Starting phenix.real_space_refine on Thu Feb 15 16:01:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_26645_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_26645.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_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_2024/7uob_26645_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_26645_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_26645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_26645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_26645_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uob_26645/02_2024/7uob_26645_neut_updated.pdb" } resolution = 2.68 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= 0.038 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.19, per 1000 atoms: 0.57 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: 6.02 Conformation dependent library (CDL) restraints added in 2.1 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: 6.15 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: 5.53 Time building geometry restraints manager: 6.18 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: 7510 35.03 - 70.05: 232 70.05 - 105.08: 28 105.08 - 140.11: 2 140.11 - 175.13: 5 Dihedral angle restraints: 7777 sinusoidal: 3690 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 7774 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 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.330 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 44.380 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 16.246 175.132 5131 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 % Allowed : 7.15 % Favored : 91.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.017 0.002 PHE A 652 TYR 0.013 0.002 TYR A 515 ARG 0.003 0.001 ARG A 132 *********************** 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 : 1.395 Fit side-chains REVERT: A 235 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.6000 (t70) outliers start: 18 outliers final: 5 residues processed: 132 average time/residue: 1.7923 time to fit residues: 252.5703 Evaluate side-chains 103 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 114 CYS 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: 0.7938 moved from start: 0.1510 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= 0.280 Angle : 0.532 8.071 17742 Z= 0.276 Chirality : 0.040 0.191 2055 Planarity : 0.004 0.043 2001 Dihedral : 16.690 179.389 2613 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 2.69 % Allowed : 9.09 % Favored : 88.22 % 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: 0.12 (0.42), residues: 146 loop : -0.85 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.021 0.002 PHE B 49 TYR 0.013 0.001 TYR A 788 ARG 0.007 0.000 ARG D 51 *********************** 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 : 1.326 Fit side-chains REVERT: A 75 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6523 (p90) REVERT: A 615 MET cc_start: 0.8204 (ptt) cc_final: 0.7969 (ptt) outliers start: 32 outliers final: 19 residues processed: 123 average time/residue: 1.7142 time to fit residues: 225.7083 Evaluate side-chains 114 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 70 MET 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: 0.9980 chunk 106 optimal weight: 0.0170 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 128 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN D 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12830 Z= 0.179 Angle : 0.490 8.399 17742 Z= 0.249 Chirality : 0.038 0.181 2055 Planarity : 0.004 0.063 2001 Dihedral : 16.497 174.333 2610 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.78 % Favored : 97.00 % Rotamer: Outliers : 2.53 % Allowed : 10.27 % Favored : 87.21 % 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: 0.52 (0.23), residues: 1367 helix: 1.29 (0.21), residues: 680 sheet: 0.25 (0.42), residues: 146 loop : -0.79 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.013 0.001 PHE B 49 TYR 0.012 0.001 TYR A 788 ARG 0.009 0.000 ARG A 105 *********************** 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 131 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 1.446 Fit side-chains outliers start: 30 outliers final: 11 residues processed: 118 average time/residue: 1.6934 time to fit residues: 213.9504 Evaluate side-chains 102 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 114 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 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: 0.9990 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12830 Z= 0.200 Angle : 0.500 8.640 17742 Z= 0.252 Chirality : 0.038 0.182 2055 Planarity : 0.004 0.045 2001 Dihedral : 16.226 176.718 2606 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 2.44 % Allowed : 10.35 % Favored : 87.21 % 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: 0.56 (0.23), residues: 1367 helix: 1.28 (0.21), residues: 682 sheet: 0.34 (0.42), residues: 146 loop : -0.75 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.024 0.001 PHE D 15 TYR 0.014 0.001 TYR A 788 ARG 0.009 0.000 ARG D 51 *********************** 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 126 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.435 Fit side-chains REVERT: A 75 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6971 (p90) REVERT: A 924 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7823 (mmm) outliers start: 29 outliers final: 13 residues processed: 117 average time/residue: 1.7279 time to fit residues: 216.5341 Evaluate side-chains 107 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET 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: 0.5980 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 0.0030 chunk 56 optimal weight: 0.0980 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12830 Z= 0.192 Angle : 0.495 9.432 17742 Z= 0.251 Chirality : 0.037 0.181 2055 Planarity : 0.004 0.039 2001 Dihedral : 15.769 167.960 2606 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 2.36 % Allowed : 10.77 % Favored : 86.87 % 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: 1.32 (0.21), residues: 683 sheet: 0.39 (0.42), residues: 146 loop : -0.74 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.001 PHE A 694 TYR 0.013 0.001 TYR A 788 ARG 0.009 0.000 ARG B 96 *********************** 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 123 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.431 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 115 average time/residue: 1.6801 time to fit residues: 207.2951 Evaluate side-chains 114 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 158 GLN 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: 0.9980 chunk 26 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.0040 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: 0.9980 chunk 131 optimal weight: 2.9990 overall best weight: 0.5370 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12830 Z= 0.169 Angle : 0.490 10.414 17742 Z= 0.246 Chirality : 0.037 0.180 2055 Planarity : 0.003 0.047 2001 Dihedral : 15.707 165.754 2606 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.63 % Rotamer: Outliers : 1.94 % Allowed : 12.04 % Favored : 86.03 % 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: 1.36 (0.21), residues: 683 sheet: 0.37 (0.41), residues: 146 loop : -0.70 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE D 15 TYR 0.013 0.001 TYR A 788 ARG 0.011 0.000 ARG D 51 *********************** 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 122 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.264 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 115 average time/residue: 1.6969 time to fit residues: 208.7466 Evaluate side-chains 109 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 137 THR 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: 0.9990 chunk 99 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 10.9990 chunk 85 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN D 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12830 Z= 0.235 Angle : 0.538 12.582 17742 Z= 0.270 Chirality : 0.038 0.182 2055 Planarity : 0.004 0.042 2001 Dihedral : 15.710 162.732 2605 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.78 % Favored : 97.00 % Rotamer: Outliers : 2.19 % Allowed : 12.63 % Favored : 85.19 % 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: 0.53 (0.23), residues: 1367 helix: 1.22 (0.20), residues: 690 sheet: 0.38 (0.41), residues: 146 loop : -0.77 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.001 PHE A 694 TYR 0.015 0.001 TYR A 788 ARG 0.011 0.001 ARG B 96 *********************** 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 125 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.499 Fit side-chains REVERT: A 924 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7814 (mmm) outliers start: 26 outliers final: 20 residues processed: 118 average time/residue: 1.7091 time to fit residues: 216.7286 Evaluate side-chains 116 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 0.0470 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 overall best weight: 0.3892 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12830 Z= 0.158 Angle : 0.531 12.243 17742 Z= 0.265 Chirality : 0.037 0.179 2055 Planarity : 0.004 0.056 2001 Dihedral : 15.651 160.266 2605 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 1.26 % Allowed : 13.97 % Favored : 84.76 % 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: 0.68 (0.23), residues: 1367 helix: 1.37 (0.21), residues: 680 sheet: 0.42 (0.41), residues: 146 loop : -0.68 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.004 0.000 HIS C 36 PHE 0.022 0.001 PHE D 49 TYR 0.012 0.001 TYR A 788 ARG 0.014 0.000 ARG D 51 *********************** 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 116 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.389 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 113 average time/residue: 1.7279 time to fit residues: 208.6892 Evaluate side-chains 108 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 119 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 133 optimal weight: 0.0030 chunk 81 optimal weight: 0.9990 overall best weight: 0.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN D 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12830 Z= 0.145 Angle : 0.527 11.859 17742 Z= 0.265 Chirality : 0.036 0.178 2055 Planarity : 0.004 0.052 2001 Dihedral : 15.629 158.946 2605 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 1.60 % Allowed : 13.80 % Favored : 84.60 % 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: 0.78 (0.23), residues: 1367 helix: 1.42 (0.21), residues: 680 sheet: 0.50 (0.41), residues: 146 loop : -0.59 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 PHE 0.012 0.001 PHE D 49 TYR 0.014 0.001 TYR B 22 ARG 0.013 0.001 ARG B 96 *********************** 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 118 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.256 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 1.6622 time to fit residues: 203.3253 Evaluate side-chains 104 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12830 Z= 0.281 Angle : 0.599 12.162 17742 Z= 0.302 Chirality : 0.039 0.183 2055 Planarity : 0.004 0.061 2001 Dihedral : 15.694 153.936 2605 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.07 % Favored : 96.71 % Rotamer: Outliers : 1.18 % Allowed : 14.65 % Favored : 84.18 % 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: 1.20 (0.20), residues: 690 sheet: 0.46 (0.41), residues: 146 loop : -0.74 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.015 0.001 PHE A 694 TYR 0.016 0.001 TYR A 788 ARG 0.014 0.001 ARG D 51 ********************** 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 110 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.477 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 109 average time/residue: 1.8792 time to fit residues: 219.5081 Evaluate side-chains 108 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.083652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.050524 restraints weight = 24749.041| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.28 r_work: 0.2593 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12830 Z= 0.209 Angle : 0.564 12.287 17742 Z= 0.284 Chirality : 0.038 0.181 2055 Planarity : 0.004 0.079 2001 Dihedral : 15.661 148.115 2605 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.85 % Favored : 96.93 % Rotamer: Outliers : 1.09 % Allowed : 14.73 % Favored : 84.18 % 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: 0.59 (0.23), residues: 1367 helix: 1.26 (0.20), residues: 688 sheet: 0.53 (0.41), residues: 146 loop : -0.74 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.016 0.001 PHE D 49 TYR 0.014 0.001 TYR A 788 ARG 0.015 0.001 ARG D 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.32 seconds wall clock time: 84 minutes 38.99 seconds (5078.99 seconds total)