Starting phenix.real_space_refine (version: dev) on Fri Feb 24 11:19:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/02_2023/7mf3_23810_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/02_2023/7mf3_23810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/02_2023/7mf3_23810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/02_2023/7mf3_23810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/02_2023/7mf3_23810_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mf3_23810/02_2023/7mf3_23810_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.009 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 "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 22938 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7230 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 24, 'TRANS': 865} Chain breaks: 2 Chain: "B" Number of atoms: 7276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7276 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 24, 'TRANS': 871} Chain breaks: 2 Chain: "C" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1169 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1277 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "E" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1270 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1169 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1742 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1737 Classifications: {'peptide': 211} Link IDs: {'TRANS': 210} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.72, per 1000 atoms: 0.60 Number of scatterers: 22938 At special positions: 0 Unit cell: (101.587, 172.608, 229.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 129 16.00 P 6 15.00 Mg 4 11.99 O 4475 8.00 N 3965 7.00 C 14359 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=0, symmetry=0 Time building additional restraints: 10.27 Conformation dependent library (CDL) restraints added in 3.5 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 9 sheets defined 58.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.907A pdb=" N PHE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 141 removed outlier: 4.199A pdb=" N MET A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.860A pdb=" N GLN A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.834A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 346 through 364 removed outlier: 4.405A pdb=" N GLY A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 420 through 450 removed outlier: 3.890A pdb=" N LEU A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 507 removed outlier: 5.037A pdb=" N LEU A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU A 501 " --> pdb=" O MET A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 538 through 545 Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.791A pdb=" N GLU A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.938A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 676 Processing helix chain 'A' and resid 698 through 706 removed outlier: 4.878A pdb=" N GLU A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 718 Processing helix chain 'A' and resid 727 through 734 Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.879A pdb=" N CYS A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 766 No H-bonds generated for 'chain 'A' and resid 764 through 766' Processing helix chain 'A' and resid 778 through 783 removed outlier: 4.039A pdb=" N LEU A 781 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 783 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 791 Processing helix chain 'A' and resid 793 through 839 removed outlier: 4.464A pdb=" N TRP A 838 " --> pdb=" O LYS A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 853 removed outlier: 4.276A pdb=" N VAL A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) Proline residue: A 849 - end of helix removed outlier: 4.113A pdb=" N GLN A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 948 removed outlier: 4.016A pdb=" N LYS A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.547A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 153 through 166 removed outlier: 3.725A pdb=" N TYR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 219 through 233 removed outlier: 4.056A pdb=" N ASN B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 329 through 342 removed outlier: 3.947A pdb=" N THR B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 363 Processing helix chain 'B' and resid 382 through 389 removed outlier: 3.869A pdb=" N CYS B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 420 through 450 Processing helix chain 'B' and resid 477 through 508 Processing helix chain 'B' and resid 522 through 528 removed outlier: 3.773A pdb=" N LEU B 527 " --> pdb=" O PRO B 523 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE B 528 " --> pdb=" O CYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 546 removed outlier: 4.128A pdb=" N TRP B 546 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 563 Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 620 through 626 Processing helix chain 'B' and resid 662 through 674 Processing helix chain 'B' and resid 698 through 708 Processing helix chain 'B' and resid 710 through 719 Processing helix chain 'B' and resid 727 through 733 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 764 through 766 No H-bonds generated for 'chain 'B' and resid 764 through 766' Processing helix chain 'B' and resid 780 through 838 removed outlier: 3.873A pdb=" N THR B 793 " --> pdb=" O ASP B 789 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 795 " --> pdb=" O LYS B 791 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 828 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B 830 " --> pdb=" O GLN B 826 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA B 831 " --> pdb=" O ARG B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 removed outlier: 3.984A pdb=" N PHE B 844 " --> pdb=" O TRP B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 852 Processing helix chain 'B' and resid 856 through 947 Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.617A pdb=" N LEU C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 85 through 95 Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.574A pdb=" N ARG C 109 " --> pdb=" O GLY C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 4.900A pdb=" N VAL C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 149 removed outlier: 3.784A pdb=" N SER C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.870A pdb=" N ASP D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 58 " --> pdb=" O HIS D 54 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 Processing helix chain 'D' and resid 82 through 92 removed outlier: 4.116A pdb=" N LYS D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 143 removed outlier: 4.235A pdb=" N GLU D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N MET D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR D 142 " --> pdb=" O VAL D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'E' and resid 27 through 40 removed outlier: 4.419A pdb=" N GLN E 31 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 removed outlier: 3.834A pdb=" N ASP E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 82 through 92 removed outlier: 4.198A pdb=" N LEU E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 89 " --> pdb=" O PHE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 109 removed outlier: 4.454A pdb=" N PHE E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 126 Processing helix chain 'E' and resid 136 through 144 removed outlier: 3.588A pdb=" N GLU E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N MET E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 155 through 163 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 28 through 37 Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.797A pdb=" N LYS F 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 Proline residue: F 71 - end of helix Processing helix chain 'F' and resid 85 through 95 Processing helix chain 'F' and resid 105 through 114 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'G' and resid 1413 through 1526 removed outlier: 3.598A pdb=" N LYS G1458 " --> pdb=" O LYS G1455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU G1465 " --> pdb=" O MET G1462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA G1484 " --> pdb=" O GLU G1481 " (cutoff:3.500A) Processing helix chain 'G' and resid 1532 through 1622 removed outlier: 3.592A pdb=" N GLU G1535 " --> pdb=" O ASN G1532 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG G1541 " --> pdb=" O LYS G1538 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G1576 " --> pdb=" O VAL G1573 " (cutoff:3.500A) Processing helix chain 'H' and resid 1415 through 1523 removed outlier: 3.908A pdb=" N ALA H1419 " --> pdb=" O GLU H1415 " (cutoff:3.500A) Processing helix chain 'H' and resid 1536 through 1620 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= B, first strand: chain 'A' and resid 115 through 117 removed outlier: 7.806A pdb=" N PHE A 681 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N VAL A 123 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG A 683 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 174 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS A 684 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 176 " --> pdb=" O CYS A 684 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.634A pdb=" N ASN A 723 " --> pdb=" O PHE A 776 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 249 through 256 removed outlier: 3.518A pdb=" N GLY A 264 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= F, first strand: chain 'B' and resid 57 through 61 removed outlier: 3.767A pdb=" N LYS B 66 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 121 through 124 removed outlier: 8.465A pdb=" N VAL B 682 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 174 " --> pdb=" O VAL B 682 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N CYS B 684 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 176 " --> pdb=" O CYS B 684 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 171 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 464 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 175 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER B 459 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 583 through 585 removed outlier: 3.528A pdb=" N GLY B 588 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 724 through 726 removed outlier: 3.691A pdb=" N ILE B 725 " --> pdb=" O ILE B 774 " (cutoff:3.500A) 1218 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7480 1.34 - 1.46: 2872 1.46 - 1.58: 12700 1.58 - 1.70: 6 1.70 - 1.82: 220 Bond restraints: 23278 Sorted by residual: bond pdb=" O3 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O3 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" O4 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" O2 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O4 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.30e+00 ... (remaining 23273 not shown) Histogram of bond angle deviations from ideal: 97.38 - 105.13: 292 105.13 - 112.87: 12160 112.87 - 120.62: 10854 120.62 - 128.36: 7854 128.36 - 136.11: 106 Bond angle restraints: 31266 Sorted by residual: angle pdb=" C GLN B 327 " pdb=" N ASP B 328 " pdb=" CA ASP B 328 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C THR B 176 " pdb=" CA THR B 176 " pdb=" CB THR B 176 " ideal model delta sigma weight residual 109.80 102.34 7.46 1.70e+00 3.46e-01 1.93e+01 angle pdb=" N GLY B 182 " pdb=" CA GLY B 182 " pdb=" C GLY B 182 " ideal model delta sigma weight residual 115.36 109.63 5.73 1.33e+00 5.65e-01 1.86e+01 angle pdb=" N LYS B 183 " pdb=" CA LYS B 183 " pdb=" C LYS B 183 " ideal model delta sigma weight residual 113.19 108.39 4.80 1.19e+00 7.06e-01 1.63e+01 angle pdb=" O ARG A 815 " pdb=" C ARG A 815 " pdb=" N GLN A 816 " ideal model delta sigma weight residual 122.03 126.10 -4.07 1.04e+00 9.25e-01 1.53e+01 ... (remaining 31261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 14110 35.84 - 71.68: 260 71.68 - 107.51: 38 107.51 - 143.35: 2 143.35 - 179.19: 1 Dihedral angle restraints: 14411 sinusoidal: 6156 harmonic: 8255 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual 300.00 120.81 179.19 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.24 116.24 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" O2A ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PA ADP A2001 " pdb=" PB ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 49.62 -109.62 1 2.00e+01 2.50e-03 3.21e+01 ... (remaining 14408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3050 0.067 - 0.134: 331 0.134 - 0.202: 17 0.202 - 0.269: 0 0.269 - 0.336: 2 Chirality restraints: 3400 Sorted by residual: chirality pdb=" CA ARG A 815 " pdb=" N ARG A 815 " pdb=" C ARG A 815 " pdb=" CB ARG A 815 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA THR B 176 " pdb=" N THR B 176 " pdb=" C THR B 176 " pdb=" CB THR B 176 " both_signs ideal model delta sigma weight residual False 2.53 2.80 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR A 404 " pdb=" CA THR A 404 " pdb=" OG1 THR A 404 " pdb=" CG2 THR A 404 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 3397 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C GLN B 327 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN B 327 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 328 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 97 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO E 98 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 228 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 229 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.029 5.00e-02 4.00e+02 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 296 2.57 - 3.15: 20032 3.15 - 3.73: 37630 3.73 - 4.32: 47985 4.32 - 4.90: 74134 Nonbonded interactions: 180077 Sorted by model distance: nonbonded pdb=" O ILE D 48 " pdb=" OD1 ASP D 49 " model vdw 1.985 3.040 nonbonded pdb=" OD1 ASP E 41 " pdb="MG MG E 200 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP E 45 " pdb="MG MG E 200 " model vdw 2.100 2.170 nonbonded pdb=" CB SER A 246 " pdb="MG MG A2003 " model vdw 2.129 2.570 nonbonded pdb=" O ASP B 618 " pdb=" OD1 ASP B 618 " model vdw 2.152 3.040 ... (remaining 180072 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 'A' selection = (chain 'B' and (resid 29 through 200 or resid 218 through 636 or resid 651 throu \ gh 949 or resid 2001 through 2003)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'D' and (resid 15 through 171 or resid 200)) selection = chain 'E' } ncs_group { reference = (chain 'G' and resid 1413 through 1623) selection = chain 'H' } 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 129 5.16 5 C 14359 2.51 5 N 3965 2.21 5 O 4475 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=0.00 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: 7.390 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: 0.020 Extract box with map and model: 28.800 Check model and map are aligned: 0.320 Process input model: 59.720 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 23278 Z= 0.178 Angle : 0.682 10.266 31266 Z= 0.361 Chirality : 0.042 0.336 3400 Planarity : 0.004 0.052 4115 Dihedral : 15.412 179.189 9031 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2798 helix: 1.04 (0.13), residues: 1601 sheet: -1.60 (0.41), residues: 148 loop : -2.05 (0.18), residues: 1049 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.4435 time to fit residues: 162.4572 Evaluate side-chains 143 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 4.9990 chunk 210 optimal weight: 0.0010 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 142 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1574 ASN G1605 HIS ** H1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23278 Z= 0.165 Angle : 0.651 9.546 31266 Z= 0.341 Chirality : 0.040 0.156 3400 Planarity : 0.005 0.055 4115 Dihedral : 6.408 154.130 3051 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.16), residues: 2798 helix: 0.87 (0.13), residues: 1620 sheet: -1.46 (0.41), residues: 148 loop : -2.11 (0.18), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 164 average time/residue: 0.3551 time to fit residues: 93.9936 Evaluate side-chains 144 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 3.060 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2230 time to fit residues: 6.6426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 69 optimal weight: 0.1980 chunk 252 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 250 optimal weight: 0.0770 chunk 86 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1607 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 23278 Z= 0.150 Angle : 0.611 9.680 31266 Z= 0.315 Chirality : 0.038 0.151 3400 Planarity : 0.004 0.045 4115 Dihedral : 6.250 145.645 3051 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2798 helix: 0.78 (0.13), residues: 1634 sheet: -1.22 (0.42), residues: 148 loop : -2.13 (0.19), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 160 average time/residue: 0.3454 time to fit residues: 90.5588 Evaluate side-chains 140 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2296 time to fit residues: 6.8295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 253 optimal weight: 0.7980 chunk 268 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN F 7 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1607 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 23278 Z= 0.158 Angle : 0.603 10.085 31266 Z= 0.310 Chirality : 0.038 0.149 3400 Planarity : 0.004 0.046 4115 Dihedral : 6.189 141.929 3051 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2798 helix: 0.73 (0.13), residues: 1636 sheet: -1.17 (0.42), residues: 148 loop : -2.14 (0.19), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 165 average time/residue: 0.3326 time to fit residues: 90.8890 Evaluate side-chains 149 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2510 time to fit residues: 10.3983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 5.9990 chunk 152 optimal weight: 0.0870 chunk 3 optimal weight: 0.0770 chunk 200 optimal weight: 0.0370 chunk 110 optimal weight: 0.5980 chunk 229 optimal weight: 0.0050 chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 241 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.1608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 502 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 ASN B 948 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 23278 Z= 0.139 Angle : 0.600 9.888 31266 Z= 0.306 Chirality : 0.038 0.177 3400 Planarity : 0.004 0.047 4115 Dihedral : 6.037 134.797 3051 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2798 helix: 0.72 (0.13), residues: 1642 sheet: -1.01 (0.43), residues: 148 loop : -2.06 (0.19), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 154 average time/residue: 0.3163 time to fit residues: 82.1571 Evaluate side-chains 141 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 2.916 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2423 time to fit residues: 4.9825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 268 optimal weight: 0.3980 chunk 223 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN B 593 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 23278 Z= 0.140 Angle : 0.595 10.928 31266 Z= 0.303 Chirality : 0.038 0.192 3400 Planarity : 0.004 0.046 4115 Dihedral : 5.957 129.784 3051 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2798 helix: 0.74 (0.13), residues: 1642 sheet: -1.07 (0.42), residues: 148 loop : -2.04 (0.19), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 155 average time/residue: 0.3302 time to fit residues: 86.4162 Evaluate side-chains 141 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2110 time to fit residues: 6.3716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1574 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 23278 Z= 0.235 Angle : 0.668 12.938 31266 Z= 0.344 Chirality : 0.041 0.410 3400 Planarity : 0.005 0.056 4115 Dihedral : 6.258 130.571 3051 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2798 helix: 0.60 (0.13), residues: 1636 sheet: -1.43 (0.41), residues: 148 loop : -2.09 (0.19), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 141 average time/residue: 0.3254 time to fit residues: 77.4910 Evaluate side-chains 135 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2226 time to fit residues: 8.1002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 182 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 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 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 23278 Z= 0.156 Angle : 0.642 17.630 31266 Z= 0.323 Chirality : 0.039 0.198 3400 Planarity : 0.004 0.045 4115 Dihedral : 6.171 127.617 3051 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2798 helix: 0.64 (0.13), residues: 1638 sheet: -1.37 (0.41), residues: 148 loop : -2.12 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 138 average time/residue: 0.3431 time to fit residues: 80.3650 Evaluate side-chains 134 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 3.159 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2301 time to fit residues: 6.6670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 0.6980 chunk 256 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23278 Z= 0.204 Angle : 0.672 17.621 31266 Z= 0.342 Chirality : 0.039 0.202 3400 Planarity : 0.004 0.043 4115 Dihedral : 6.277 123.020 3051 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2798 helix: 0.53 (0.13), residues: 1638 sheet: -1.57 (0.40), residues: 148 loop : -2.17 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 140 average time/residue: 0.3443 time to fit residues: 81.6559 Evaluate side-chains 133 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 3.334 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2583 time to fit residues: 7.0710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1432 GLN ** G1433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 23278 Z= 0.260 Angle : 0.737 15.393 31266 Z= 0.377 Chirality : 0.042 0.220 3400 Planarity : 0.005 0.044 4115 Dihedral : 6.569 113.989 3051 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2798 helix: 0.38 (0.13), residues: 1624 sheet: -1.98 (0.40), residues: 145 loop : -2.22 (0.19), residues: 1029 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 131 average time/residue: 0.3450 time to fit residues: 75.7376 Evaluate side-chains 130 residues out of total 2479 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2341 time to fit residues: 6.9952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 220 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 226 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** F 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1445 GLN ** G1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.054389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.043275 restraints weight = 244404.180| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 7.50 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 23278 Z= 0.157 Angle : 0.682 18.379 31266 Z= 0.342 Chirality : 0.040 0.204 3400 Planarity : 0.004 0.045 4115 Dihedral : 6.253 100.641 3051 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2798 helix: 0.51 (0.13), residues: 1631 sheet: -1.71 (0.40), residues: 150 loop : -2.20 (0.19), residues: 1017 =============================================================================== Job complete usr+sys time: 4305.99 seconds wall clock time: 79 minutes 58.25 seconds (4798.25 seconds total)