Starting phenix.real_space_refine on Wed Jan 22 12:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lmb_23439/01_2025/7lmb_23439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lmb_23439/01_2025/7lmb_23439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lmb_23439/01_2025/7lmb_23439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lmb_23439/01_2025/7lmb_23439.map" model { file = "/net/cci-nas-00/data/ceres_data/7lmb_23439/01_2025/7lmb_23439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lmb_23439/01_2025/7lmb_23439.cif" } resolution = 3.8 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 162 5.49 5 S 65 5.16 5 C 11247 2.51 5 N 3115 2.21 5 O 3908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3189 Classifications: {'RNA': 151} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 18, 'rna3p_pur': 64, 'rna3p_pyr': 60} Link IDs: {'rna2p': 26, 'rna3p': 124} Chain breaks: 1 Chain: "C" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain breaks: 1 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1367 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1188 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 885 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1542 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 1, 'TRANS': 182} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13842 SG CYS D 572 72.985 72.349 83.189 1.00 61.65 S ATOM 13863 SG CYS D 575 74.480 73.378 86.248 1.00 63.38 S Time building chain proxies: 10.32, per 1000 atoms: 0.56 Number of scatterers: 18498 At special positions: 0 Unit cell: (148.24, 160.48, 118.32, 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) Zn 1 29.99 S 65 16.00 P 162 15.00 O 3908 8.00 N 3115 7.00 C 11247 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 575 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3562 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 19 sheets defined 47.3% alpha, 16.7% beta 43 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 6.58 Creating SS restraints... Processing helix chain 'H' and resid 115 through 131 removed outlier: 3.784A pdb=" N CYS H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 138 removed outlier: 4.021A pdb=" N HIS H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 147 Processing helix chain 'H' and resid 155 through 160 removed outlier: 3.700A pdb=" N LEU H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 155 through 160' Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.530A pdb=" N GLN H 166 " --> pdb=" O ASN H 162 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE H 167 " --> pdb=" O LYS H 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 162 through 167' Processing helix chain 'H' and resid 203 through 215 Processing helix chain 'H' and resid 391 through 401 removed outlier: 4.185A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 480 removed outlier: 4.828A pdb=" N GLN H 477 " --> pdb=" O ARG H 473 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS H 478 " --> pdb=" O LEU H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 531 Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.890A pdb=" N VAL A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 134 through 144 Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.645A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.878A pdb=" N GLN A 228 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.562A pdb=" N ARG A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.845A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.160A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.573A pdb=" N PHE A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.676A pdb=" N TYR A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 467 removed outlier: 3.640A pdb=" N TYR A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.532A pdb=" N GLU A 508 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 560 through 577 removed outlier: 5.556A pdb=" N ASP A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.676A pdb=" N ILE A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 794 removed outlier: 4.080A pdb=" N SER A 783 " --> pdb=" O GLY A 779 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 removed outlier: 4.253A pdb=" N LYS A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 removed outlier: 3.579A pdb=" N ALA A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.794A pdb=" N GLN A 848 " --> pdb=" O PHE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 911 through 926 removed outlier: 3.987A pdb=" N LYS A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.648A pdb=" N MET A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 972 through 980 removed outlier: 4.736A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 removed outlier: 4.013A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A1009 " --> pdb=" O CYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1038 removed outlier: 3.754A pdb=" N LYS A1018 " --> pdb=" O ASN A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1075 removed outlier: 3.894A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 removed outlier: 3.846A pdb=" N ASN A1094 " --> pdb=" O PHE A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 4.354A pdb=" N THR A1102 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1109 removed outlier: 4.342A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 526 removed outlier: 3.793A pdb=" N ILE D 520 " --> pdb=" O SER D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 622 through 634 removed outlier: 3.561A pdb=" N GLY D 634 " --> pdb=" O CYS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 679 through 696 removed outlier: 3.667A pdb=" N LYS D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 123 removed outlier: 4.205A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 175 removed outlier: 3.871A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY E 173 " --> pdb=" O GLN E 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 22 removed outlier: 3.874A pdb=" N ALA F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG F 22 " --> pdb=" O MET F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.902A pdb=" N PHE F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 114 through 119' Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.032A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.952A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 156 removed outlier: 3.516A pdb=" N ILE G 155 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 161 Processing helix chain 'G' and resid 162 through 184 Processing sheet with id=AA1, first strand: chain 'H' and resid 153 through 154 Processing sheet with id=AA2, first strand: chain 'H' and resid 407 through 411 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.724A pdb=" N ALA A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 159 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 168 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.724A pdb=" N ALA A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 159 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 168 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA7, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 532 through 535 Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 615 Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 537 removed outlier: 6.398A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 669 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR D 670 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 541 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 649 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AB3, first strand: chain 'D' and resid 661 through 662 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 33 Processing sheet with id=AB5, first strand: chain 'E' and resid 31 through 33 removed outlier: 5.886A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL E 98 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 85 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 59 removed outlier: 3.800A pdb=" N PHE E 64 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.809A pdb=" N HIS F 53 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS F 24 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.866A pdb=" N ILE G 114 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG G 49 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR G 112 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER G 51 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TRP G 110 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 15.980A pdb=" N LYS G 80 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 13.061A pdb=" N LEU G 125 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N ILE G 82 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ILE G 127 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN G 84 " --> pdb=" O ILE G 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.866A pdb=" N ILE G 114 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG G 49 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR G 112 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER G 51 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TRP G 110 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 15.980A pdb=" N LYS G 80 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 13.061A pdb=" N LEU G 125 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N ILE G 82 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ILE G 127 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN G 84 " --> pdb=" O ILE G 127 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.995A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 106 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS G 132 " --> pdb=" O ILE G 106 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 9.59 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4796 1.33 - 1.45: 4335 1.45 - 1.57: 9620 1.57 - 1.69: 320 1.69 - 1.81: 97 Bond restraints: 19168 Sorted by residual: bond pdb=" CA ASN A 465 " pdb=" C ASN A 465 " ideal model delta sigma weight residual 1.522 1.481 0.040 1.72e-02 3.38e+03 5.47e+00 bond pdb=" CB VAL A 119 " pdb=" CG2 VAL A 119 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" O5' C B 49 " pdb=" C5' C B 49 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.66e+00 bond pdb=" CB CYS A1001 " pdb=" SG CYS A1001 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CB ILE A 478 " pdb=" CG2 ILE A 478 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.47e+00 ... (remaining 19163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 25349 1.37 - 2.74: 1085 2.74 - 4.11: 104 4.11 - 5.48: 28 5.48 - 6.85: 10 Bond angle restraints: 26576 Sorted by residual: angle pdb=" N LYS A 657 " pdb=" CA LYS A 657 " pdb=" C LYS A 657 " ideal model delta sigma weight residual 113.18 118.56 -5.38 1.21e+00 6.83e-01 1.97e+01 angle pdb=" CA ASN A 465 " pdb=" C ASN A 465 " pdb=" N LYS A 466 " ideal model delta sigma weight residual 118.59 124.16 -5.57 1.63e+00 3.76e-01 1.17e+01 angle pdb=" N GLY D 596 " pdb=" CA GLY D 596 " pdb=" C GLY D 596 " ideal model delta sigma weight residual 110.73 117.21 -6.48 1.90e+00 2.77e-01 1.16e+01 angle pdb=" CA TYR G 26 " pdb=" CB TYR G 26 " pdb=" CG TYR G 26 " ideal model delta sigma weight residual 113.90 119.18 -5.28 1.80e+00 3.09e-01 8.61e+00 angle pdb=" C PHE G 25 " pdb=" N TYR G 26 " pdb=" CA TYR G 26 " ideal model delta sigma weight residual 122.31 116.81 5.50 2.00e+00 2.50e-01 7.55e+00 ... (remaining 26571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 11115 35.73 - 71.45: 531 71.45 - 107.18: 61 107.18 - 142.91: 1 142.91 - 178.63: 8 Dihedral angle restraints: 11716 sinusoidal: 6238 harmonic: 5478 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 200.00 53.91 146.09 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' C B 43 " pdb=" C1' C B 43 " pdb=" N1 C B 43 " pdb=" C2 C B 43 " ideal model delta sinusoidal sigma weight residual -160.00 -26.18 -133.82 1 1.50e+01 4.44e-03 7.22e+01 dihedral pdb=" O4' U B 41 " pdb=" C1' U B 41 " pdb=" N1 U B 41 " pdb=" C2 U B 41 " ideal model delta sinusoidal sigma weight residual -128.00 50.63 -178.63 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2334 0.047 - 0.094: 604 0.094 - 0.141: 112 0.141 - 0.188: 14 0.188 - 0.234: 1 Chirality restraints: 3065 Sorted by residual: chirality pdb=" CA LYS A 657 " pdb=" N LYS A 657 " pdb=" C LYS A 657 " pdb=" CB LYS A 657 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' C B 49 " pdb=" C4' C B 49 " pdb=" O3' C B 49 " pdb=" C2' C B 49 " both_signs ideal model delta sigma weight residual False -2.48 -2.64 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CB ILE H 464 " pdb=" CA ILE H 464 " pdb=" CG1 ILE H 464 " pdb=" CG2 ILE H 464 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 3062 not shown) Planarity restraints: 2809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " 0.015 2.00e-02 2.50e+03 1.54e-02 7.10e+00 pdb=" N9 DG C 17 " -0.012 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " -0.041 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 536 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO A 537 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 656 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ASN A 656 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN A 656 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 657 " -0.011 2.00e-02 2.50e+03 ... (remaining 2806 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 914 2.71 - 3.26: 18684 3.26 - 3.80: 29429 3.80 - 4.35: 36553 4.35 - 4.90: 58013 Nonbonded interactions: 143593 Sorted by model distance: nonbonded pdb=" N CYS D 575 " pdb="ZN ZN D 900 " model vdw 2.160 2.310 nonbonded pdb=" OG SER A 823 " pdb=" OD1 ASN A 826 " model vdw 2.198 3.040 nonbonded pdb=" OP1 A B 136 " pdb=" OG SER A 972 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLN A1008 " pdb=" OH TYR A1025 " model vdw 2.206 3.040 nonbonded pdb=" O PHE A 525 " pdb=" NZ LYS A 555 " model vdw 2.213 3.120 ... (remaining 143588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 51.300 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.004 0.045 19168 Z= 0.259 Angle : 0.634 6.849 26576 Z= 0.358 Chirality : 0.043 0.234 3065 Planarity : 0.004 0.051 2809 Dihedral : 19.411 178.633 8154 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % 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: -3.71 (0.17), residues: 1809 helix: -1.80 (0.16), residues: 731 sheet: -2.61 (0.30), residues: 242 loop : -3.01 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 604 HIS 0.006 0.001 HIS A 949 PHE 0.022 0.002 PHE D 662 TYR 0.021 0.002 TYR G 26 ARG 0.003 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 PHE cc_start: 0.4481 (t80) cc_final: 0.4007 (t80) REVERT: F 21 PHE cc_start: 0.7468 (m-10) cc_final: 0.7122 (m-10) REVERT: F 120 ASP cc_start: 0.5892 (p0) cc_final: 0.5206 (p0) REVERT: G 130 MET cc_start: 0.7285 (mtm) cc_final: 0.7052 (mtm) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.3177 time to fit residues: 161.9938 Evaluate side-chains 198 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.0050 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 468 ASN H 484 ASN H 485 ASN ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 248 ASN A 320 ASN A 324 ASN A 349 GLN A 364 ASN A 440 GLN A 482 HIS A 733 ASN A 747 ASN A 748 HIS ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 841 ASN A 872 ASN A 901 GLN ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN D 531 GLN D 629 ASN D 633 ASN D 635 GLN E 159 HIS ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS G 34 GLN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.149504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.119092 restraints weight = 35590.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118751 restraints weight = 40389.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119445 restraints weight = 42008.974| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19168 Z= 0.199 Angle : 0.592 8.042 26576 Z= 0.316 Chirality : 0.041 0.155 3065 Planarity : 0.004 0.048 2809 Dihedral : 20.140 179.307 4331 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.88 % Allowed : 11.93 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1809 helix: -0.10 (0.18), residues: 746 sheet: -2.03 (0.32), residues: 239 loop : -2.40 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 604 HIS 0.005 0.001 HIS F 53 PHE 0.030 0.002 PHE H 524 TYR 0.029 0.001 TYR G 26 ARG 0.005 0.000 ARG E 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 1.775 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: H 473 ARG cc_start: 0.5819 (tpp-160) cc_final: 0.5350 (ptp-170) REVERT: H 497 ASP cc_start: 0.6450 (t0) cc_final: 0.5936 (m-30) REVERT: A 285 ILE cc_start: 0.7485 (mt) cc_final: 0.7218 (mm) REVERT: A 508 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 570 LEU cc_start: 0.8739 (mt) cc_final: 0.8254 (mt) REVERT: A 578 MET cc_start: 0.7400 (mtp) cc_final: 0.6806 (mmp) REVERT: A 590 ASN cc_start: 0.8559 (m110) cc_final: 0.8326 (m-40) REVERT: A 790 GLU cc_start: 0.6071 (pt0) cc_final: 0.5870 (pt0) REVERT: A 991 ASP cc_start: 0.7491 (t0) cc_final: 0.6995 (m-30) REVERT: G 130 MET cc_start: 0.7503 (mtm) cc_final: 0.7264 (mtm) outliers start: 31 outliers final: 15 residues processed: 257 average time/residue: 0.3145 time to fit residues: 125.2016 Evaluate side-chains 211 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 388 GLN ** H 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 636 ASN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 151 ASN F 53 HIS G 36 GLN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.145084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.113924 restraints weight = 35873.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.114285 restraints weight = 45489.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.115252 restraints weight = 43348.393| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19168 Z= 0.362 Angle : 0.681 8.816 26576 Z= 0.360 Chirality : 0.044 0.176 3065 Planarity : 0.004 0.065 2809 Dihedral : 20.173 179.580 4331 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.67 % Allowed : 14.72 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.88 (0.19), residues: 1809 helix: 0.12 (0.19), residues: 739 sheet: -2.18 (0.30), residues: 260 loop : -2.23 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 604 HIS 0.010 0.001 HIS F 53 PHE 0.059 0.002 PHE H 524 TYR 0.025 0.002 TYR G 26 ARG 0.007 0.001 ARG A 812 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 TYR cc_start: 0.8728 (m-80) cc_final: 0.8519 (m-80) REVERT: A 285 ILE cc_start: 0.7338 (mt) cc_final: 0.6978 (mm) REVERT: A 508 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: A 575 LEU cc_start: 0.8267 (tp) cc_final: 0.7955 (tt) REVERT: D 586 MET cc_start: 0.7915 (ppp) cc_final: 0.7689 (ppp) REVERT: D 654 GLU cc_start: 0.5419 (tt0) cc_final: 0.5150 (tt0) REVERT: E 86 MET cc_start: 0.7386 (mpp) cc_final: 0.7170 (mpp) REVERT: F 21 PHE cc_start: 0.8073 (m-80) cc_final: 0.7799 (m-80) REVERT: G 1 MET cc_start: 0.8613 (tpp) cc_final: 0.8317 (tpp) outliers start: 44 outliers final: 33 residues processed: 224 average time/residue: 0.3228 time to fit residues: 113.5460 Evaluate side-chains 219 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 HIS Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 133 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 140 optimal weight: 0.0370 chunk 169 optimal weight: 2.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 477 GLN ** H 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS G 84 ASN ** G 109 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 = 0.4134 r_free = 0.4134 target = 0.146037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115168 restraints weight = 35757.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114813 restraints weight = 43833.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.115832 restraints weight = 43521.702| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19168 Z= 0.286 Angle : 0.630 9.088 26576 Z= 0.335 Chirality : 0.042 0.156 3065 Planarity : 0.004 0.046 2809 Dihedral : 20.102 179.482 4331 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.85 % Allowed : 16.47 % Favored : 80.68 % 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: -1.54 (0.19), residues: 1809 helix: 0.40 (0.19), residues: 747 sheet: -1.83 (0.31), residues: 264 loop : -2.13 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 604 HIS 0.010 0.001 HIS F 53 PHE 0.063 0.002 PHE H 524 TYR 0.023 0.002 TYR G 26 ARG 0.010 0.001 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 497 ASP cc_start: 0.6556 (t0) cc_final: 0.5901 (m-30) REVERT: A 228 GLN cc_start: 0.8455 (mm110) cc_final: 0.8204 (tt0) REVERT: A 285 ILE cc_start: 0.7277 (mt) cc_final: 0.6954 (mm) REVERT: D 654 GLU cc_start: 0.5596 (tt0) cc_final: 0.5199 (tt0) REVERT: E 86 MET cc_start: 0.7318 (mpp) cc_final: 0.7118 (mpp) REVERT: E 158 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8214 (ttp80) REVERT: G 130 MET cc_start: 0.7470 (mtm) cc_final: 0.7235 (mtm) outliers start: 47 outliers final: 37 residues processed: 223 average time/residue: 0.3012 time to fit residues: 106.4188 Evaluate side-chains 221 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 512 ASN Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 HIS Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.1735 > 50: distance: 99 - 105: 4.132 distance: 100 - 130: 8.908 distance: 105 - 106: 3.178 distance: 106 - 107: 16.134 distance: 106 - 109: 9.841 distance: 107 - 108: 36.789 distance: 107 - 113: 15.695 distance: 108 - 138: 18.781 distance: 109 - 110: 4.260 distance: 110 - 111: 5.709 distance: 110 - 112: 4.326 distance: 113 - 114: 30.598 distance: 114 - 115: 15.309 distance: 114 - 117: 29.445 distance: 115 - 116: 18.875 distance: 115 - 122: 15.844 distance: 116 - 147: 23.306 distance: 117 - 118: 28.453 distance: 118 - 119: 39.084 distance: 119 - 120: 26.413 distance: 120 - 121: 34.848 distance: 122 - 123: 12.287 distance: 123 - 124: 6.554 distance: 123 - 126: 6.804 distance: 124 - 125: 4.779 distance: 124 - 130: 7.573 distance: 125 - 156: 6.658 distance: 127 - 128: 15.150 distance: 127 - 129: 12.431 distance: 130 - 131: 6.842 distance: 132 - 133: 4.992 distance: 132 - 138: 3.494 distance: 133 - 164: 6.895 distance: 134 - 135: 13.244 distance: 135 - 136: 9.863 distance: 135 - 137: 13.008 distance: 138 - 139: 5.685 distance: 139 - 142: 4.888 distance: 140 - 141: 5.516 distance: 140 - 147: 7.511 distance: 142 - 143: 3.019 distance: 143 - 144: 3.343 distance: 147 - 148: 4.821 distance: 148 - 149: 3.212 distance: 148 - 151: 7.178 distance: 149 - 150: 3.718 distance: 149 - 156: 4.487 distance: 150 - 184: 5.854 distance: 151 - 152: 3.916 distance: 152 - 153: 3.184 distance: 153 - 154: 5.825 distance: 154 - 155: 7.267 distance: 159 - 190: 3.453 distance: 160 - 162: 4.644 distance: 161 - 163: 3.482 distance: 165 - 166: 5.293 distance: 165 - 168: 4.321 distance: 168 - 169: 6.664 distance: 169 - 170: 3.257 distance: 171 - 172: 7.434 distance: 172 - 173: 3.736 distance: 172 - 174: 6.678 distance: 175 - 176: 4.772 distance: 176 - 177: 7.652 distance: 176 - 179: 5.547 distance: 177 - 178: 7.234 distance: 177 - 184: 3.670 distance: 178 - 208: 9.902 distance: 179 - 180: 7.081 distance: 180 - 181: 4.899 distance: 181 - 182: 7.143 distance: 182 - 183: 13.243 distance: 185 - 186: 3.953 distance: 186 - 187: 4.083 distance: 186 - 190: 4.664 distance: 187 - 215: 4.488 distance: 188 - 189: 4.220