 2.00e-02 2.50e+03 pdb=" N7 GTP A1007 " -0.000 2.00e-02 2.50e+03 pdb=" N9 GTP A1007 " 0.020 2.00e-02 2.50e+03 pdb=" O6 GTP A1007 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP A1006 " -0.018 2.00e-02 2.50e+03 9.69e-03 2.82e+00 pdb=" C2 GTP A1006 " -0.005 2.00e-02 2.50e+03 pdb=" C4 GTP A1006 " 0.015 2.00e-02 2.50e+03 pdb=" C5 GTP A1006 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GTP A1006 " -0.002 2.00e-02 2.50e+03 pdb=" C8 GTP A1006 " -0.002 2.00e-02 2.50e+03 pdb=" N1 GTP A1006 " -0.009 2.00e-02 2.50e+03 pdb=" N2 GTP A1006 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP A1006 " 0.007 2.00e-02 2.50e+03 pdb=" N7 GTP A1006 " -0.009 2.00e-02 2.50e+03 pdb=" N9 GTP A1006 " 0.018 2.00e-02 2.50e+03 pdb=" O6 GTP A1006 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 927 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " -0.023 5.00e-02 4.00e+02 ... (remaining 1998 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 172 2.60 - 3.18: 10732 3.18 - 3.75: 20011 3.75 - 4.33: 30805 4.33 - 4.90: 47397 Nonbonded interactions: 109117 Sorted by model distance: nonbonded pdb=" OH TYR A 719 " pdb=" O HOH A1101 " model vdw 2.030 2.440 nonbonded pdb=" O HOH A1108 " pdb=" O HOH A1247 " model vdw 2.068 2.440 nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.083 2.440 nonbonded pdb=" N GLU A 665 " pdb=" OE1 GLU A 665 " model vdw 2.150 2.520 nonbonded pdb=" O GLY A 486 " pdb=" O HOH A1102 " model vdw 2.164 2.440 ... (remaining 109112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 76 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 7592 2.51 5 N 2104 2.21 5 O 2859 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.460 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: 12.620 Check model and map are aligned: 0.180 Process input model: 41.960 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.242 12830 Z= 0.398 Angle : 0.613 16.546 17742 Z= 0.298 Chirality : 0.039 0.224 2055 Planarity : 0.004 0.044 2001 Dihedral : 13.351 175.132 4877 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.16 (0.22), residues: 1367 helix: 1.01 (0.20), residues: 680 sheet: 0.20 (0.43), residues: 145 loop : -1.04 (0.24), residues: 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.289 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 132 average time/residue: 1.8160 time to fit residues: 255.7184 Evaluate side-chains 103 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.2001 time to fit residues: 2.2886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12830 Z= 0.281 Angle : 0.532 8.072 17742 Z= 0.276 Chirality : 0.040 0.189 2055 Planarity : 0.004 0.043 2001 Dihedral : 10.263 179.767 2350 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.40 (0.22), residues: 1367 helix: 1.19 (0.20), residues: 681 sheet: 0.13 (0.42), residues: 146 loop : -0.85 (0.25), residues: 540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 1.487 Fit side-chains outliers start: 32 outliers final: 18 residues processed: 122 average time/residue: 1.6346 time to fit residues: 214.1803 Evaluate side-chains 113 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 4 average time/residue: 1.0603 time to fit residues: 6.3174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 0.0040 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 128 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12830 Z= 0.176 Angle : 0.484 8.310 17742 Z= 0.246 Chirality : 0.038 0.181 2055 Planarity : 0.004 0.057 2001 Dihedral : 9.869 173.008 2350 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.63 % Favored : 97.15 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.55 (0.23), residues: 1367 helix: 1.32 (0.21), residues: 680 sheet: 0.27 (0.42), residues: 146 loop : -0.80 (0.25), residues: 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 1.349 Fit side-chains outliers start: 37 outliers final: 18 residues processed: 123 average time/residue: 1.5987 time to fit residues: 211.7687 Evaluate side-chains 108 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 3 average time/residue: 0.5709 time to fit residues: 3.9952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12830 Z= 0.212 Angle : 0.501 8.606 17742 Z= 0.254 Chirality : 0.038 0.183 2055 Planarity : 0.004 0.044 2001 Dihedral : 9.383 174.770 2350 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.54 (0.23), residues: 1367 helix: 1.27 (0.21), residues: 685 sheet: 0.33 (0.42), residues: 146 loop : -0.77 (0.25), residues: 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 1.453 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 120 average time/residue: 1.6828 time to fit residues: 217.0282 Evaluate side-chains 113 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 5 average time/residue: 0.7770 time to fit residues: 6.2662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 GLN D 158 GLN D 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12830 Z= 0.235 Angle : 0.499 9.251 17742 Z= 0.254 Chirality : 0.038 0.182 2055 Planarity : 0.004 0.037 2001 Dihedral : 8.758 166.386 2350 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.07 % Favored : 96.71 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.54 (0.23), residues: 1367 helix: 1.28 (0.21), residues: 684 sheet: 0.33 (0.42), residues: 146 loop : -0.79 (0.25), residues: 537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 1.425 Fit side-chains outliers start: 34 outliers final: 22 residues processed: 121 average time/residue: 1.6559 time to fit residues: 215.7052 Evaluate side-chains 115 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.8722 time to fit residues: 4.7973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.0040 chunk 33 optimal weight: 0.0670 chunk 136 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 12830 Z= 0.157 Angle : 0.484 10.466 17742 Z= 0.244 Chirality : 0.037 0.180 2055 Planarity : 0.003 0.046 2001 Dihedral : 8.413 162.934 2350 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.66 (0.23), residues: 1367 helix: 1.35 (0.21), residues: 687 sheet: 0.32 (0.42), residues: 146 loop : -0.69 (0.25), residues: 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.334 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 123 average time/residue: 1.5835 time to fit residues: 209.6093 Evaluate side-chains 115 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.7022 time to fit residues: 3.5069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.0370 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 85 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12830 Z= 0.180 Angle : 0.513 12.597 17742 Z= 0.256 Chirality : 0.037 0.181 2055 Planarity : 0.003 0.043 2001 Dihedral : 8.283 160.666 2350 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.71 % Favored : 97.07 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.67 (0.23), residues: 1367 helix: 1.33 (0.21), residues: 687 sheet: 0.36 (0.42), residues: 146 loop : -0.64 (0.26), residues: 534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 117 average time/residue: 1.5677 time to fit residues: 198.0280 Evaluate side-chains 114 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 1 average time/residue: 0.5764 time to fit residues: 2.7057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12830 Z= 0.211 Angle : 0.536 10.922 17742 Z= 0.269 Chirality : 0.038 0.181 2055 Planarity : 0.004 0.054 2001 Dihedral : 8.238 155.472 2350 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.07 % Favored : 96.71 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.57 (0.23), residues: 1367 helix: 1.22 (0.20), residues: 694 sheet: 0.35 (0.41), residues: 146 loop : -0.70 (0.26), residues: 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.380 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 121 average time/residue: 1.6379 time to fit residues: 212.7112 Evaluate side-chains 115 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 1 average time/residue: 0.3127 time to fit residues: 2.1247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0000 chunk 130 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 0.0570 chunk 133 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 overall best weight: 0.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12830 Z= 0.138 Angle : 0.511 11.831 17742 Z= 0.256 Chirality : 0.036 0.179 2055 Planarity : 0.003 0.050 2001 Dihedral : 8.011 152.093 2350 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.78 % Favored : 97.00 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.77 (0.23), residues: 1367 helix: 1.41 (0.21), residues: 684 sheet: 0.35 (0.41), residues: 149 loop : -0.57 (0.26), residues: 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.317 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 1.6130 time to fit residues: 212.0123 Evaluate side-chains 112 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.9054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 12830 Z= 0.230 Angle : 0.562 12.257 17742 Z= 0.287 Chirality : 0.038 0.181 2055 Planarity : 0.004 0.062 2001 Dihedral : 8.089 148.152 2350 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.63 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.61 (0.23), residues: 1367 helix: 1.25 (0.20), residues: 695 sheet: 0.39 (0.41), residues: 146 loop : -0.67 (0.26), residues: 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 21 residues processed: 115 average time/residue: 1.7079 time to fit residues: 211.8425 Evaluate side-chains 113 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.0020 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056308 restraints weight = 25914.302| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.34 r_work: 0.2591 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12830 Z= 0.201 Angle : 0.567 13.705 17742 Z= 0.285 Chirality : 0.037 0.180 2055 Planarity : 0.004 0.059 2001 Dihedral : 8.009 142.154 2350 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.07 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.63 (0.23), residues: 1367 helix: 1.26 (0.20), residues: 694 sheet: 0.43 (0.41), residues: 146 loop : -0.66 (0.26), residues: 527 =============================================================================== Job complete usr+sys time: 4477.14 seconds wall clock time: 81 minutes 4.24 seconds (4864.24 seconds total)