Starting phenix.real_space_refine on Sun Jun 15 12:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iqw_9708/06_2025/6iqw_9708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iqw_9708/06_2025/6iqw_9708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6iqw_9708/06_2025/6iqw_9708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iqw_9708/06_2025/6iqw_9708.map" model { file = "/net/cci-nas-00/data/ceres_data/6iqw_9708/06_2025/6iqw_9708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iqw_9708/06_2025/6iqw_9708.cif" } resolution = 3.35 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= -0.008 sd= 1.289 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: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 50 5.16 5 C 10766 2.51 5 N 2947 2.21 5 O 3146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16935 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6131 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1094 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "C" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2113 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2177 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 510 Classifications: {'RNA': 24} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 11, 'rna3p': 12} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.32, per 1000 atoms: 0.55 Number of scatterers: 16935 At special positions: 0 Unit cell: (134.16, 147.68, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 26 15.00 O 3146 8.00 N 2947 7.00 C 10766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 274 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.9 seconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 18 sheets defined 41.6% alpha, 8.2% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.898A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 22 removed outlier: 4.008A pdb=" N VAL A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 removed outlier: 3.654A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.698A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.780A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 5.979A pdb=" N GLU A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 102 removed outlier: 4.072A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.552A pdb=" N TYR A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 Proline residue: A 177 - end of helix removed outlier: 3.672A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.545A pdb=" N TYR A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 282 removed outlier: 3.726A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 305 through 325 Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.502A pdb=" N PHE A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 344 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 369 Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.698A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.843A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 561 through 566 removed outlier: 3.636A pdb=" N GLY A 566 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.988A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 4.107A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.855A pdb=" N GLU A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 689 removed outlier: 3.579A pdb=" N ILE A 688 " --> pdb=" O TYR A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 719 removed outlier: 3.753A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 711 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.969A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 735 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.688A pdb=" N VAL A 746 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY A 747 " --> pdb=" O PRO A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 749 through 755 removed outlier: 3.878A pdb=" N VAL A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 773 removed outlier: 4.442A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 70 through 88 removed outlier: 3.586A pdb=" N ARG B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.932A pdb=" N GLN B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.641A pdb=" N ASP B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 134 removed outlier: 4.402A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 removed outlier: 4.439A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 4.521A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 177 removed outlier: 3.971A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.910A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.584A pdb=" N TRP C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 75' Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.831A pdb=" N LEU C 120 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.522A pdb=" N PHE C 128 " --> pdb=" O CYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.621A pdb=" N GLU C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 220 Processing helix chain 'C' and resid 248 through 253 removed outlier: 4.100A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 276 through 287 removed outlier: 4.934A pdb=" N GLU C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 71 removed outlier: 3.629A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 removed outlier: 3.671A pdb=" N ASN D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 122 removed outlier: 3.886A pdb=" N ALA D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.545A pdb=" N ALA D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 206 through 223 removed outlier: 3.628A pdb=" N ILE D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 removed outlier: 3.538A pdb=" N GLY D 232 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.337A pdb=" N ASP D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 76 through 81 Processing helix chain 'E' and resid 88 through 95 removed outlier: 3.521A pdb=" N ALA E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'F' and resid 36 through 46 removed outlier: 4.577A pdb=" N ASN F 46 " --> pdb=" O ASN F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 64 through 71 removed outlier: 3.616A pdb=" N TRP F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 134 removed outlier: 3.540A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 144 removed outlier: 3.554A pdb=" N MET F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 removed outlier: 3.792A pdb=" N ASP F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 169 removed outlier: 3.671A pdb=" N TYR F 163 " --> pdb=" O ASP F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 4.587A pdb=" N ASP F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 200 through 207 Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.854A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 removed outlier: 3.705A pdb=" N GLU F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 305 removed outlier: 3.602A pdb=" N VAL F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 285 " --> pdb=" O PRO F 281 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 298 " --> pdb=" O ASP F 294 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET F 301 " --> pdb=" O TYR F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 315 through 323 removed outlier: 3.553A pdb=" N ARG F 319 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.649A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 450 through 454 removed outlier: 3.968A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE A 465 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR A 485 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL A 467 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 580 through 586 removed outlier: 6.798A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA A 585 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 590 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU A 620 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE A 656 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL A 622 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AA6, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AA7, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AA8, first strand: chain 'D' and resid 141 through 143 Processing sheet with id=AA9, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AB1, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AB2, first strand: chain 'D' and resid 167 through 169 Processing sheet with id=AB3, first strand: chain 'E' and resid 56 through 59 removed outlier: 6.177A pdb=" N SER E 56 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU E 160 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE E 58 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 229 through 230 Processing sheet with id=AB5, first strand: chain 'E' and resid 262 through 263 Processing sheet with id=AB6, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 28 removed outlier: 3.887A pdb=" N TYR F 85 " --> pdb=" O VAL F 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 89 through 90 removed outlier: 4.706A pdb=" N ILE F 238 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 89 through 90 543 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 4.53 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: 3929 1.33 - 1.45: 3922 1.45 - 1.57: 9395 1.57 - 1.69: 51 1.69 - 1.82: 82 Bond restraints: 17379 Sorted by residual: bond pdb=" C LEU F 20 " pdb=" N THR F 21 " ideal model delta sigma weight residual 1.331 1.207 0.124 1.59e-02 3.96e+03 6.11e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.65e+01 bond pdb=" N ARG E 89 " pdb=" CA ARG E 89 " ideal model delta sigma weight residual 1.459 1.400 0.059 1.16e-02 7.43e+03 2.56e+01 bond pdb=" C5 ATP A 801 " pdb=" N7 ATP A 801 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 17374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 23343 3.81 - 7.61: 238 7.61 - 11.42: 29 11.42 - 15.23: 2 15.23 - 19.04: 3 Bond angle restraints: 23615 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 119.70 17.13 1.00e+00 1.00e+00 2.93e+02 angle pdb=" C GLU E 88 " pdb=" N ARG E 89 " pdb=" CA ARG E 89 " ideal model delta sigma weight residual 120.79 108.58 12.21 1.39e+00 5.18e-01 7.71e+01 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.56 8.24 1.00e+00 1.00e+00 6.79e+01 angle pdb=" N3 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N9 ATP A 801 " ideal model delta sigma weight residual 127.04 135.05 -8.01 1.15e+00 7.59e-01 4.87e+01 ... (remaining 23610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.01: 9107 19.01 - 38.02: 1065 38.02 - 57.03: 196 57.03 - 76.03: 51 76.03 - 95.04: 2 Dihedral angle restraints: 10421 sinusoidal: 4478 harmonic: 5943 Sorted by residual: dihedral pdb=" CA PHE A 325 " pdb=" C PHE A 325 " pdb=" N GLU A 326 " pdb=" CA GLU A 326 " ideal model delta harmonic sigma weight residual -180.00 -145.33 -34.67 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA VAL D 39 " pdb=" C VAL D 39 " pdb=" N ILE D 40 " pdb=" CA ILE D 40 " ideal model delta harmonic sigma weight residual -180.00 -146.38 -33.62 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA ARG A 394 " pdb=" C ARG A 394 " pdb=" N GLU A 395 " pdb=" CA GLU A 395 " ideal model delta harmonic sigma weight residual 180.00 146.74 33.26 0 5.00e+00 4.00e-02 4.43e+01 ... (remaining 10418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1886 0.060 - 0.119: 548 0.119 - 0.179: 119 0.179 - 0.238: 14 0.238 - 0.298: 4 Chirality restraints: 2571 Sorted by residual: chirality pdb=" C1' A I 18 " pdb=" O4' A I 18 " pdb=" C2' A I 18 " pdb=" N9 A I 18 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE D 196 " pdb=" CA ILE D 196 " pdb=" CG1 ILE D 196 " pdb=" CG2 ILE D 196 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE C 15 " pdb=" CA ILE C 15 " pdb=" CG1 ILE C 15 " pdb=" CG2 ILE C 15 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2568 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 141 " -0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C SER E 141 " 0.068 2.00e-02 2.50e+03 pdb=" O SER E 141 " -0.025 2.00e-02 2.50e+03 pdb=" N SER E 142 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 58 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO E 59 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 59 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 59 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 494 " -0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 495 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.046 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 48 2.39 - 3.01: 8682 3.01 - 3.64: 25978 3.64 - 4.27: 38459 4.27 - 4.90: 62685 Nonbonded interactions: 135852 Sorted by model distance: nonbonded pdb=" O ALA B 51 " pdb=" CD2 TYR B 55 " model vdw 1.757 3.340 nonbonded pdb=" O ARG E 89 " pdb=" OG1 THR E 92 " model vdw 2.168 3.040 nonbonded pdb=" O GLY F 15 " pdb=" O2' C I 21 " model vdw 2.210 3.040 nonbonded pdb=" O GLU E 88 " pdb=" O ARG E 89 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 727 " pdb=" O GLN B 173 " model vdw 2.254 3.040 ... (remaining 135847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 4 through 25 or resid 38 through 194 or (resid 195 and (na \ me N or name CA or name C or name O or name CB )) or resid 196 through 282)) selection = (chain 'D' and (resid 4 through 25 or resid 38 through 63 or (resid 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 through 223 or (resi \ d 224 and (name N or name CA or name C or name O or name CB )) or resid 225 thro \ ugh 234 or (resid 235 and (name N or name CA or name C or name O or name CB )) o \ r resid 236 through 282)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.280 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.007 0.124 17380 Z= 0.328 Angle : 1.051 19.035 23617 Z= 0.594 Chirality : 0.059 0.298 2571 Planarity : 0.008 0.090 2941 Dihedral : 16.456 95.044 6622 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.52 % Favored : 86.09 % Rotamer: Outliers : 0.35 % Allowed : 10.34 % Favored : 89.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.25 % 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: -4.93 (0.14), residues: 2049 helix: -3.21 (0.12), residues: 730 sheet: -3.15 (0.34), residues: 185 loop : -3.44 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 131 HIS 0.009 0.002 HIS A 60 PHE 0.038 0.003 PHE E 159 TYR 0.031 0.003 TYR E 272 ARG 0.014 0.001 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.18302 ( 541) hydrogen bonds : angle 7.90657 ( 1515) SS BOND : bond 0.00496 ( 1) SS BOND : angle 1.83450 ( 2) covalent geometry : bond 0.00683 (17379) covalent geometry : angle 1.05077 (23615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 678 time to evaluate : 1.758 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 revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.6145 (m-80) cc_final: 0.4458 (m-80) REVERT: A 36 ARG cc_start: 0.8522 (tpt90) cc_final: 0.8135 (tpt90) REVERT: A 99 GLU cc_start: 0.8918 (tp30) cc_final: 0.8275 (tp30) REVERT: A 114 GLN cc_start: 0.8173 (pt0) cc_final: 0.7249 (mp10) REVERT: A 121 SER cc_start: 0.9111 (t) cc_final: 0.8782 (m) REVERT: A 169 LYS cc_start: 0.7336 (mtpp) cc_final: 0.6610 (mtmm) REVERT: A 181 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8438 (ptmm) REVERT: A 192 GLU cc_start: 0.8343 (tt0) cc_final: 0.8004 (pm20) REVERT: A 199 TYR cc_start: 0.8822 (t80) cc_final: 0.8314 (t80) REVERT: A 200 ASP cc_start: 0.8518 (m-30) cc_final: 0.8244 (m-30) REVERT: A 204 MET cc_start: 0.9359 (mmp) cc_final: 0.9113 (mmt) REVERT: A 237 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 241 SER cc_start: 0.9125 (t) cc_final: 0.8639 (p) REVERT: A 272 ASP cc_start: 0.8512 (t0) cc_final: 0.7973 (t70) REVERT: A 276 GLU cc_start: 0.7941 (tp30) cc_final: 0.7482 (tp30) REVERT: A 283 LEU cc_start: 0.9398 (mt) cc_final: 0.9012 (mp) REVERT: A 287 ASN cc_start: 0.9168 (m110) cc_final: 0.8201 (m110) REVERT: A 299 ILE cc_start: 0.9406 (mt) cc_final: 0.8999 (mt) REVERT: A 301 GLN cc_start: 0.8876 (pm20) cc_final: 0.8521 (pm20) REVERT: A 359 LEU cc_start: 0.9225 (tp) cc_final: 0.8101 (tp) REVERT: A 430 LEU cc_start: 0.7981 (mt) cc_final: 0.7716 (tp) REVERT: A 435 THR cc_start: 0.8718 (t) cc_final: 0.8252 (p) REVERT: A 454 TYR cc_start: 0.7905 (t80) cc_final: 0.6925 (t80) REVERT: A 464 GLN cc_start: 0.8708 (mp10) cc_final: 0.7826 (mp10) REVERT: A 490 TYR cc_start: 0.8071 (t80) cc_final: 0.7318 (t80) REVERT: A 503 GLU cc_start: 0.8563 (tt0) cc_final: 0.8138 (mt-10) REVERT: A 513 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8054 (ttm-80) REVERT: A 550 LYS cc_start: 0.8316 (mttt) cc_final: 0.7970 (mttm) REVERT: A 629 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6545 (mt-10) REVERT: A 638 ASP cc_start: 0.8348 (m-30) cc_final: 0.7837 (t0) REVERT: A 664 LEU cc_start: 0.8889 (mt) cc_final: 0.8687 (mp) REVERT: A 708 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8370 (mmtp) REVERT: A 725 TRP cc_start: 0.9004 (p-90) cc_final: 0.7564 (p-90) REVERT: A 745 LEU cc_start: 0.8413 (mt) cc_final: 0.7948 (mt) REVERT: A 762 TYR cc_start: 0.8413 (t80) cc_final: 0.8048 (t80) REVERT: B 74 ARG cc_start: 0.8407 (mtm110) cc_final: 0.8186 (mtm-85) REVERT: B 86 THR cc_start: 0.9324 (t) cc_final: 0.9104 (p) REVERT: B 97 LYS cc_start: 0.8808 (tptp) cc_final: 0.8269 (mttm) REVERT: B 122 LYS cc_start: 0.9294 (ptpt) cc_final: 0.8451 (mmmm) REVERT: B 129 TYR cc_start: 0.8663 (t80) cc_final: 0.8311 (t80) REVERT: C 14 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7724 (mtpp) REVERT: C 68 ASN cc_start: 0.8968 (t0) cc_final: 0.8663 (t0) REVERT: C 94 GLN cc_start: 0.7616 (mt0) cc_final: 0.7069 (mm-40) REVERT: C 95 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7580 (mp0) REVERT: C 106 ASN cc_start: 0.8219 (t0) cc_final: 0.7800 (t0) REVERT: C 142 ILE cc_start: 0.8590 (mt) cc_final: 0.8371 (mm) REVERT: C 143 VAL cc_start: 0.9042 (t) cc_final: 0.8841 (t) REVERT: C 183 ASN cc_start: 0.8700 (m-40) cc_final: 0.7543 (m-40) REVERT: C 237 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7992 (ttpp) REVERT: C 249 ASP cc_start: 0.6923 (t70) cc_final: 0.6397 (t0) REVERT: D 70 ARG cc_start: 0.7491 (mmm160) cc_final: 0.7155 (mmp80) REVERT: D 136 ASN cc_start: 0.8586 (m110) cc_final: 0.8280 (m110) REVERT: D 202 ASN cc_start: 0.8138 (m-40) cc_final: 0.7886 (p0) REVERT: E 43 GLU cc_start: 0.7733 (tm-30) cc_final: 0.6989 (mt-10) REVERT: E 63 ASP cc_start: 0.8698 (p0) cc_final: 0.8486 (p0) REVERT: E 105 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8024 (mtpp) REVERT: E 128 ASP cc_start: 0.8255 (t0) cc_final: 0.7738 (t0) REVERT: E 148 GLU cc_start: 0.7371 (mp0) cc_final: 0.6715 (mt-10) REVERT: E 200 HIS cc_start: 0.7972 (t-170) cc_final: 0.7435 (t70) REVERT: E 262 ARG cc_start: 0.6698 (mtt-85) cc_final: 0.5945 (mtt180) REVERT: F 36 ASP cc_start: 0.8474 (t0) cc_final: 0.8241 (t0) REVERT: F 86 THR cc_start: 0.9104 (p) cc_final: 0.8774 (t) REVERT: F 98 MET cc_start: 0.5745 (mtt) cc_final: 0.5410 (mpp) REVERT: F 163 TYR cc_start: 0.8294 (t80) cc_final: 0.7751 (t80) REVERT: F 220 LYS cc_start: 0.8495 (pttt) cc_final: 0.7769 (ttpt) REVERT: F 275 LEU cc_start: 0.8864 (mt) cc_final: 0.8302 (tt) REVERT: F 290 TRP cc_start: 0.8578 (m100) cc_final: 0.8266 (m100) REVERT: F 297 TYR cc_start: 0.7358 (m-80) cc_final: 0.6890 (m-80) REVERT: F 298 THR cc_start: 0.8774 (m) cc_final: 0.8464 (p) REVERT: F 319 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8734 (mmt-90) REVERT: F 385 LEU cc_start: 0.8343 (mt) cc_final: 0.7784 (tp) REVERT: F 389 MET cc_start: 0.7573 (mpp) cc_final: 0.7176 (mpp) outliers start: 6 outliers final: 3 residues processed: 680 average time/residue: 0.3141 time to fit residues: 310.4718 Evaluate side-chains 484 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 481 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain F residue 305 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 124 ASN C 22 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 205 HIS D 136 ASN E 36 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116095 restraints weight = 33023.372| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.08 r_work: 0.3399 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17380 Z= 0.172 Angle : 0.754 11.874 23617 Z= 0.393 Chirality : 0.049 0.319 2571 Planarity : 0.007 0.087 2941 Dihedral : 12.307 94.819 2704 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.66 % Favored : 88.19 % Rotamer: Outliers : 4.09 % Allowed : 19.51 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.88 (0.16), residues: 2049 helix: -1.78 (0.16), residues: 754 sheet: -2.82 (0.34), residues: 195 loop : -3.21 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 206 HIS 0.009 0.001 HIS C 44 PHE 0.021 0.002 PHE D 194 TYR 0.032 0.002 TYR B 55 ARG 0.010 0.001 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 541) hydrogen bonds : angle 5.85105 ( 1515) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.84983 ( 2) covalent geometry : bond 0.00374 (17379) covalent geometry : angle 0.75415 (23615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 525 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.6385 (m-80) cc_final: 0.5586 (m-80) REVERT: A 71 MET cc_start: 0.8234 (tpt) cc_final: 0.7664 (tpt) REVERT: A 99 GLU cc_start: 0.9065 (tp30) cc_final: 0.8561 (tp30) REVERT: A 114 GLN cc_start: 0.8090 (pt0) cc_final: 0.7268 (mp10) REVERT: A 121 SER cc_start: 0.9182 (t) cc_final: 0.8751 (m) REVERT: A 169 LYS cc_start: 0.7239 (mtpp) cc_final: 0.6562 (mtmm) REVERT: A 181 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8727 (ptmm) REVERT: A 192 GLU cc_start: 0.8761 (tt0) cc_final: 0.8169 (pm20) REVERT: A 203 ARG cc_start: 0.9191 (ttm170) cc_final: 0.8835 (ptm-80) REVERT: A 237 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 253 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8748 (mmmt) REVERT: A 272 ASP cc_start: 0.8853 (t0) cc_final: 0.8171 (t0) REVERT: A 276 GLU cc_start: 0.8751 (tp30) cc_final: 0.8168 (tp30) REVERT: A 287 ASN cc_start: 0.9270 (m110) cc_final: 0.8993 (m-40) REVERT: A 299 ILE cc_start: 0.9432 (mt) cc_final: 0.9214 (mt) REVERT: A 342 GLU cc_start: 0.9233 (mt-10) cc_final: 0.9031 (mt-10) REVERT: A 359 LEU cc_start: 0.9235 (tp) cc_final: 0.8257 (tp) REVERT: A 430 LEU cc_start: 0.7936 (mt) cc_final: 0.7593 (tp) REVERT: A 439 ASP cc_start: 0.8323 (m-30) cc_final: 0.8118 (m-30) REVERT: A 454 TYR cc_start: 0.8148 (t80) cc_final: 0.7264 (t80) REVERT: A 464 GLN cc_start: 0.8559 (mp10) cc_final: 0.7863 (mp10) REVERT: A 490 TYR cc_start: 0.8405 (t80) cc_final: 0.7620 (t80) REVERT: A 503 GLU cc_start: 0.8713 (tt0) cc_final: 0.8184 (mt-10) REVERT: A 513 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8154 (ttm-80) REVERT: A 527 GLU cc_start: 0.8678 (tt0) cc_final: 0.7772 (tp30) REVERT: A 550 LYS cc_start: 0.8315 (mttt) cc_final: 0.8028 (mttm) REVERT: A 573 ASP cc_start: 0.8553 (m-30) cc_final: 0.8296 (p0) REVERT: A 577 GLU cc_start: 0.7785 (tt0) cc_final: 0.6975 (pp20) REVERT: A 629 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 638 ASP cc_start: 0.8727 (m-30) cc_final: 0.8129 (t0) REVERT: A 650 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7849 (mm-30) REVERT: A 718 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8062 (ttp-170) REVERT: A 725 TRP cc_start: 0.9115 (p-90) cc_final: 0.7480 (p-90) REVERT: A 745 LEU cc_start: 0.8384 (mt) cc_final: 0.7826 (mt) REVERT: A 755 ARG cc_start: 0.7929 (ptt180) cc_final: 0.7462 (ptt180) REVERT: B 96 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7382 (mtp180) REVERT: B 97 LYS cc_start: 0.8830 (tptp) cc_final: 0.8483 (mttm) REVERT: B 103 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7196 (mtt180) REVERT: B 110 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8659 (mtmt) REVERT: B 122 LYS cc_start: 0.9320 (ptpt) cc_final: 0.8431 (mmmm) REVERT: B 123 MET cc_start: 0.9382 (mtp) cc_final: 0.9094 (ttm) REVERT: B 133 LYS cc_start: 0.8596 (tptp) cc_final: 0.8121 (mtmt) REVERT: C 14 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8038 (mtpp) REVERT: C 68 ASN cc_start: 0.9044 (t0) cc_final: 0.8836 (t0) REVERT: C 85 SER cc_start: 0.9006 (m) cc_final: 0.8745 (p) REVERT: C 89 CYS cc_start: 0.8130 (m) cc_final: 0.7901 (m) REVERT: C 94 GLN cc_start: 0.7607 (mt0) cc_final: 0.7031 (mm-40) REVERT: C 95 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7905 (mp0) REVERT: C 106 ASN cc_start: 0.8394 (t0) cc_final: 0.7984 (t0) REVERT: C 133 LYS cc_start: 0.8940 (tptt) cc_final: 0.8309 (pttp) REVERT: C 237 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8411 (ttpp) REVERT: C 244 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7577 (tp30) REVERT: C 249 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6793 (t0) REVERT: D 70 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7205 (mmt90) REVERT: D 140 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.8054 (mtp-110) REVERT: D 267 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6057 (mtpp) REVERT: E 43 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7324 (mt-10) REVERT: E 58 PHE cc_start: 0.8264 (t80) cc_final: 0.7978 (t80) REVERT: E 63 ASP cc_start: 0.8698 (p0) cc_final: 0.8471 (p0) REVERT: E 86 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8031 (tp30) REVERT: E 124 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: E 148 GLU cc_start: 0.7669 (mp0) cc_final: 0.7411 (mt-10) REVERT: E 158 TYR cc_start: 0.8874 (p90) cc_final: 0.8402 (p90) REVERT: E 200 HIS cc_start: 0.8306 (t-170) cc_final: 0.7785 (t70) REVERT: E 237 PHE cc_start: 0.8383 (m-80) cc_final: 0.7896 (m-10) REVERT: E 262 ARG cc_start: 0.7014 (mtt-85) cc_final: 0.6428 (mtt180) REVERT: E 264 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7395 (mm-30) REVERT: F 26 TYR cc_start: 0.7961 (t80) cc_final: 0.7543 (t80) REVERT: F 36 ASP cc_start: 0.8718 (t0) cc_final: 0.8485 (t0) REVERT: F 86 THR cc_start: 0.9142 (p) cc_final: 0.8850 (m) REVERT: F 99 GLN cc_start: 0.8484 (pm20) cc_final: 0.8260 (pm20) REVERT: F 127 TYR cc_start: 0.6706 (t80) cc_final: 0.6417 (t80) REVERT: F 131 LYS cc_start: 0.8396 (tttp) cc_final: 0.7642 (tppt) REVERT: F 183 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: F 198 ARG cc_start: 0.7382 (tmm-80) cc_final: 0.6673 (ttp-110) REVERT: F 204 ASP cc_start: 0.9156 (t0) cc_final: 0.8711 (t70) REVERT: F 220 LYS cc_start: 0.8488 (pttt) cc_final: 0.7835 (ttpt) REVERT: F 238 ILE cc_start: 0.7763 (tt) cc_final: 0.7518 (pt) REVERT: F 241 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8493 (mt-10) REVERT: F 275 LEU cc_start: 0.8735 (mt) cc_final: 0.8415 (tt) REVERT: F 297 TYR cc_start: 0.7762 (m-80) cc_final: 0.7168 (m-80) REVERT: F 319 ARG cc_start: 0.9281 (ttp80) cc_final: 0.8804 (mmt-90) REVERT: F 385 LEU cc_start: 0.8463 (mt) cc_final: 0.7513 (pp) REVERT: F 389 MET cc_start: 0.7728 (mpp) cc_final: 0.7514 (mpp) outliers start: 70 outliers final: 42 residues processed: 560 average time/residue: 0.3055 time to fit residues: 250.6495 Evaluate side-chains 501 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 454 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 120 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 212 ASN F 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113724 restraints weight = 33081.527| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.00 r_work: 0.3367 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17380 Z= 0.209 Angle : 0.754 10.751 23617 Z= 0.392 Chirality : 0.049 0.308 2571 Planarity : 0.006 0.096 2941 Dihedral : 12.029 90.757 2702 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.01 % Favored : 87.90 % Rotamer: Outliers : 5.26 % Allowed : 21.61 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.31 (0.17), residues: 2049 helix: -1.16 (0.17), residues: 758 sheet: -2.45 (0.35), residues: 187 loop : -3.01 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 235 HIS 0.007 0.001 HIS D 111 PHE 0.042 0.002 PHE E 116 TYR 0.032 0.002 TYR B 55 ARG 0.009 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 541) hydrogen bonds : angle 5.58657 ( 1515) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.69764 ( 2) covalent geometry : bond 0.00472 (17379) covalent geometry : angle 0.75383 (23615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 491 time to evaluate : 1.753 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: A 71 MET cc_start: 0.8199 (tpt) cc_final: 0.7651 (tpt) REVERT: A 99 GLU cc_start: 0.9003 (tp30) cc_final: 0.8601 (tp30) REVERT: A 114 GLN cc_start: 0.8162 (pt0) cc_final: 0.7462 (mp10) REVERT: A 121 SER cc_start: 0.9192 (t) cc_final: 0.8699 (m) REVERT: A 152 GLN cc_start: 0.8239 (pt0) cc_final: 0.7229 (tp40) REVERT: A 169 LYS cc_start: 0.7274 (mtpp) cc_final: 0.6591 (mtmm) REVERT: A 192 GLU cc_start: 0.8793 (tt0) cc_final: 0.8259 (pm20) REVERT: A 203 ARG cc_start: 0.9327 (ttm170) cc_final: 0.8918 (ptm-80) REVERT: A 237 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 245 ASP cc_start: 0.9158 (m-30) cc_final: 0.8355 (t0) REVERT: A 253 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8819 (mmmt) REVERT: A 266 LEU cc_start: 0.9269 (tp) cc_final: 0.9053 (tt) REVERT: A 272 ASP cc_start: 0.8855 (t0) cc_final: 0.8241 (t0) REVERT: A 287 ASN cc_start: 0.9308 (m110) cc_final: 0.9025 (m-40) REVERT: A 359 LEU cc_start: 0.9269 (tp) cc_final: 0.8299 (tp) REVERT: A 391 VAL cc_start: 0.9048 (t) cc_final: 0.8716 (p) REVERT: A 430 LEU cc_start: 0.7902 (mt) cc_final: 0.7622 (tp) REVERT: A 454 TYR cc_start: 0.8174 (t80) cc_final: 0.7364 (t80) REVERT: A 464 GLN cc_start: 0.8612 (mp10) cc_final: 0.7778 (mp10) REVERT: A 490 TYR cc_start: 0.8475 (t80) cc_final: 0.7702 (t80) REVERT: A 513 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8221 (ttm-80) REVERT: A 537 LYS cc_start: 0.8908 (mttt) cc_final: 0.8672 (mttp) REVERT: A 549 PHE cc_start: 0.8699 (m-80) cc_final: 0.8487 (m-80) REVERT: A 550 LYS cc_start: 0.8299 (mttt) cc_final: 0.8099 (mttm) REVERT: A 560 LYS cc_start: 0.8623 (mttp) cc_final: 0.8190 (mmmt) REVERT: A 573 ASP cc_start: 0.8556 (m-30) cc_final: 0.8314 (p0) REVERT: A 601 GLU cc_start: 0.8778 (tt0) cc_final: 0.8520 (tt0) REVERT: A 629 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7100 (mt-10) REVERT: A 638 ASP cc_start: 0.8729 (m-30) cc_final: 0.8072 (t0) REVERT: A 708 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8640 (mptt) REVERT: A 718 ARG cc_start: 0.8436 (ttm170) cc_final: 0.8107 (ttp-170) REVERT: A 724 ARG cc_start: 0.8672 (mtp180) cc_final: 0.7462 (mmp-170) REVERT: A 725 TRP cc_start: 0.9154 (p-90) cc_final: 0.7532 (p-90) REVERT: A 745 LEU cc_start: 0.8514 (mt) cc_final: 0.7954 (mp) REVERT: B 96 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7088 (mtp180) REVERT: B 97 LYS cc_start: 0.8714 (tptp) cc_final: 0.8394 (mttm) REVERT: B 103 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7295 (mtt180) REVERT: B 122 LYS cc_start: 0.9307 (ptpt) cc_final: 0.8523 (mmmt) REVERT: B 123 MET cc_start: 0.9309 (mtp) cc_final: 0.9033 (ttm) REVERT: B 133 LYS cc_start: 0.8685 (tptp) cc_final: 0.8287 (ptpt) REVERT: C 14 LYS cc_start: 0.8539 (ptpt) cc_final: 0.8017 (mtpp) REVERT: C 85 SER cc_start: 0.9022 (m) cc_final: 0.8783 (p) REVERT: C 89 CYS cc_start: 0.8341 (m) cc_final: 0.7101 (m) REVERT: C 94 GLN cc_start: 0.7543 (mt0) cc_final: 0.6828 (mm-40) REVERT: C 95 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7890 (mp0) REVERT: C 106 ASN cc_start: 0.8466 (t0) cc_final: 0.8031 (t0) REVERT: C 109 TRP cc_start: 0.8504 (m100) cc_final: 0.6775 (m-10) REVERT: C 133 LYS cc_start: 0.8812 (tptt) cc_final: 0.8242 (pttp) REVERT: C 142 ILE cc_start: 0.8982 (mt) cc_final: 0.8720 (mm) REVERT: C 237 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8465 (ttpp) REVERT: C 244 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7580 (tp30) REVERT: D 70 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7311 (mmt90) REVERT: D 84 TYR cc_start: 0.8137 (m-80) cc_final: 0.7803 (m-80) REVERT: D 115 ASP cc_start: 0.8269 (t0) cc_final: 0.7891 (t70) REVERT: D 140 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.8255 (mtp-110) REVERT: E 43 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7434 (mt-10) REVERT: E 63 ASP cc_start: 0.8656 (p0) cc_final: 0.8419 (p0) REVERT: E 86 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7975 (tp30) REVERT: E 89 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7907 (tpt170) REVERT: E 118 ILE cc_start: 0.9412 (tp) cc_final: 0.9114 (mt) REVERT: E 124 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7221 (m-10) REVERT: E 148 GLU cc_start: 0.7547 (mp0) cc_final: 0.7322 (mt-10) REVERT: E 158 TYR cc_start: 0.8941 (p90) cc_final: 0.8450 (p90) REVERT: E 200 HIS cc_start: 0.8247 (t-170) cc_final: 0.7731 (t70) REVERT: E 262 ARG cc_start: 0.7120 (mtt-85) cc_final: 0.6891 (ttm170) REVERT: E 264 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7546 (mm-30) REVERT: F 26 TYR cc_start: 0.7845 (t80) cc_final: 0.7376 (t80) REVERT: F 36 ASP cc_start: 0.8811 (t0) cc_final: 0.8598 (t0) REVERT: F 45 MET cc_start: 0.5505 (tpt) cc_final: 0.4590 (mtm) REVERT: F 86 THR cc_start: 0.9147 (p) cc_final: 0.8906 (m) REVERT: F 99 GLN cc_start: 0.8672 (pm20) cc_final: 0.8390 (pm20) REVERT: F 127 TYR cc_start: 0.6788 (t80) cc_final: 0.6548 (t80) REVERT: F 131 LYS cc_start: 0.8379 (tttp) cc_final: 0.7621 (tppt) REVERT: F 204 ASP cc_start: 0.9151 (t0) cc_final: 0.8719 (t70) REVERT: F 220 LYS cc_start: 0.8545 (pttt) cc_final: 0.7872 (ttpt) REVERT: F 238 ILE cc_start: 0.7691 (tt) cc_final: 0.7394 (pt) REVERT: F 241 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8544 (mt-10) REVERT: F 275 LEU cc_start: 0.8750 (mt) cc_final: 0.8400 (tt) REVERT: F 290 TRP cc_start: 0.8460 (m100) cc_final: 0.8125 (m100) REVERT: F 297 TYR cc_start: 0.7700 (m-80) cc_final: 0.7231 (m-80) REVERT: F 304 GLU cc_start: 0.8350 (tt0) cc_final: 0.8149 (tt0) REVERT: F 319 ARG cc_start: 0.9250 (ttp80) cc_final: 0.8796 (mmt-90) REVERT: F 327 ASP cc_start: 0.7004 (t0) cc_final: 0.6462 (p0) REVERT: F 385 LEU cc_start: 0.8429 (mt) cc_final: 0.7532 (pp) outliers start: 90 outliers final: 61 residues processed: 538 average time/residue: 0.2995 time to fit residues: 236.8311 Evaluate side-chains 514 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 450 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 10 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN C 44 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 212 ASN E 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116840 restraints weight = 33116.990| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.10 r_work: 0.3395 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17380 Z= 0.158 Angle : 0.711 12.527 23617 Z= 0.365 Chirality : 0.048 0.279 2571 Planarity : 0.006 0.095 2941 Dihedral : 11.860 96.145 2702 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.18 % Favored : 88.73 % Rotamer: Outliers : 5.43 % Allowed : 23.25 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.98 (0.18), residues: 2049 helix: -0.80 (0.18), residues: 751 sheet: -2.46 (0.35), residues: 192 loop : -2.84 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 152 HIS 0.007 0.001 HIS A 60 PHE 0.033 0.002 PHE E 58 TYR 0.029 0.002 TYR F 303 ARG 0.011 0.001 ARG C 60 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 541) hydrogen bonds : angle 5.37102 ( 1515) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.64326 ( 2) covalent geometry : bond 0.00363 (17379) covalent geometry : angle 0.71057 (23615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 492 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7364 (mtt) cc_final: 0.6812 (mmm) REVERT: A 71 MET cc_start: 0.8075 (tpt) cc_final: 0.7535 (tpt) REVERT: A 99 GLU cc_start: 0.9021 (tp30) cc_final: 0.8642 (tp30) REVERT: A 114 GLN cc_start: 0.8213 (pt0) cc_final: 0.7469 (mp10) REVERT: A 121 SER cc_start: 0.9088 (t) cc_final: 0.8519 (m) REVERT: A 152 GLN cc_start: 0.8210 (pt0) cc_final: 0.7246 (tp40) REVERT: A 166 SER cc_start: 0.8421 (m) cc_final: 0.8067 (p) REVERT: A 169 LYS cc_start: 0.7177 (mtpp) cc_final: 0.6515 (mtmm) REVERT: A 181 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8659 (ptmm) REVERT: A 192 GLU cc_start: 0.8718 (tt0) cc_final: 0.8243 (pm20) REVERT: A 203 ARG cc_start: 0.9260 (ttm170) cc_final: 0.8996 (ptm-80) REVERT: A 204 MET cc_start: 0.9248 (mmp) cc_final: 0.8909 (mmp) REVERT: A 237 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 253 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8817 (mmmt) REVERT: A 266 LEU cc_start: 0.9253 (tp) cc_final: 0.9019 (tt) REVERT: A 272 ASP cc_start: 0.8803 (t0) cc_final: 0.8228 (t0) REVERT: A 329 LEU cc_start: 0.9534 (tt) cc_final: 0.9297 (tt) REVERT: A 342 GLU cc_start: 0.9249 (mt-10) cc_final: 0.9046 (mt-10) REVERT: A 359 LEU cc_start: 0.9223 (tp) cc_final: 0.8206 (tp) REVERT: A 430 LEU cc_start: 0.7884 (mt) cc_final: 0.7570 (tp) REVERT: A 454 TYR cc_start: 0.8183 (t80) cc_final: 0.7310 (t80) REVERT: A 464 GLN cc_start: 0.8635 (mp10) cc_final: 0.8010 (mp10) REVERT: A 490 TYR cc_start: 0.8390 (t80) cc_final: 0.7612 (t80) REVERT: A 513 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8195 (ttm-80) REVERT: A 537 LYS cc_start: 0.8910 (mttt) cc_final: 0.8626 (mttp) REVERT: A 558 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 560 LYS cc_start: 0.8619 (mttp) cc_final: 0.8202 (mmmt) REVERT: A 577 GLU cc_start: 0.7721 (tt0) cc_final: 0.6964 (pp20) REVERT: A 600 PHE cc_start: 0.8945 (t80) cc_final: 0.8317 (t80) REVERT: A 629 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 638 ASP cc_start: 0.8692 (m-30) cc_final: 0.8117 (t0) REVERT: A 650 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7974 (mm-30) REVERT: A 708 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8614 (mptt) REVERT: A 718 ARG cc_start: 0.8370 (ttm170) cc_final: 0.8163 (ttp-170) REVERT: A 725 TRP cc_start: 0.9112 (p-90) cc_final: 0.7525 (p-90) REVERT: A 745 LEU cc_start: 0.8450 (mt) cc_final: 0.7878 (mp) REVERT: B 96 ARG cc_start: 0.7697 (ttm110) cc_final: 0.6776 (tpp-160) REVERT: B 97 LYS cc_start: 0.8678 (tptp) cc_final: 0.8353 (mttm) REVERT: B 133 LYS cc_start: 0.8678 (tptp) cc_final: 0.8281 (mtmt) REVERT: C 14 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8014 (mtpp) REVERT: C 85 SER cc_start: 0.9004 (m) cc_final: 0.8769 (p) REVERT: C 89 CYS cc_start: 0.8081 (m) cc_final: 0.6505 (m) REVERT: C 94 GLN cc_start: 0.7519 (mt0) cc_final: 0.6789 (tp40) REVERT: C 95 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7724 (mp0) REVERT: C 106 ASN cc_start: 0.8478 (t0) cc_final: 0.8076 (t0) REVERT: C 109 TRP cc_start: 0.8490 (m100) cc_final: 0.6737 (m-10) REVERT: C 133 LYS cc_start: 0.8809 (tptt) cc_final: 0.8181 (ptpp) REVERT: C 142 ILE cc_start: 0.8907 (mt) cc_final: 0.8675 (mm) REVERT: C 195 GLU cc_start: 0.8650 (tt0) cc_final: 0.8016 (tt0) REVERT: C 237 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8452 (ttpp) REVERT: D 70 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7384 (mpt-90) REVERT: D 115 ASP cc_start: 0.8278 (t0) cc_final: 0.8005 (t70) REVERT: D 140 ARG cc_start: 0.8450 (mtp-110) cc_final: 0.8098 (mtp-110) REVERT: D 224 TYR cc_start: 0.8676 (p90) cc_final: 0.8348 (p90) REVERT: E 43 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7429 (mt-10) REVERT: E 63 ASP cc_start: 0.8598 (p0) cc_final: 0.8358 (p0) REVERT: E 74 GLU cc_start: 0.8656 (mp0) cc_final: 0.8360 (mp0) REVERT: E 86 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7890 (tp30) REVERT: E 89 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7961 (tpt170) REVERT: E 95 ARG cc_start: 0.8367 (tpp80) cc_final: 0.8163 (tpp80) REVERT: E 118 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9175 (mt) REVERT: E 124 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6838 (m-10) REVERT: E 200 HIS cc_start: 0.8255 (t-170) cc_final: 0.7826 (t70) REVERT: E 237 PHE cc_start: 0.8292 (m-80) cc_final: 0.7824 (m-10) REVERT: E 262 ARG cc_start: 0.7081 (mtt-85) cc_final: 0.6736 (ttm170) REVERT: E 264 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7466 (mm-30) REVERT: F 23 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8230 (p) REVERT: F 36 ASP cc_start: 0.8811 (t0) cc_final: 0.8583 (t0) REVERT: F 45 MET cc_start: 0.5400 (tpt) cc_final: 0.4582 (mtm) REVERT: F 86 THR cc_start: 0.9110 (p) cc_final: 0.8864 (m) REVERT: F 99 GLN cc_start: 0.8665 (pm20) cc_final: 0.8413 (pm20) REVERT: F 131 LYS cc_start: 0.8478 (tttp) cc_final: 0.7713 (tppt) REVERT: F 204 ASP cc_start: 0.9126 (t0) cc_final: 0.8800 (t70) REVERT: F 220 LYS cc_start: 0.8567 (pttt) cc_final: 0.7934 (ttpt) REVERT: F 238 ILE cc_start: 0.7742 (tt) cc_final: 0.7221 (pt) REVERT: F 241 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8555 (mt-10) REVERT: F 275 LEU cc_start: 0.8666 (mt) cc_final: 0.8347 (tt) REVERT: F 290 TRP cc_start: 0.8487 (m100) cc_final: 0.8119 (m100) REVERT: F 297 TYR cc_start: 0.7775 (m-80) cc_final: 0.7222 (m-80) REVERT: F 327 ASP cc_start: 0.7027 (t0) cc_final: 0.6427 (p0) outliers start: 93 outliers final: 65 residues processed: 541 average time/residue: 0.3731 time to fit residues: 303.2442 Evaluate side-chains 522 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 453 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 47 optimal weight: 0.0030 chunk 88 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS B 179 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 212 ASN F 13 HIS F 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115443 restraints weight = 33231.147| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.95 r_work: 0.3417 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17380 Z= 0.178 Angle : 0.716 12.979 23617 Z= 0.368 Chirality : 0.049 0.255 2571 Planarity : 0.006 0.099 2941 Dihedral : 11.750 93.378 2702 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.81 % Favored : 88.09 % Rotamer: Outliers : 5.67 % Allowed : 24.59 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.80 (0.18), residues: 2049 helix: -0.60 (0.18), residues: 754 sheet: -2.47 (0.35), residues: 192 loop : -2.75 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 239 HIS 0.007 0.001 HIS A 60 PHE 0.022 0.002 PHE C 101 TYR 0.041 0.002 TYR F 322 ARG 0.008 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 541) hydrogen bonds : angle 5.36318 ( 1515) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.66139 ( 2) covalent geometry : bond 0.00405 (17379) covalent geometry : angle 0.71574 (23615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 480 time to evaluate : 1.930 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: A 65 MET cc_start: 0.7352 (mtt) cc_final: 0.6758 (mmm) REVERT: A 71 MET cc_start: 0.8108 (tpt) cc_final: 0.7551 (tpt) REVERT: A 99 GLU cc_start: 0.9046 (tp30) cc_final: 0.8624 (tp30) REVERT: A 114 GLN cc_start: 0.8186 (pt0) cc_final: 0.7480 (mp10) REVERT: A 121 SER cc_start: 0.9024 (t) cc_final: 0.8431 (m) REVERT: A 152 GLN cc_start: 0.8153 (pt0) cc_final: 0.7149 (tp40) REVERT: A 166 SER cc_start: 0.8471 (m) cc_final: 0.8117 (p) REVERT: A 169 LYS cc_start: 0.7134 (mtpp) cc_final: 0.6412 (mtmm) REVERT: A 181 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8605 (ptmm) REVERT: A 192 GLU cc_start: 0.8762 (tt0) cc_final: 0.8246 (pm20) REVERT: A 203 ARG cc_start: 0.9193 (ttm170) cc_final: 0.8928 (ptm-80) REVERT: A 237 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 253 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8812 (mmmt) REVERT: A 272 ASP cc_start: 0.8808 (t0) cc_final: 0.8296 (t0) REVERT: A 289 VAL cc_start: 0.9729 (t) cc_final: 0.9504 (p) REVERT: A 295 HIS cc_start: 0.8059 (t-90) cc_final: 0.7785 (t70) REVERT: A 359 LEU cc_start: 0.9226 (tp) cc_final: 0.8248 (tp) REVERT: A 430 LEU cc_start: 0.7903 (mt) cc_final: 0.7545 (tp) REVERT: A 454 TYR cc_start: 0.8145 (t80) cc_final: 0.7139 (t80) REVERT: A 464 GLN cc_start: 0.8610 (mp10) cc_final: 0.7928 (mp10) REVERT: A 490 TYR cc_start: 0.8469 (t80) cc_final: 0.7687 (t80) REVERT: A 513 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8224 (ttm-80) REVERT: A 537 LYS cc_start: 0.8912 (mttt) cc_final: 0.8592 (mttm) REVERT: A 560 LYS cc_start: 0.8680 (mttp) cc_final: 0.8185 (mmmt) REVERT: A 600 PHE cc_start: 0.8946 (t80) cc_final: 0.8308 (t80) REVERT: A 629 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 638 ASP cc_start: 0.8647 (m-30) cc_final: 0.8106 (t0) REVERT: A 708 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8636 (mptt) REVERT: A 718 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8158 (ttp-170) REVERT: A 724 ARG cc_start: 0.8549 (mtp180) cc_final: 0.7309 (mmp-170) REVERT: A 725 TRP cc_start: 0.9164 (p-90) cc_final: 0.7547 (p-90) REVERT: A 742 PHE cc_start: 0.9475 (m-80) cc_final: 0.9212 (m-80) REVERT: A 745 LEU cc_start: 0.8543 (mt) cc_final: 0.7880 (mt) REVERT: B 66 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.6076 (t80) REVERT: B 97 LYS cc_start: 0.8648 (tptp) cc_final: 0.8353 (mttm) REVERT: B 133 LYS cc_start: 0.8666 (tptp) cc_final: 0.8363 (mtpt) REVERT: C 14 LYS cc_start: 0.8485 (ptpt) cc_final: 0.7971 (mtpp) REVERT: C 59 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9076 (mp) REVERT: C 85 SER cc_start: 0.9026 (m) cc_final: 0.8790 (p) REVERT: C 89 CYS cc_start: 0.8122 (m) cc_final: 0.6500 (m) REVERT: C 92 ASP cc_start: 0.7014 (p0) cc_final: 0.6571 (p0) REVERT: C 94 GLN cc_start: 0.7569 (mt0) cc_final: 0.6859 (tp40) REVERT: C 95 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7724 (mp0) REVERT: C 106 ASN cc_start: 0.8433 (t0) cc_final: 0.8025 (t0) REVERT: C 109 TRP cc_start: 0.8446 (m100) cc_final: 0.6770 (m-10) REVERT: C 133 LYS cc_start: 0.8780 (tptt) cc_final: 0.8145 (ptpp) REVERT: C 142 ILE cc_start: 0.8911 (mt) cc_final: 0.8660 (mm) REVERT: C 195 GLU cc_start: 0.8671 (tt0) cc_final: 0.8071 (tt0) REVERT: C 237 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8322 (ttpp) REVERT: C 259 ILE cc_start: 0.8140 (mp) cc_final: 0.7831 (mt) REVERT: D 55 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8647 (tt) REVERT: D 70 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7391 (mpt-90) REVERT: D 115 ASP cc_start: 0.8260 (t0) cc_final: 0.8007 (t70) REVERT: D 140 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8169 (mtp-110) REVERT: D 224 TYR cc_start: 0.8700 (p90) cc_final: 0.8396 (p90) REVERT: E 43 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7458 (mt-10) REVERT: E 63 ASP cc_start: 0.8612 (p0) cc_final: 0.8358 (p0) REVERT: E 86 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7743 (tp30) REVERT: E 124 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: E 200 HIS cc_start: 0.8207 (t-170) cc_final: 0.7793 (t70) REVERT: E 237 PHE cc_start: 0.8271 (m-80) cc_final: 0.7813 (m-80) REVERT: E 262 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6671 (ttm170) REVERT: E 264 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7097 (mm-30) REVERT: F 23 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8240 (p) REVERT: F 26 TYR cc_start: 0.7808 (t80) cc_final: 0.7386 (t80) REVERT: F 36 ASP cc_start: 0.8814 (t0) cc_final: 0.8581 (t0) REVERT: F 45 MET cc_start: 0.5342 (tpt) cc_final: 0.4515 (mtm) REVERT: F 86 THR cc_start: 0.9138 (p) cc_final: 0.8883 (m) REVERT: F 99 GLN cc_start: 0.8736 (pm20) cc_final: 0.8500 (pm20) REVERT: F 131 LYS cc_start: 0.8417 (tttp) cc_final: 0.7451 (mptt) REVERT: F 189 MET cc_start: 0.8284 (ttm) cc_final: 0.8058 (tpp) REVERT: F 198 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7238 (ttt-90) REVERT: F 220 LYS cc_start: 0.8561 (pttt) cc_final: 0.7945 (ttpt) REVERT: F 241 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8552 (mt-10) REVERT: F 275 LEU cc_start: 0.8696 (mt) cc_final: 0.8382 (tt) REVERT: F 290 TRP cc_start: 0.8518 (m100) cc_final: 0.8119 (m100) REVERT: F 297 TYR cc_start: 0.7760 (m-80) cc_final: 0.7139 (m-80) REVERT: F 298 THR cc_start: 0.8558 (m) cc_final: 0.8345 (p) REVERT: F 327 ASP cc_start: 0.7102 (t0) cc_final: 0.6516 (p0) REVERT: F 391 MET cc_start: 0.7285 (mmm) cc_final: 0.7080 (ptt) outliers start: 97 outliers final: 79 residues processed: 531 average time/residue: 0.3083 time to fit residues: 245.2162 Evaluate side-chains 532 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 447 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN D 183 ASN E 30 ASN F 13 HIS ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114137 restraints weight = 33495.080| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.02 r_work: 0.3392 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17380 Z= 0.206 Angle : 0.739 14.941 23617 Z= 0.379 Chirality : 0.049 0.250 2571 Planarity : 0.006 0.098 2941 Dihedral : 11.711 90.281 2698 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.20 % Favored : 87.70 % Rotamer: Outliers : 6.60 % Allowed : 25.70 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.64 (0.18), residues: 2049 helix: -0.46 (0.18), residues: 747 sheet: -2.30 (0.35), residues: 202 loop : -2.66 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 239 HIS 0.007 0.001 HIS A 60 PHE 0.026 0.002 PHE E 58 TYR 0.045 0.002 TYR F 322 ARG 0.007 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 541) hydrogen bonds : angle 5.40054 ( 1515) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.60028 ( 2) covalent geometry : bond 0.00469 (17379) covalent geometry : angle 0.73942 (23615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 463 time to evaluate : 3.117 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: A 65 MET cc_start: 0.7314 (mtt) cc_final: 0.6664 (mmm) REVERT: A 71 MET cc_start: 0.8219 (tpt) cc_final: 0.7756 (tpt) REVERT: A 99 GLU cc_start: 0.9062 (tp30) cc_final: 0.8659 (tp30) REVERT: A 114 GLN cc_start: 0.8228 (pt0) cc_final: 0.7572 (mp10) REVERT: A 121 SER cc_start: 0.9087 (t) cc_final: 0.8495 (m) REVERT: A 152 GLN cc_start: 0.8180 (pt0) cc_final: 0.7234 (tp40) REVERT: A 166 SER cc_start: 0.8451 (m) cc_final: 0.8097 (p) REVERT: A 169 LYS cc_start: 0.7167 (mtpp) cc_final: 0.6500 (mtmm) REVERT: A 180 GLU cc_start: 0.9214 (tt0) cc_final: 0.8976 (mm-30) REVERT: A 181 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8635 (ptmm) REVERT: A 192 GLU cc_start: 0.8804 (tt0) cc_final: 0.8299 (pm20) REVERT: A 203 ARG cc_start: 0.9249 (ttm170) cc_final: 0.8932 (ptm-80) REVERT: A 237 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 245 ASP cc_start: 0.9057 (m-30) cc_final: 0.8267 (t0) REVERT: A 253 LYS cc_start: 0.9081 (mmtp) cc_final: 0.8852 (mmmt) REVERT: A 272 ASP cc_start: 0.8768 (t0) cc_final: 0.8202 (t0) REVERT: A 283 LEU cc_start: 0.9436 (mt) cc_final: 0.9125 (mt) REVERT: A 295 HIS cc_start: 0.8086 (t-90) cc_final: 0.7845 (t70) REVERT: A 334 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 359 LEU cc_start: 0.9248 (tp) cc_final: 0.8363 (tp) REVERT: A 391 VAL cc_start: 0.9063 (t) cc_final: 0.8823 (t) REVERT: A 430 LEU cc_start: 0.7930 (mt) cc_final: 0.7580 (tp) REVERT: A 454 TYR cc_start: 0.8194 (t80) cc_final: 0.7198 (t80) REVERT: A 464 GLN cc_start: 0.8636 (mp10) cc_final: 0.7990 (mp10) REVERT: A 490 TYR cc_start: 0.8469 (t80) cc_final: 0.7919 (t80) REVERT: A 513 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8280 (ttm-80) REVERT: A 537 LYS cc_start: 0.8938 (mttt) cc_final: 0.8605 (mttm) REVERT: A 601 GLU cc_start: 0.8638 (tt0) cc_final: 0.8337 (tt0) REVERT: A 629 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7113 (mt-10) REVERT: A 638 ASP cc_start: 0.8695 (m-30) cc_final: 0.8195 (t0) REVERT: A 707 TRP cc_start: 0.8462 (m100) cc_final: 0.8254 (m100) REVERT: A 708 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8671 (mptt) REVERT: A 718 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8189 (ttp-170) REVERT: A 724 ARG cc_start: 0.8591 (mtp180) cc_final: 0.7193 (tpm170) REVERT: A 725 TRP cc_start: 0.9170 (p-90) cc_final: 0.7592 (p-90) REVERT: A 742 PHE cc_start: 0.9477 (m-80) cc_final: 0.9174 (m-80) REVERT: A 745 LEU cc_start: 0.8510 (mt) cc_final: 0.7856 (mt) REVERT: B 66 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.5908 (t80) REVERT: B 96 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7027 (mtp180) REVERT: B 97 LYS cc_start: 0.8654 (tptp) cc_final: 0.8303 (mttp) REVERT: B 133 LYS cc_start: 0.8713 (tptp) cc_final: 0.8443 (mtpt) REVERT: C 14 LYS cc_start: 0.8505 (ptpt) cc_final: 0.7975 (mtpp) REVERT: C 59 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9125 (mp) REVERT: C 85 SER cc_start: 0.9029 (m) cc_final: 0.8799 (p) REVERT: C 89 CYS cc_start: 0.8166 (m) cc_final: 0.6620 (m) REVERT: C 92 ASP cc_start: 0.6971 (p0) cc_final: 0.6521 (p0) REVERT: C 94 GLN cc_start: 0.7600 (mt0) cc_final: 0.6996 (tp40) REVERT: C 95 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7753 (mp0) REVERT: C 106 ASN cc_start: 0.8452 (t0) cc_final: 0.8045 (t0) REVERT: C 109 TRP cc_start: 0.8541 (m100) cc_final: 0.6975 (m-10) REVERT: C 133 LYS cc_start: 0.8808 (tptt) cc_final: 0.8174 (ptpp) REVERT: C 142 ILE cc_start: 0.8937 (mt) cc_final: 0.8690 (mm) REVERT: C 195 GLU cc_start: 0.8691 (tt0) cc_final: 0.8158 (tt0) REVERT: C 237 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8406 (ttpp) REVERT: C 259 ILE cc_start: 0.8121 (mp) cc_final: 0.7898 (mt) REVERT: D 70 ARG cc_start: 0.7958 (mmm160) cc_final: 0.7449 (mpt-90) REVERT: D 96 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7353 (m-40) REVERT: D 115 ASP cc_start: 0.8326 (t0) cc_final: 0.8076 (t70) REVERT: D 140 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.8309 (ttm110) REVERT: D 201 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: D 224 TYR cc_start: 0.8766 (p90) cc_final: 0.8469 (p90) REVERT: E 43 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7485 (mt-10) REVERT: E 63 ASP cc_start: 0.8599 (p0) cc_final: 0.8334 (p0) REVERT: E 86 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7719 (tp30) REVERT: E 124 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: E 200 HIS cc_start: 0.8224 (t-170) cc_final: 0.7818 (t70) REVERT: E 237 PHE cc_start: 0.8250 (m-80) cc_final: 0.7830 (m-10) REVERT: E 262 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6915 (ttm170) REVERT: F 23 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8291 (p) REVERT: F 36 ASP cc_start: 0.8830 (t0) cc_final: 0.8590 (t0) REVERT: F 45 MET cc_start: 0.5361 (tpt) cc_final: 0.4456 (mtm) REVERT: F 86 THR cc_start: 0.9124 (p) cc_final: 0.8883 (m) REVERT: F 99 GLN cc_start: 0.8776 (pm20) cc_final: 0.8434 (pm20) REVERT: F 131 LYS cc_start: 0.8445 (tttp) cc_final: 0.7402 (mptt) REVERT: F 189 MET cc_start: 0.8434 (ttm) cc_final: 0.8204 (tpp) REVERT: F 220 LYS cc_start: 0.8537 (pttt) cc_final: 0.7932 (ttpt) REVERT: F 241 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8506 (mt-10) REVERT: F 290 TRP cc_start: 0.8547 (m100) cc_final: 0.8130 (m100) REVERT: F 297 TYR cc_start: 0.7768 (m-80) cc_final: 0.7125 (m-80) REVERT: F 298 THR cc_start: 0.8501 (m) cc_final: 0.8289 (p) REVERT: F 327 ASP cc_start: 0.7044 (t0) cc_final: 0.6455 (p0) outliers start: 113 outliers final: 95 residues processed: 529 average time/residue: 0.3231 time to fit residues: 252.4156 Evaluate side-chains 540 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 438 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111758 restraints weight = 33368.248| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.95 r_work: 0.3348 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17380 Z= 0.253 Angle : 0.781 15.770 23617 Z= 0.402 Chirality : 0.050 0.254 2571 Planarity : 0.006 0.100 2941 Dihedral : 11.780 85.395 2698 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.18 % Favored : 86.68 % Rotamer: Outliers : 7.01 % Allowed : 25.70 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.67 (0.18), residues: 2049 helix: -0.54 (0.18), residues: 762 sheet: -2.16 (0.36), residues: 198 loop : -2.69 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 235 HIS 0.009 0.002 HIS C 205 PHE 0.027 0.002 PHE C 101 TYR 0.039 0.003 TYR F 322 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 541) hydrogen bonds : angle 5.52017 ( 1515) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.73863 ( 2) covalent geometry : bond 0.00570 (17379) covalent geometry : angle 0.78053 (23615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 448 time to evaluate : 1.832 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: A 65 MET cc_start: 0.7352 (mtt) cc_final: 0.7090 (mmm) REVERT: A 71 MET cc_start: 0.8163 (tpt) cc_final: 0.7719 (tpt) REVERT: A 99 GLU cc_start: 0.9151 (tp30) cc_final: 0.8803 (tp30) REVERT: A 114 GLN cc_start: 0.8287 (pt0) cc_final: 0.7604 (mp10) REVERT: A 121 SER cc_start: 0.9168 (t) cc_final: 0.8560 (m) REVERT: A 152 GLN cc_start: 0.8179 (pt0) cc_final: 0.7260 (tp40) REVERT: A 166 SER cc_start: 0.8481 (m) cc_final: 0.8126 (p) REVERT: A 169 LYS cc_start: 0.7193 (mtpp) cc_final: 0.6485 (mtmm) REVERT: A 180 GLU cc_start: 0.9249 (tt0) cc_final: 0.8925 (mm-30) REVERT: A 181 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8598 (ptmm) REVERT: A 192 GLU cc_start: 0.8873 (tt0) cc_final: 0.8345 (pm20) REVERT: A 194 ASN cc_start: 0.8550 (t0) cc_final: 0.8007 (t0) REVERT: A 203 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8959 (ptm-80) REVERT: A 237 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 245 ASP cc_start: 0.9057 (m-30) cc_final: 0.8336 (t0) REVERT: A 253 LYS cc_start: 0.9117 (mmtp) cc_final: 0.8901 (mmmt) REVERT: A 272 ASP cc_start: 0.8779 (t0) cc_final: 0.8262 (t0) REVERT: A 283 LEU cc_start: 0.9508 (mt) cc_final: 0.9204 (mt) REVERT: A 334 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 359 LEU cc_start: 0.9281 (tp) cc_final: 0.8506 (tp) REVERT: A 373 GLU cc_start: 0.8860 (mp0) cc_final: 0.8594 (pm20) REVERT: A 391 VAL cc_start: 0.9087 (t) cc_final: 0.8862 (t) REVERT: A 430 LEU cc_start: 0.7955 (mt) cc_final: 0.7597 (tp) REVERT: A 454 TYR cc_start: 0.8181 (t80) cc_final: 0.7205 (t80) REVERT: A 464 GLN cc_start: 0.8659 (mp10) cc_final: 0.8005 (mp10) REVERT: A 490 TYR cc_start: 0.8504 (t80) cc_final: 0.7976 (t80) REVERT: A 513 ARG cc_start: 0.8708 (mtp85) cc_final: 0.8260 (ttm-80) REVERT: A 537 LYS cc_start: 0.8968 (mttt) cc_final: 0.8640 (mttm) REVERT: A 629 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 638 ASP cc_start: 0.8735 (m-30) cc_final: 0.8246 (t0) REVERT: A 707 TRP cc_start: 0.8565 (m100) cc_final: 0.8142 (m100) REVERT: A 708 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8688 (mptt) REVERT: A 718 ARG cc_start: 0.8435 (ttm170) cc_final: 0.8207 (ttp-170) REVERT: A 724 ARG cc_start: 0.8612 (mtp180) cc_final: 0.7271 (tpm170) REVERT: A 725 TRP cc_start: 0.9206 (p-90) cc_final: 0.7596 (p-90) REVERT: A 742 PHE cc_start: 0.9499 (m-80) cc_final: 0.9200 (m-80) REVERT: A 745 LEU cc_start: 0.8579 (mt) cc_final: 0.7903 (mt) REVERT: B 66 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5769 (t80) REVERT: B 96 ARG cc_start: 0.7546 (ttm110) cc_final: 0.6497 (tpt170) REVERT: B 97 LYS cc_start: 0.8661 (tptp) cc_final: 0.8311 (mttp) REVERT: B 133 LYS cc_start: 0.8670 (tptp) cc_final: 0.8369 (ptpt) REVERT: C 14 LYS cc_start: 0.8552 (ptpt) cc_final: 0.8019 (mtpp) REVERT: C 59 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9140 (mp) REVERT: C 85 SER cc_start: 0.9076 (m) cc_final: 0.8843 (p) REVERT: C 89 CYS cc_start: 0.8235 (m) cc_final: 0.6806 (m) REVERT: C 94 GLN cc_start: 0.7659 (mt0) cc_final: 0.7100 (tp40) REVERT: C 95 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7830 (mp0) REVERT: C 106 ASN cc_start: 0.8504 (t0) cc_final: 0.8154 (t0) REVERT: C 109 TRP cc_start: 0.8674 (m100) cc_final: 0.7128 (m-10) REVERT: C 133 LYS cc_start: 0.8821 (tptt) cc_final: 0.8289 (pttp) REVERT: C 142 ILE cc_start: 0.8939 (mt) cc_final: 0.8689 (mm) REVERT: C 195 GLU cc_start: 0.8809 (tt0) cc_final: 0.8338 (tt0) REVERT: C 207 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8039 (ttt-90) REVERT: C 237 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8362 (ttpp) REVERT: C 259 ILE cc_start: 0.8160 (mp) cc_final: 0.7891 (mt) REVERT: D 70 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7465 (mpt-90) REVERT: D 96 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7464 (m-40) REVERT: D 115 ASP cc_start: 0.8365 (t0) cc_final: 0.8144 (t70) REVERT: D 140 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8268 (mtp-110) REVERT: D 224 TYR cc_start: 0.8804 (p90) cc_final: 0.8509 (p90) REVERT: E 8 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7806 (ttmt) REVERT: E 43 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7489 (mt-10) REVERT: E 63 ASP cc_start: 0.8592 (p0) cc_final: 0.8303 (p0) REVERT: E 86 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7694 (tp30) REVERT: E 118 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9171 (mt) REVERT: E 124 TYR cc_start: 0.7411 (m-10) cc_final: 0.6994 (m-10) REVERT: E 200 HIS cc_start: 0.8184 (t-170) cc_final: 0.7770 (t70) REVERT: E 237 PHE cc_start: 0.8211 (m-80) cc_final: 0.7782 (m-10) REVERT: E 264 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7467 (mm-30) REVERT: F 23 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8349 (p) REVERT: F 36 ASP cc_start: 0.8842 (t0) cc_final: 0.8589 (t0) REVERT: F 86 THR cc_start: 0.9115 (p) cc_final: 0.8868 (m) REVERT: F 131 LYS cc_start: 0.8466 (tttp) cc_final: 0.7418 (mptt) REVERT: F 163 TYR cc_start: 0.8127 (t80) cc_final: 0.7509 (t80) REVERT: F 204 ASP cc_start: 0.9193 (t0) cc_final: 0.8963 (t70) REVERT: F 220 LYS cc_start: 0.8519 (pttt) cc_final: 0.7904 (ttpt) REVERT: F 241 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8461 (mt-10) REVERT: F 275 LEU cc_start: 0.8684 (mt) cc_final: 0.8399 (tt) REVERT: F 290 TRP cc_start: 0.8547 (m100) cc_final: 0.8103 (m100) REVERT: F 297 TYR cc_start: 0.7666 (m-80) cc_final: 0.7004 (m-80) REVERT: F 327 ASP cc_start: 0.7064 (t0) cc_final: 0.6536 (p0) REVERT: F 390 PRO cc_start: 0.8416 (Cg_exo) cc_final: 0.8215 (Cg_endo) outliers start: 120 outliers final: 103 residues processed: 518 average time/residue: 0.3129 time to fit residues: 241.1791 Evaluate side-chains 540 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 431 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 24 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 123 optimal weight: 0.0770 chunk 183 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS D 96 ASN D 183 ASN E 30 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118147 restraints weight = 33003.615| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.06 r_work: 0.3428 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17380 Z= 0.138 Angle : 0.714 13.139 23617 Z= 0.363 Chirality : 0.048 0.232 2571 Planarity : 0.006 0.099 2941 Dihedral : 11.561 83.834 2698 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.22 % Favored : 88.73 % Rotamer: Outliers : 4.50 % Allowed : 28.80 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.44 (0.18), residues: 2049 helix: -0.29 (0.19), residues: 745 sheet: -2.33 (0.35), residues: 198 loop : -2.52 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 272 HIS 0.009 0.001 HIS A 60 PHE 0.042 0.002 PHE E 58 TYR 0.034 0.002 TYR C 250 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 541) hydrogen bonds : angle 5.25289 ( 1515) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.70612 ( 2) covalent geometry : bond 0.00319 (17379) covalent geometry : angle 0.71358 (23615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 489 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7163 (mtt) cc_final: 0.6741 (mmt) REVERT: A 99 GLU cc_start: 0.9089 (tp30) cc_final: 0.8726 (tp30) REVERT: A 114 GLN cc_start: 0.8239 (pt0) cc_final: 0.7623 (mp10) REVERT: A 121 SER cc_start: 0.9001 (t) cc_final: 0.8373 (m) REVERT: A 152 GLN cc_start: 0.8046 (pt0) cc_final: 0.7148 (tp40) REVERT: A 166 SER cc_start: 0.8396 (m) cc_final: 0.8052 (p) REVERT: A 169 LYS cc_start: 0.7044 (mtpp) cc_final: 0.6356 (mtmm) REVERT: A 180 GLU cc_start: 0.9140 (tt0) cc_final: 0.8790 (mm-30) REVERT: A 181 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8573 (ptmm) REVERT: A 192 GLU cc_start: 0.8696 (tt0) cc_final: 0.8196 (pm20) REVERT: A 194 ASN cc_start: 0.8487 (t0) cc_final: 0.7918 (t0) REVERT: A 199 TYR cc_start: 0.9023 (t80) cc_final: 0.8303 (t80) REVERT: A 203 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8959 (ptm-80) REVERT: A 237 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 253 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8833 (mmmt) REVERT: A 272 ASP cc_start: 0.8516 (t0) cc_final: 0.8062 (t0) REVERT: A 283 LEU cc_start: 0.9494 (mt) cc_final: 0.9176 (mt) REVERT: A 342 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8420 (mp0) REVERT: A 359 LEU cc_start: 0.9182 (tp) cc_final: 0.8355 (tp) REVERT: A 391 VAL cc_start: 0.9040 (t) cc_final: 0.8801 (t) REVERT: A 403 PRO cc_start: 0.7998 (Cg_endo) cc_final: 0.7666 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7934 (mt) cc_final: 0.7575 (tp) REVERT: A 454 TYR cc_start: 0.8137 (t80) cc_final: 0.7133 (t80) REVERT: A 464 GLN cc_start: 0.8602 (mp10) cc_final: 0.7961 (mp10) REVERT: A 490 TYR cc_start: 0.8267 (t80) cc_final: 0.7504 (t80) REVERT: A 513 ARG cc_start: 0.8753 (mtp85) cc_final: 0.8366 (ttm-80) REVERT: A 537 LYS cc_start: 0.8960 (mttt) cc_final: 0.8562 (mttm) REVERT: A 558 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 577 GLU cc_start: 0.7539 (tt0) cc_final: 0.6916 (pp20) REVERT: A 600 PHE cc_start: 0.8854 (t80) cc_final: 0.8592 (t80) REVERT: A 629 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 638 ASP cc_start: 0.8643 (m-30) cc_final: 0.8177 (t0) REVERT: A 707 TRP cc_start: 0.8520 (m100) cc_final: 0.8064 (m100) REVERT: A 708 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8561 (mptt) REVERT: A 724 ARG cc_start: 0.8519 (mtp180) cc_final: 0.7112 (tpm170) REVERT: A 725 TRP cc_start: 0.9146 (p-90) cc_final: 0.7592 (p-90) REVERT: A 742 PHE cc_start: 0.9450 (m-80) cc_final: 0.9182 (m-80) REVERT: A 745 LEU cc_start: 0.8493 (mt) cc_final: 0.7816 (mt) REVERT: A 768 LEU cc_start: 0.8697 (mt) cc_final: 0.8425 (tp) REVERT: B 66 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.5821 (t80) REVERT: B 96 ARG cc_start: 0.7352 (ttm110) cc_final: 0.6264 (tpt170) REVERT: B 97 LYS cc_start: 0.8523 (tptp) cc_final: 0.8257 (mttm) REVERT: C 14 LYS cc_start: 0.8449 (ptpt) cc_final: 0.7929 (mtpp) REVERT: C 59 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8923 (mp) REVERT: C 85 SER cc_start: 0.8988 (m) cc_final: 0.8741 (p) REVERT: C 89 CYS cc_start: 0.7953 (m) cc_final: 0.7150 (m) REVERT: C 92 ASP cc_start: 0.6927 (p0) cc_final: 0.6714 (p0) REVERT: C 94 GLN cc_start: 0.7596 (mt0) cc_final: 0.7098 (tp40) REVERT: C 102 ASN cc_start: 0.7160 (p0) cc_final: 0.6557 (m-40) REVERT: C 106 ASN cc_start: 0.8378 (t0) cc_final: 0.8014 (t0) REVERT: C 133 LYS cc_start: 0.8850 (tptt) cc_final: 0.8315 (pttp) REVERT: C 195 GLU cc_start: 0.8612 (tt0) cc_final: 0.8131 (tt0) REVERT: C 207 ARG cc_start: 0.8264 (ttm110) cc_final: 0.7972 (ttt-90) REVERT: C 237 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8325 (ttpp) REVERT: C 244 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7577 (tp30) REVERT: C 259 ILE cc_start: 0.8234 (mp) cc_final: 0.7494 (mt) REVERT: D 70 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7550 (mpt-90) REVERT: D 93 ASN cc_start: 0.8935 (p0) cc_final: 0.8429 (p0) REVERT: D 96 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7299 (m-40) REVERT: D 97 CYS cc_start: 0.6776 (p) cc_final: 0.6542 (m) REVERT: D 115 ASP cc_start: 0.8255 (t0) cc_final: 0.8046 (t70) REVERT: E 43 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7363 (mt-10) REVERT: E 63 ASP cc_start: 0.8513 (p0) cc_final: 0.8231 (p0) REVERT: E 86 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7627 (tp30) REVERT: E 116 PHE cc_start: 0.8695 (p90) cc_final: 0.8394 (p90) REVERT: E 118 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9088 (mt) REVERT: E 124 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6730 (m-10) REVERT: E 200 HIS cc_start: 0.8045 (t-170) cc_final: 0.7573 (t70) REVERT: E 237 PHE cc_start: 0.8380 (m-80) cc_final: 0.7689 (m-80) REVERT: E 262 ARG cc_start: 0.6707 (ttm170) cc_final: 0.5872 (mtt180) REVERT: E 264 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7435 (mm-30) REVERT: F 23 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8208 (p) REVERT: F 26 TYR cc_start: 0.7951 (t80) cc_final: 0.7581 (t80) REVERT: F 36 ASP cc_start: 0.8791 (t0) cc_final: 0.8549 (t0) REVERT: F 45 MET cc_start: 0.5425 (tpt) cc_final: 0.4813 (mtm) REVERT: F 86 THR cc_start: 0.9063 (p) cc_final: 0.8837 (m) REVERT: F 131 LYS cc_start: 0.8496 (tttp) cc_final: 0.7462 (mptt) REVERT: F 220 LYS cc_start: 0.8524 (pttt) cc_final: 0.7910 (ttpt) REVERT: F 241 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8437 (mt-10) REVERT: F 290 TRP cc_start: 0.8584 (m100) cc_final: 0.8069 (m100) REVERT: F 297 TYR cc_start: 0.7761 (m-80) cc_final: 0.6917 (m-80) REVERT: F 327 ASP cc_start: 0.7023 (t0) cc_final: 0.6483 (p0) outliers start: 77 outliers final: 57 residues processed: 532 average time/residue: 0.2937 time to fit residues: 233.9031 Evaluate side-chains 515 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 451 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 172 optimal weight: 7.9990 chunk 18 optimal weight: 0.0370 chunk 104 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.0010 chunk 124 optimal weight: 7.9990 overall best weight: 1.9868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 200 HIS ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118157 restraints weight = 33028.692| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.05 r_work: 0.3423 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17380 Z= 0.153 Angle : 0.718 13.211 23617 Z= 0.367 Chirality : 0.049 0.218 2571 Planarity : 0.006 0.095 2941 Dihedral : 11.475 82.476 2698 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.57 % Favored : 88.34 % Rotamer: Outliers : 4.32 % Allowed : 29.50 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.38 (0.18), residues: 2049 helix: -0.25 (0.19), residues: 755 sheet: -2.24 (0.35), residues: 198 loop : -2.50 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 596 HIS 0.025 0.002 HIS C 205 PHE 0.036 0.002 PHE E 58 TYR 0.031 0.002 TYR A 727 ARG 0.008 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 541) hydrogen bonds : angle 5.26876 ( 1515) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.61707 ( 2) covalent geometry : bond 0.00357 (17379) covalent geometry : angle 0.71777 (23615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 469 time to evaluate : 1.897 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: A 65 MET cc_start: 0.7147 (mtt) cc_final: 0.6877 (mmm) REVERT: A 99 GLU cc_start: 0.9083 (tp30) cc_final: 0.8704 (tp30) REVERT: A 114 GLN cc_start: 0.8260 (pt0) cc_final: 0.7641 (mp10) REVERT: A 121 SER cc_start: 0.9033 (t) cc_final: 0.8407 (m) REVERT: A 152 GLN cc_start: 0.8063 (pt0) cc_final: 0.7172 (tp40) REVERT: A 166 SER cc_start: 0.8414 (m) cc_final: 0.8075 (p) REVERT: A 169 LYS cc_start: 0.7068 (mtpp) cc_final: 0.6378 (mtmm) REVERT: A 180 GLU cc_start: 0.9134 (tt0) cc_final: 0.8865 (mm-30) REVERT: A 181 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8605 (ptmm) REVERT: A 192 GLU cc_start: 0.8727 (tt0) cc_final: 0.8212 (pm20) REVERT: A 203 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.9003 (ptm-80) REVERT: A 237 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 253 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8858 (mmmt) REVERT: A 272 ASP cc_start: 0.8521 (t0) cc_final: 0.8072 (t0) REVERT: A 342 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8471 (mp0) REVERT: A 359 LEU cc_start: 0.9190 (tp) cc_final: 0.8439 (tp) REVERT: A 391 VAL cc_start: 0.9040 (t) cc_final: 0.8794 (t) REVERT: A 403 PRO cc_start: 0.7914 (Cg_endo) cc_final: 0.7535 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7934 (mt) cc_final: 0.7561 (tp) REVERT: A 454 TYR cc_start: 0.8155 (t80) cc_final: 0.7188 (t80) REVERT: A 464 GLN cc_start: 0.8601 (mp10) cc_final: 0.7957 (mp10) REVERT: A 490 TYR cc_start: 0.8322 (t80) cc_final: 0.7772 (t80) REVERT: A 513 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8389 (ttm-80) REVERT: A 537 LYS cc_start: 0.8948 (mttt) cc_final: 0.8537 (mttm) REVERT: A 558 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 577 GLU cc_start: 0.7570 (tt0) cc_final: 0.6932 (pp20) REVERT: A 600 PHE cc_start: 0.8909 (t80) cc_final: 0.8699 (t80) REVERT: A 629 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 638 ASP cc_start: 0.8667 (m-30) cc_final: 0.8214 (t0) REVERT: A 707 TRP cc_start: 0.8554 (m100) cc_final: 0.8272 (m100) REVERT: A 708 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8585 (mptt) REVERT: A 724 ARG cc_start: 0.8524 (mtp180) cc_final: 0.7141 (tpm170) REVERT: A 725 TRP cc_start: 0.9157 (p-90) cc_final: 0.7604 (p-90) REVERT: A 745 LEU cc_start: 0.8530 (mt) cc_final: 0.7924 (mt) REVERT: A 768 LEU cc_start: 0.8711 (mt) cc_final: 0.8438 (tp) REVERT: B 66 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.5871 (t80) REVERT: B 96 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6291 (tpt170) REVERT: B 97 LYS cc_start: 0.8528 (tptp) cc_final: 0.8262 (mttm) REVERT: C 14 LYS cc_start: 0.8479 (ptpt) cc_final: 0.7980 (mtpp) REVERT: C 59 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8863 (mp) REVERT: C 85 SER cc_start: 0.8980 (m) cc_final: 0.8730 (p) REVERT: C 89 CYS cc_start: 0.7995 (m) cc_final: 0.5696 (m) REVERT: C 92 ASP cc_start: 0.6860 (p0) cc_final: 0.6417 (p0) REVERT: C 94 GLN cc_start: 0.7810 (mt0) cc_final: 0.6978 (tp40) REVERT: C 102 ASN cc_start: 0.7022 (p0) cc_final: 0.6599 (m110) REVERT: C 106 ASN cc_start: 0.8419 (t0) cc_final: 0.8043 (t0) REVERT: C 109 TRP cc_start: 0.8539 (m100) cc_final: 0.6965 (m100) REVERT: C 133 LYS cc_start: 0.8798 (tptt) cc_final: 0.8248 (pttp) REVERT: C 195 GLU cc_start: 0.8609 (tt0) cc_final: 0.8124 (tt0) REVERT: C 207 ARG cc_start: 0.8293 (ttm110) cc_final: 0.8006 (ttt-90) REVERT: C 237 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8302 (ttpt) REVERT: C 244 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7543 (tp30) REVERT: C 259 ILE cc_start: 0.8277 (mp) cc_final: 0.7392 (mt) REVERT: D 70 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7611 (mpt-90) REVERT: D 93 ASN cc_start: 0.8874 (p0) cc_final: 0.8465 (p0) REVERT: D 115 ASP cc_start: 0.8258 (t0) cc_final: 0.8053 (t70) REVERT: D 131 SER cc_start: 0.8671 (p) cc_final: 0.8458 (p) REVERT: E 43 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7371 (mt-10) REVERT: E 63 ASP cc_start: 0.8493 (p0) cc_final: 0.8261 (p0) REVERT: E 86 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7655 (tp30) REVERT: E 116 PHE cc_start: 0.8731 (p90) cc_final: 0.8521 (p90) REVERT: E 118 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9070 (mt) REVERT: E 237 PHE cc_start: 0.8331 (m-80) cc_final: 0.7985 (m-80) REVERT: E 244 MET cc_start: 0.8150 (mmm) cc_final: 0.7890 (mmm) REVERT: E 262 ARG cc_start: 0.6724 (ttm170) cc_final: 0.5799 (mtt180) REVERT: E 264 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7395 (mm-30) REVERT: F 23 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8233 (p) REVERT: F 26 TYR cc_start: 0.7901 (t80) cc_final: 0.7512 (t80) REVERT: F 36 ASP cc_start: 0.8785 (t0) cc_final: 0.8548 (t0) REVERT: F 45 MET cc_start: 0.5433 (tpt) cc_final: 0.4779 (mtm) REVERT: F 86 THR cc_start: 0.9079 (p) cc_final: 0.8860 (m) REVERT: F 131 LYS cc_start: 0.8479 (tttp) cc_final: 0.7439 (mptt) REVERT: F 189 MET cc_start: 0.7913 (tpp) cc_final: 0.7461 (tpp) REVERT: F 220 LYS cc_start: 0.8513 (pttt) cc_final: 0.7912 (ttpt) REVERT: F 241 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8434 (mt-10) REVERT: F 275 LEU cc_start: 0.8683 (mt) cc_final: 0.8453 (tt) REVERT: F 290 TRP cc_start: 0.8587 (m100) cc_final: 0.8188 (m100) REVERT: F 297 TYR cc_start: 0.7628 (m-80) cc_final: 0.6862 (m-80) REVERT: F 327 ASP cc_start: 0.7055 (t0) cc_final: 0.6529 (p0) outliers start: 74 outliers final: 62 residues processed: 510 average time/residue: 0.2801 time to fit residues: 214.5417 Evaluate side-chains 530 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 463 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 125 CYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 64.3913 > 50: distance: 20 - 29: 8.439 distance: 29 - 30: 9.442 distance: 30 - 31: 7.126 distance: 30 - 33: 16.133 distance: 31 - 32: 13.147 distance: 31 - 35: 18.510 distance: 33 - 34: 6.672 distance: 35 - 36: 3.032 distance: 36 - 37: 26.052 distance: 37 - 38: 7.893 distance: 39 - 40: 4.858 distance: 41 - 42: 13.920 distance: 43 - 44: 12.369 distance: 44 - 45: 6.820 distance: 44 - 46: 6.511 distance: 49 - 50: 6.513 distance: 49 - 54: 3.651 distance: 51 - 53: 5.424 distance: 55 - 56: 4.303 distance: 55 - 58: 4.695 distance: 56 - 57: 13.579 distance: 56 - 66: 3.815 distance: 58 - 59: 17.930 distance: 59 - 60: 6.035 distance: 59 - 61: 9.052 distance: 60 - 62: 28.553 distance: 61 - 63: 12.541 distance: 62 - 64: 4.855 distance: 63 - 64: 15.262 distance: 66 - 67: 7.690 distance: 67 - 68: 9.297 distance: 67 - 70: 8.526 distance: 68 - 69: 38.005 distance: 68 - 78: 8.287 distance: 70 - 71: 8.621 distance: 71 - 72: 13.233 distance: 71 - 73: 25.454 distance: 72 - 74: 9.269 distance: 73 - 75: 17.759 distance: 74 - 76: 24.928 distance: 75 - 76: 3.866 distance: 76 - 77: 10.686 distance: 78 - 79: 20.229 distance: 79 - 80: 20.689 distance: 80 - 81: 30.931 distance: 80 - 86: 10.044 distance: 82 - 83: 17.921 distance: 83 - 84: 13.477 distance: 83 - 85: 25.243 distance: 86 - 87: 24.197 distance: 86 - 92: 15.344 distance: 87 - 88: 13.675 distance: 87 - 90: 13.508 distance: 88 - 89: 11.578 distance: 88 - 93: 10.384 distance: 90 - 91: 15.122 distance: 91 - 92: 9.337 distance: 93 - 94: 7.375 distance: 94 - 95: 8.192 distance: 94 - 97: 20.344 distance: 95 - 96: 22.083 distance: 95 - 102: 40.273 distance: 97 - 98: 9.911 distance: 98 - 99: 6.928 distance: 99 - 100: 3.147 distance: 100 - 101: 41.154 distance: 102 - 103: 33.701 distance: 102 - 108: 8.067 distance: 103 - 104: 7.584 distance: 103 - 106: 16.106 distance: 104 - 109: 34.573 distance: 106 - 107: 16.755 distance: 107 - 108: 8.743