Starting phenix.real_space_refine on Tue Jan 21 19:58:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iqw_9708/01_2025/6iqw_9708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iqw_9708/01_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_9708/01_2025/6iqw_9708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iqw_9708/01_2025/6iqw_9708.map" model { file = "/net/cci-nas-00/data/ceres_data/6iqw_9708/01_2025/6iqw_9708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iqw_9708/01_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-5571/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: 9.29, 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: 4.25 Conformation dependent library (CDL) restraints added in 2.0 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: 5.03 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: 5.42 Time building geometry restraints manager: 4.88 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.900 Find NCS groups from input model: 0.330 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- 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 17379 Z= 0.445 Angle : 1.051 19.035 23615 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 *********************** 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 : 1.768 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: 0.3210 time to fit residues: 315.8805 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 : 2.032 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.141195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116217 restraints weight = 32942.687| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 4.05 r_work: 0.3401 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 17379 Z= 0.243 Angle : 0.754 11.877 23615 Z= 0.393 Chirality : 0.049 0.319 2571 Planarity : 0.007 0.087 2941 Dihedral : 12.307 94.817 2704 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.21 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 *********************** 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 : 1.963 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: 0.6390 (m-80) cc_final: 0.5592 (m-80) REVERT: A 71 MET cc_start: 0.8239 (tpt) cc_final: 0.7670 (tpt) REVERT: A 99 GLU cc_start: 0.9064 (tp30) cc_final: 0.8561 (tp30) REVERT: A 114 GLN cc_start: 0.8094 (pt0) cc_final: 0.7269 (mp10) REVERT: A 121 SER cc_start: 0.9183 (t) cc_final: 0.8750 (m) REVERT: A 169 LYS cc_start: 0.7238 (mtpp) cc_final: 0.6560 (mtmm) REVERT: A 181 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8726 (ptmm) REVERT: A 192 GLU cc_start: 0.8758 (tt0) cc_final: 0.8167 (pm20) REVERT: A 203 ARG cc_start: 0.9191 (ttm170) cc_final: 0.8834 (ptm-80) REVERT: A 237 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7473 (mt-10) REVERT: A 253 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8745 (mmmt) REVERT: A 272 ASP cc_start: 0.8855 (t0) cc_final: 0.8172 (t0) REVERT: A 276 GLU cc_start: 0.8751 (tp30) cc_final: 0.8167 (tp30) REVERT: A 287 ASN cc_start: 0.9270 (m110) cc_final: 0.8993 (m-40) REVERT: A 299 ILE cc_start: 0.9430 (mt) cc_final: 0.9212 (mt) REVERT: A 342 GLU cc_start: 0.9234 (mt-10) cc_final: 0.9031 (mt-10) REVERT: A 359 LEU cc_start: 0.9236 (tp) cc_final: 0.8261 (tp) REVERT: A 430 LEU cc_start: 0.7937 (mt) cc_final: 0.7595 (tp) REVERT: A 439 ASP cc_start: 0.8326 (m-30) cc_final: 0.8121 (m-30) REVERT: A 454 TYR cc_start: 0.8144 (t80) cc_final: 0.7260 (t80) REVERT: A 464 GLN cc_start: 0.8560 (mp10) cc_final: 0.7863 (mp10) REVERT: A 490 TYR cc_start: 0.8404 (t80) cc_final: 0.7618 (t80) REVERT: A 503 GLU cc_start: 0.8712 (tt0) cc_final: 0.8183 (mt-10) REVERT: A 513 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8153 (ttm-80) REVERT: A 527 GLU cc_start: 0.8674 (tt0) cc_final: 0.7765 (tp30) REVERT: A 550 LYS cc_start: 0.8314 (mttt) cc_final: 0.8028 (mttm) REVERT: A 573 ASP cc_start: 0.8554 (m-30) cc_final: 0.8296 (p0) REVERT: A 577 GLU cc_start: 0.7787 (tt0) cc_final: 0.6976 (pp20) REVERT: A 629 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7027 (mt-10) REVERT: A 638 ASP cc_start: 0.8727 (m-30) cc_final: 0.8128 (t0) REVERT: A 650 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7850 (mm-30) REVERT: A 718 ARG cc_start: 0.8432 (ttm170) cc_final: 0.8061 (ttp-170) REVERT: A 725 TRP cc_start: 0.9114 (p-90) cc_final: 0.7479 (p-90) REVERT: A 745 LEU cc_start: 0.8383 (mt) cc_final: 0.7828 (mt) REVERT: A 755 ARG cc_start: 0.7929 (ptt180) cc_final: 0.7463 (ptt180) REVERT: B 96 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7385 (mtp180) REVERT: B 97 LYS cc_start: 0.8830 (tptp) cc_final: 0.8484 (mttm) REVERT: B 103 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7212 (mtt180) REVERT: B 122 LYS cc_start: 0.9319 (ptpt) cc_final: 0.8430 (mmmm) REVERT: B 123 MET cc_start: 0.9380 (mtp) cc_final: 0.9091 (ttm) REVERT: B 133 LYS cc_start: 0.8596 (tptp) cc_final: 0.8125 (mtmt) REVERT: C 14 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8037 (mtpp) REVERT: C 68 ASN cc_start: 0.9045 (t0) cc_final: 0.8836 (t0) REVERT: C 85 SER cc_start: 0.9004 (m) cc_final: 0.8744 (p) REVERT: C 89 CYS cc_start: 0.8129 (m) cc_final: 0.7901 (m) REVERT: C 94 GLN cc_start: 0.7603 (mt0) cc_final: 0.7028 (mm-40) REVERT: C 95 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7907 (mp0) REVERT: C 106 ASN cc_start: 0.8395 (t0) cc_final: 0.7984 (t0) REVERT: C 133 LYS cc_start: 0.8939 (tptt) cc_final: 0.8307 (pttp) REVERT: C 237 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8410 (ttpp) REVERT: C 244 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7573 (tp30) REVERT: C 249 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6787 (t0) REVERT: D 70 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7202 (mmt90) REVERT: D 140 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.8053 (mtp-110) REVERT: D 267 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6061 (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: 0.7976 (t80) REVERT: E 63 ASP cc_start: 0.8696 (p0) cc_final: 0.8469 (p0) REVERT: E 86 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8029 (tp30) REVERT: E 124 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7157 (m-10) REVERT: E 148 GLU cc_start: 0.7670 (mp0) cc_final: 0.7410 (mt-10) REVERT: E 158 TYR cc_start: 0.8874 (p90) cc_final: 0.8401 (p90) REVERT: E 200 HIS cc_start: 0.8303 (t-170) cc_final: 0.7783 (t70) REVERT: E 237 PHE cc_start: 0.8379 (m-80) cc_final: 0.7894 (m-10) REVERT: E 262 ARG cc_start: 0.7017 (mtt-85) cc_final: 0.6431 (mtt180) REVERT: E 264 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7397 (mm-30) REVERT: F 26 TYR cc_start: 0.7962 (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: 0.9141 (p) cc_final: 0.8850 (m) REVERT: F 99 GLN cc_start: 0.8485 (pm20) cc_final: 0.8260 (pm20) REVERT: F 127 TYR cc_start: 0.6714 (t80) cc_final: 0.6425 (t80) REVERT: F 131 LYS cc_start: 0.8399 (tttp) cc_final: 0.7643 (tppt) REVERT: F 183 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7453 (pp20) REVERT: F 198 ARG cc_start: 0.7383 (tmm-80) cc_final: 0.6674 (ttp-110) REVERT: F 204 ASP cc_start: 0.9156 (t0) cc_final: 0.8710 (t70) REVERT: F 220 LYS cc_start: 0.8490 (pttt) cc_final: 0.7836 (ttpt) REVERT: F 238 ILE cc_start: 0.7768 (tt) cc_final: 0.7524 (pt) REVERT: F 241 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8494 (mt-10) REVERT: F 275 LEU cc_start: 0.8735 (mt) cc_final: 0.8416 (tt) REVERT: F 297 TYR cc_start: 0.7765 (m-80) cc_final: 0.7171 (m-80) REVERT: F 319 ARG cc_start: 0.9278 (ttp80) cc_final: 0.8803 (mmt-90) REVERT: F 385 LEU cc_start: 0.8465 (mt) cc_final: 0.7518 (pp) REVERT: F 389 MET cc_start: 0.7729 (mpp) cc_final: 0.7515 (mpp) outliers start: 70 outliers final: 42 residues processed: 560 average time/residue: 0.3091 time to fit residues: 252.9151 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 : 1.740 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 212 ASN F 13 HIS F 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113895 restraints weight = 33249.147| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.03 r_work: 0.3354 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 17379 Z= 0.334 Angle : 0.768 10.661 23615 Z= 0.400 Chirality : 0.050 0.310 2571 Planarity : 0.006 0.096 2941 Dihedral : 12.067 90.732 2702 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.25 % Favored : 87.60 % Rotamer: Outliers : 5.37 % Allowed : 21.85 % Favored : 72.78 % 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: -3.33 (0.17), residues: 2049 helix: -1.20 (0.17), residues: 761 sheet: -2.48 (0.35), residues: 187 loop : -3.00 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 235 HIS 0.007 0.001 HIS D 111 PHE 0.038 0.002 PHE E 116 TYR 0.035 0.002 TYR B 55 ARG 0.008 0.001 ARG E 53 *********************** 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 578 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 486 time to evaluate : 1.911 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 26 TYR cc_start: 0.6285 (m-80) cc_final: 0.5979 (m-80) REVERT: A 71 MET cc_start: 0.8216 (tpt) cc_final: 0.7661 (tpt) REVERT: A 99 GLU cc_start: 0.9010 (tp30) cc_final: 0.8600 (tp30) REVERT: A 114 GLN cc_start: 0.8178 (pt0) cc_final: 0.7477 (mp10) REVERT: A 121 SER cc_start: 0.9206 (t) cc_final: 0.8710 (m) REVERT: A 152 GLN cc_start: 0.8257 (pt0) cc_final: 0.7254 (tp40) REVERT: A 169 LYS cc_start: 0.7289 (mtpp) cc_final: 0.6575 (mtmm) REVERT: A 192 GLU cc_start: 0.8809 (tt0) cc_final: 0.8276 (pm20) REVERT: A 203 ARG cc_start: 0.9323 (ttm170) cc_final: 0.8910 (ptm-80) REVERT: A 237 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 245 ASP cc_start: 0.9185 (m-30) cc_final: 0.8405 (t0) REVERT: A 253 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8826 (mmmt) REVERT: A 266 LEU cc_start: 0.9279 (tp) cc_final: 0.9067 (tt) REVERT: A 272 ASP cc_start: 0.8874 (t0) cc_final: 0.8249 (t0) REVERT: A 359 LEU cc_start: 0.9281 (tp) cc_final: 0.8350 (tp) REVERT: A 391 VAL cc_start: 0.9086 (t) cc_final: 0.8764 (p) REVERT: A 430 LEU cc_start: 0.7908 (mt) cc_final: 0.7632 (tp) REVERT: A 454 TYR cc_start: 0.8186 (t80) cc_final: 0.7378 (t80) REVERT: A 464 GLN cc_start: 0.8628 (mp10) cc_final: 0.7793 (mp10) REVERT: A 490 TYR cc_start: 0.8494 (t80) cc_final: 0.7716 (t80) REVERT: A 513 ARG cc_start: 0.8709 (mtp85) cc_final: 0.8214 (ttm-80) REVERT: A 537 LYS cc_start: 0.8910 (mttt) cc_final: 0.8674 (mttp) REVERT: A 549 PHE cc_start: 0.8717 (m-80) cc_final: 0.8501 (m-80) REVERT: A 550 LYS cc_start: 0.8344 (mttt) cc_final: 0.8086 (mttm) REVERT: A 560 LYS cc_start: 0.8636 (mttp) cc_final: 0.8200 (mmmt) REVERT: A 573 ASP cc_start: 0.8542 (m-30) cc_final: 0.8323 (p0) REVERT: A 601 GLU cc_start: 0.8794 (tt0) cc_final: 0.8532 (tt0) REVERT: A 629 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 638 ASP cc_start: 0.8724 (m-30) cc_final: 0.8081 (t0) REVERT: A 708 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8657 (mptt) REVERT: A 718 ARG cc_start: 0.8439 (ttm170) cc_final: 0.8006 (ttp-170) REVERT: A 724 ARG cc_start: 0.8676 (mtp180) cc_final: 0.7421 (mmp-170) REVERT: A 725 TRP cc_start: 0.9161 (p-90) cc_final: 0.7544 (p-90) REVERT: A 745 LEU cc_start: 0.8465 (mt) cc_final: 0.7920 (mp) REVERT: B 96 ARG cc_start: 0.7747 (ttm110) cc_final: 0.6757 (tpp-160) REVERT: B 97 LYS cc_start: 0.8726 (tptp) cc_final: 0.8425 (mttm) REVERT: B 103 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7221 (mtt180) REVERT: B 122 LYS cc_start: 0.9314 (ptpt) cc_final: 0.8538 (mmmt) REVERT: B 123 MET cc_start: 0.9321 (mtp) cc_final: 0.9037 (ttm) REVERT: B 133 LYS cc_start: 0.8700 (tptp) cc_final: 0.8297 (ptpt) REVERT: C 14 LYS cc_start: 0.8543 (ptpt) cc_final: 0.8016 (mtpp) REVERT: C 85 SER cc_start: 0.9034 (m) cc_final: 0.8797 (p) REVERT: C 89 CYS cc_start: 0.8235 (m) cc_final: 0.7829 (m) REVERT: C 94 GLN cc_start: 0.7547 (mt0) cc_final: 0.6926 (mm-40) REVERT: C 95 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7908 (mp0) REVERT: C 106 ASN cc_start: 0.8483 (t0) cc_final: 0.8076 (t0) REVERT: C 109 TRP cc_start: 0.8532 (m100) cc_final: 0.8167 (m100) REVERT: C 127 LEU cc_start: 0.9113 (tt) cc_final: 0.8896 (tt) REVERT: C 133 LYS cc_start: 0.8810 (tptt) cc_final: 0.8236 (pttp) REVERT: C 142 ILE cc_start: 0.8924 (mt) cc_final: 0.8663 (mm) REVERT: C 237 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8466 (ttpp) REVERT: C 244 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7619 (tp30) REVERT: C 249 ASP cc_start: 0.7176 (t70) cc_final: 0.6887 (t0) REVERT: D 70 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7313 (mmt90) REVERT: D 84 TYR cc_start: 0.8160 (m-80) cc_final: 0.7835 (m-80) REVERT: D 115 ASP cc_start: 0.8313 (t0) cc_final: 0.7939 (t70) REVERT: D 140 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8304 (mtp-110) REVERT: E 43 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7441 (mt-10) REVERT: E 63 ASP cc_start: 0.8666 (p0) cc_final: 0.8442 (p0) REVERT: E 86 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7983 (tp30) REVERT: E 89 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7914 (tpt170) REVERT: E 118 ILE cc_start: 0.9414 (tp) cc_final: 0.9123 (mt) REVERT: E 124 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7250 (m-10) REVERT: E 148 GLU cc_start: 0.7563 (mp0) cc_final: 0.7344 (mt-10) REVERT: E 158 TYR cc_start: 0.8971 (p90) cc_final: 0.8505 (p90) REVERT: E 200 HIS cc_start: 0.8247 (t-170) cc_final: 0.7728 (t70) REVERT: E 264 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 36 ASP cc_start: 0.8818 (t0) cc_final: 0.8602 (t0) REVERT: F 86 THR cc_start: 0.9147 (p) cc_final: 0.8906 (m) REVERT: F 99 GLN cc_start: 0.8684 (pm20) cc_final: 0.8405 (pm20) REVERT: F 127 TYR cc_start: 0.6801 (t80) cc_final: 0.6599 (t80) REVERT: F 131 LYS cc_start: 0.8386 (tttp) cc_final: 0.7658 (tppt) REVERT: F 204 ASP cc_start: 0.9170 (t0) cc_final: 0.8723 (t70) REVERT: F 220 LYS cc_start: 0.8551 (pttt) cc_final: 0.7876 (ttpt) REVERT: F 238 ILE cc_start: 0.7709 (tt) cc_final: 0.7406 (pt) REVERT: F 241 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8575 (mt-10) REVERT: F 275 LEU cc_start: 0.8725 (mt) cc_final: 0.8384 (tt) REVERT: F 290 TRP cc_start: 0.8517 (m100) cc_final: 0.8186 (m100) REVERT: F 297 TYR cc_start: 0.7689 (m-80) cc_final: 0.7221 (m-80) REVERT: F 319 ARG cc_start: 0.9248 (ttp80) cc_final: 0.8816 (mmt180) REVERT: F 327 ASP cc_start: 0.7010 (t0) cc_final: 0.6465 (p0) REVERT: F 385 LEU cc_start: 0.8444 (mt) cc_final: 0.7534 (pp) outliers start: 92 outliers final: 63 residues processed: 536 average time/residue: 0.3162 time to fit residues: 248.7691 Evaluate side-chains 520 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 454 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 444 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 13 HIS 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: 6.9990 chunk 100 optimal weight: 0.0470 chunk 16 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- 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 598 GLN B 179 HIS C 44 HIS D 183 ASN E 30 ASN F 13 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112833 restraints weight = 33251.831| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.97 r_work: 0.3351 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17379 Z= 0.309 Angle : 0.749 12.750 23615 Z= 0.387 Chirality : 0.049 0.290 2571 Planarity : 0.006 0.099 2941 Dihedral : 11.976 94.890 2702 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.76 % Favored : 88.14 % Rotamer: Outliers : 5.96 % Allowed : 23.95 % Favored : 70.09 % 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: -3.02 (0.17), residues: 2049 helix: -0.82 (0.18), residues: 749 sheet: -2.48 (0.35), residues: 188 loop : -2.87 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 152 HIS 0.010 0.001 HIS F 13 PHE 0.026 0.002 PHE E 58 TYR 0.030 0.002 TYR B 55 ARG 0.007 0.001 ARG E 53 *********************** 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 584 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 482 time to evaluate : 1.544 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: symmetry clash REVERT: A 26 TYR cc_start: 0.6444 (m-80) cc_final: 0.6220 (m-80) REVERT: A 65 MET cc_start: 0.7292 (mtt) cc_final: 0.7036 (mtt) REVERT: A 71 MET cc_start: 0.8120 (tpt) cc_final: 0.7563 (tpt) REVERT: A 99 GLU cc_start: 0.9018 (tp30) cc_final: 0.8659 (tp30) REVERT: A 114 GLN cc_start: 0.8214 (pt0) cc_final: 0.7449 (mp10) REVERT: A 121 SER cc_start: 0.9173 (t) cc_final: 0.8645 (m) REVERT: A 152 GLN cc_start: 0.8219 (pt0) cc_final: 0.7262 (tp40) REVERT: A 166 SER cc_start: 0.8445 (m) cc_final: 0.8086 (p) REVERT: A 169 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6525 (mtmm) REVERT: A 192 GLU cc_start: 0.8807 (tt0) cc_final: 0.8300 (pm20) REVERT: A 203 ARG cc_start: 0.9264 (ttm170) cc_final: 0.8950 (ptm-80) REVERT: A 237 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 245 ASP cc_start: 0.9197 (m-30) cc_final: 0.8350 (t0) REVERT: A 253 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8842 (mmmt) REVERT: A 266 LEU cc_start: 0.9258 (tp) cc_final: 0.9052 (tt) REVERT: A 272 ASP cc_start: 0.8843 (t0) cc_final: 0.8246 (t0) REVERT: A 276 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: A 283 LEU cc_start: 0.9424 (mt) cc_final: 0.9171 (mt) REVERT: A 289 VAL cc_start: 0.9716 (t) cc_final: 0.9461 (p) REVERT: A 334 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8180 (mm-30) REVERT: A 359 LEU cc_start: 0.9265 (tp) cc_final: 0.8333 (tp) REVERT: A 430 LEU cc_start: 0.7901 (mt) cc_final: 0.7539 (tp) REVERT: A 454 TYR cc_start: 0.8207 (t80) cc_final: 0.7211 (t80) REVERT: A 464 GLN cc_start: 0.8620 (mp10) cc_final: 0.7838 (mp10) REVERT: A 490 TYR cc_start: 0.8424 (t80) cc_final: 0.7644 (t80) REVERT: A 513 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8217 (ttm-80) REVERT: A 537 LYS cc_start: 0.8886 (mttt) cc_final: 0.8633 (mttp) REVERT: A 560 LYS cc_start: 0.8673 (mttp) cc_final: 0.8212 (mmmt) REVERT: A 629 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 638 ASP cc_start: 0.8730 (m-30) cc_final: 0.8149 (t0) REVERT: A 708 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8647 (mptt) REVERT: A 718 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8137 (ttp-170) REVERT: A 724 ARG cc_start: 0.8675 (mtp180) cc_final: 0.7463 (mmp-170) REVERT: A 725 TRP cc_start: 0.9167 (p-90) cc_final: 0.7575 (p-90) REVERT: A 745 LEU cc_start: 0.8489 (mt) cc_final: 0.7867 (mt) REVERT: B 96 ARG cc_start: 0.7719 (ttm110) cc_final: 0.6778 (tpp-160) REVERT: B 97 LYS cc_start: 0.8721 (tptp) cc_final: 0.8382 (mttm) REVERT: B 103 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7249 (mtt180) REVERT: B 117 LYS cc_start: 0.7588 (ptpp) cc_final: 0.7224 (mmmt) REVERT: B 133 LYS cc_start: 0.8702 (tptp) cc_final: 0.8320 (ptpt) REVERT: C 14 LYS cc_start: 0.8552 (ptpt) cc_final: 0.8036 (mtpp) REVERT: C 58 ARG cc_start: 0.7826 (tpt170) cc_final: 0.7342 (tpt170) REVERT: C 85 SER cc_start: 0.9042 (m) cc_final: 0.8804 (p) REVERT: C 89 CYS cc_start: 0.8235 (m) cc_final: 0.6739 (m) REVERT: C 94 GLN cc_start: 0.7540 (mt0) cc_final: 0.6837 (tp40) REVERT: C 95 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7824 (mp0) REVERT: C 106 ASN cc_start: 0.8490 (t0) cc_final: 0.8092 (t0) REVERT: C 109 TRP cc_start: 0.8578 (m100) cc_final: 0.6801 (m-10) REVERT: C 133 LYS cc_start: 0.8779 (tptt) cc_final: 0.8174 (pttp) REVERT: C 142 ILE cc_start: 0.8958 (mt) cc_final: 0.8695 (mm) REVERT: C 237 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8451 (ttpp) REVERT: D 70 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7415 (mpt-90) REVERT: D 115 ASP cc_start: 0.8288 (t0) cc_final: 0.8033 (t70) REVERT: E 20 ARG cc_start: 0.8649 (mmp80) cc_final: 0.8427 (mmp80) REVERT: E 43 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7437 (mt-10) REVERT: E 63 ASP cc_start: 0.8650 (p0) cc_final: 0.8408 (p0) REVERT: E 86 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7831 (tp30) REVERT: E 89 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8013 (tpt170) REVERT: E 118 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9193 (mt) REVERT: E 124 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: E 148 GLU cc_start: 0.7586 (mp0) cc_final: 0.7363 (mt-10) REVERT: E 200 HIS cc_start: 0.8283 (t-170) cc_final: 0.7760 (t70) REVERT: E 237 PHE cc_start: 0.8323 (m-80) cc_final: 0.7798 (m-10) REVERT: E 262 ARG cc_start: 0.6850 (ttm170) cc_final: 0.6326 (ttm170) REVERT: E 264 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7592 (mm-30) REVERT: F 23 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8307 (p) REVERT: F 26 TYR cc_start: 0.7820 (t80) cc_final: 0.7360 (t80) REVERT: F 36 ASP cc_start: 0.8838 (t0) cc_final: 0.8603 (t0) REVERT: F 45 MET cc_start: 0.6211 (mmm) cc_final: 0.5481 (mtm) REVERT: F 86 THR cc_start: 0.9136 (p) cc_final: 0.8887 (m) REVERT: F 99 GLN cc_start: 0.8722 (pm20) cc_final: 0.8482 (pm20) REVERT: F 127 TYR cc_start: 0.6857 (t80) cc_final: 0.6653 (t80) REVERT: F 131 LYS cc_start: 0.8377 (tttp) cc_final: 0.7657 (tppt) REVERT: F 220 LYS cc_start: 0.8557 (pttt) cc_final: 0.7913 (ttpt) REVERT: F 238 ILE cc_start: 0.7786 (tt) cc_final: 0.7239 (pt) REVERT: F 241 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8617 (mt-10) REVERT: F 275 LEU cc_start: 0.8729 (mt) cc_final: 0.8414 (tt) REVERT: F 290 TRP cc_start: 0.8503 (m100) cc_final: 0.8122 (m100) REVERT: F 297 TYR cc_start: 0.7760 (m-80) cc_final: 0.7255 (m-80) REVERT: F 327 ASP cc_start: 0.7041 (t0) cc_final: 0.6432 (p0) outliers start: 102 outliers final: 75 residues processed: 536 average time/residue: 0.3091 time to fit residues: 243.6027 Evaluate side-chains 523 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 442 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 175 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 276 GLU 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 518 MET 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 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 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 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 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 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 127 LEU 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 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 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 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** 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 = 0.3858 r_free = 0.3858 target = 0.140630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115411 restraints weight = 33339.344| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 4.06 r_work: 0.3385 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17379 Z= 0.238 Angle : 0.719 12.715 23615 Z= 0.369 Chirality : 0.048 0.272 2571 Planarity : 0.006 0.101 2941 Dihedral : 11.833 93.777 2702 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.91 % Favored : 87.99 % Rotamer: Outliers : 5.49 % Allowed : 25.99 % Favored : 68.52 % 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: -2.74 (0.18), residues: 2049 helix: -0.58 (0.18), residues: 741 sheet: -2.34 (0.36), residues: 187 loop : -2.68 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 152 HIS 0.007 0.001 HIS A 60 PHE 0.023 0.002 PHE D 238 TYR 0.042 0.002 TYR F 322 ARG 0.007 0.001 ARG B 74 *********************** 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 574 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 480 time to evaluate : 1.760 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: A 26 TYR cc_start: 0.6540 (m-80) cc_final: 0.6303 (m-80) REVERT: A 65 MET cc_start: 0.7109 (mtt) cc_final: 0.6884 (mtt) REVERT: A 71 MET cc_start: 0.8144 (tpt) cc_final: 0.7602 (tpt) REVERT: A 99 GLU cc_start: 0.9069 (tp30) cc_final: 0.8654 (tp30) REVERT: A 114 GLN cc_start: 0.8199 (pt0) cc_final: 0.7496 (mp10) REVERT: A 121 SER cc_start: 0.9021 (t) cc_final: 0.8430 (m) REVERT: A 152 GLN cc_start: 0.8152 (pt0) cc_final: 0.7185 (tp40) REVERT: A 166 SER cc_start: 0.8415 (m) cc_final: 0.8053 (p) REVERT: A 169 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6495 (mtmm) REVERT: A 181 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8653 (ptmm) REVERT: A 192 GLU cc_start: 0.8744 (tt0) cc_final: 0.8233 (pm20) REVERT: A 203 ARG cc_start: 0.9218 (ttm170) cc_final: 0.8954 (ptm-80) REVERT: A 237 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 245 ASP cc_start: 0.9185 (m-30) cc_final: 0.8318 (t0) REVERT: A 253 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8829 (mmmt) REVERT: A 272 ASP cc_start: 0.8763 (t0) cc_final: 0.8192 (t0) REVERT: A 276 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: A 283 LEU cc_start: 0.9437 (mt) cc_final: 0.9224 (mt) REVERT: A 359 LEU cc_start: 0.9220 (tp) cc_final: 0.8273 (tp) REVERT: A 430 LEU cc_start: 0.7910 (mt) cc_final: 0.7554 (tp) REVERT: A 454 TYR cc_start: 0.8166 (t80) cc_final: 0.7168 (t80) REVERT: A 464 GLN cc_start: 0.8592 (mp10) cc_final: 0.7911 (mp10) REVERT: A 490 TYR cc_start: 0.8413 (t80) cc_final: 0.7645 (t80) REVERT: A 513 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8212 (ttm-80) REVERT: A 537 LYS cc_start: 0.8909 (mttt) cc_final: 0.8621 (mttp) REVERT: A 560 LYS cc_start: 0.8657 (mttp) cc_final: 0.8184 (mmmt) REVERT: A 600 PHE cc_start: 0.8951 (t80) cc_final: 0.8305 (t80) REVERT: A 629 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 638 ASP cc_start: 0.8693 (m-30) cc_final: 0.8144 (t0) REVERT: A 708 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8648 (mptt) REVERT: A 718 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8187 (ttp-170) REVERT: A 724 ARG cc_start: 0.8644 (mtp180) cc_final: 0.7436 (mmp-170) REVERT: A 725 TRP cc_start: 0.9134 (p-90) cc_final: 0.7501 (p-90) REVERT: A 745 LEU cc_start: 0.8488 (mt) cc_final: 0.7941 (mp) REVERT: B 66 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.6004 (t80) REVERT: B 96 ARG cc_start: 0.7514 (ttm110) cc_final: 0.6506 (tpp-160) REVERT: B 97 LYS cc_start: 0.8651 (tptp) cc_final: 0.8328 (mttm) REVERT: B 110 LYS cc_start: 0.8943 (tptp) cc_final: 0.8489 (mtmt) REVERT: B 117 LYS cc_start: 0.7603 (ptpp) cc_final: 0.7265 (mmmt) REVERT: B 133 LYS cc_start: 0.8694 (tptp) cc_final: 0.8303 (ptpt) REVERT: C 14 LYS cc_start: 0.8454 (ptpt) cc_final: 0.7953 (mtpp) REVERT: C 85 SER cc_start: 0.9024 (m) cc_final: 0.8790 (p) REVERT: C 89 CYS cc_start: 0.8120 (m) cc_final: 0.6424 (m) REVERT: C 92 ASP cc_start: 0.7108 (p0) cc_final: 0.6677 (p0) REVERT: C 94 GLN cc_start: 0.7579 (mt0) cc_final: 0.6860 (tp40) REVERT: C 95 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7722 (mp0) REVERT: C 106 ASN cc_start: 0.8445 (t0) cc_final: 0.8092 (t0) REVERT: C 109 TRP cc_start: 0.8500 (m100) cc_final: 0.6801 (m-10) REVERT: C 142 ILE cc_start: 0.8909 (mt) cc_final: 0.8648 (mm) REVERT: C 195 GLU cc_start: 0.8645 (tt0) cc_final: 0.7933 (tt0) REVERT: C 237 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8385 (ttpp) REVERT: C 259 ILE cc_start: 0.8098 (mp) cc_final: 0.7838 (mt) REVERT: D 70 ARG cc_start: 0.7918 (mmm160) cc_final: 0.7432 (mpt-90) REVERT: D 115 ASP cc_start: 0.8301 (t0) cc_final: 0.8048 (t70) REVERT: D 224 TYR cc_start: 0.8645 (p90) cc_final: 0.8414 (p90) REVERT: E 43 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7449 (mt-10) REVERT: E 63 ASP cc_start: 0.8609 (p0) cc_final: 0.8353 (p0) REVERT: E 86 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7742 (tp30) REVERT: E 89 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8053 (tpt170) REVERT: E 118 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9161 (mt) REVERT: E 124 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: E 200 HIS cc_start: 0.8194 (t-170) cc_final: 0.7739 (t70) REVERT: E 262 ARG cc_start: 0.6876 (ttm170) cc_final: 0.5944 (mtt180) REVERT: E 264 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7662 (mm-30) REVERT: F 23 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8305 (p) REVERT: F 26 TYR cc_start: 0.7876 (t80) cc_final: 0.7428 (t80) REVERT: F 36 ASP cc_start: 0.8832 (t0) cc_final: 0.8594 (t0) REVERT: F 45 MET cc_start: 0.6790 (mmm) cc_final: 0.6238 (mtm) REVERT: F 86 THR cc_start: 0.9143 (p) cc_final: 0.8901 (m) REVERT: F 99 GLN cc_start: 0.8713 (pm20) cc_final: 0.8487 (pm20) REVERT: F 198 ARG cc_start: 0.7537 (ttt-90) cc_final: 0.7133 (ttt-90) REVERT: F 220 LYS cc_start: 0.8563 (pttt) cc_final: 0.7947 (ttpt) REVERT: F 241 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8548 (mt-10) REVERT: F 275 LEU cc_start: 0.8672 (mt) cc_final: 0.8372 (tt) REVERT: F 290 TRP cc_start: 0.8505 (m100) cc_final: 0.8095 (m100) REVERT: F 297 TYR cc_start: 0.7721 (m-80) cc_final: 0.7162 (m-80) REVERT: F 298 THR cc_start: 0.8367 (m) cc_final: 0.8160 (p) REVERT: F 327 ASP cc_start: 0.7071 (t0) cc_final: 0.6472 (p0) outliers start: 94 outliers final: 68 residues processed: 531 average time/residue: 0.3068 time to fit residues: 240.4736 Evaluate side-chains 520 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 446 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU 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 733 LEU 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 40 ILE 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 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 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 67 VAL Chi-restraints excluded: chain D residue 80 SER 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 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 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 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 276 LEU Chi-restraints excluded: chain E residue 280 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 106 ASN E 200 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 = 0.3812 r_free = 0.3812 target = 0.136715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111660 restraints weight = 33725.695| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.98 r_work: 0.3348 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17379 Z= 0.359 Angle : 0.777 13.675 23615 Z= 0.400 Chirality : 0.050 0.267 2571 Planarity : 0.006 0.098 2941 Dihedral : 11.877 89.269 2702 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.54 % Favored : 87.31 % Rotamer: Outliers : 7.18 % Allowed : 25.82 % Favored : 67.00 % 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: -2.72 (0.18), residues: 2049 helix: -0.57 (0.18), residues: 754 sheet: -2.28 (0.35), residues: 202 loop : -2.70 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 239 HIS 0.008 0.002 HIS D 205 PHE 0.028 0.002 PHE E 58 TYR 0.043 0.003 TYR F 322 ARG 0.012 0.001 ARG C 60 *********************** 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 580 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 457 time to evaluate : 1.881 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 26 TYR cc_start: 0.6475 (m-80) cc_final: 0.6232 (m-80) REVERT: A 65 MET cc_start: 0.7216 (mtt) cc_final: 0.6997 (mmm) REVERT: A 71 MET cc_start: 0.8251 (tpt) cc_final: 0.7782 (tpt) REVERT: A 99 GLU cc_start: 0.9098 (tp30) cc_final: 0.8741 (tp30) REVERT: A 114 GLN cc_start: 0.8255 (pt0) cc_final: 0.7567 (mp10) REVERT: A 121 SER cc_start: 0.9073 (t) cc_final: 0.8463 (m) REVERT: A 152 GLN cc_start: 0.8169 (pt0) cc_final: 0.7287 (tp40) REVERT: A 166 SER cc_start: 0.8466 (m) cc_final: 0.8111 (p) REVERT: A 169 LYS cc_start: 0.7229 (mtpp) cc_final: 0.6569 (mtmm) REVERT: A 181 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8634 (ptmm) REVERT: A 192 GLU cc_start: 0.8884 (tt0) cc_final: 0.8352 (pm20) REVERT: A 203 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8320 (ttm170) REVERT: A 237 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 245 ASP cc_start: 0.9231 (m-30) cc_final: 0.8487 (t0) REVERT: A 253 LYS cc_start: 0.9102 (mmtp) cc_final: 0.8874 (mmmt) REVERT: A 272 ASP cc_start: 0.8787 (t0) cc_final: 0.8241 (t0) REVERT: A 276 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: A 359 LEU cc_start: 0.9285 (tp) cc_final: 0.8514 (tp) REVERT: A 391 VAL cc_start: 0.9075 (t) cc_final: 0.8846 (t) REVERT: A 430 LEU cc_start: 0.7936 (mt) cc_final: 0.7611 (tp) REVERT: A 454 TYR cc_start: 0.8185 (t80) cc_final: 0.7218 (t80) REVERT: A 464 GLN cc_start: 0.8664 (mp10) cc_final: 0.7984 (mp10) REVERT: A 490 TYR cc_start: 0.8501 (t80) cc_final: 0.7929 (t80) REVERT: A 513 ARG cc_start: 0.8635 (mtp85) cc_final: 0.8183 (ttm-80) REVERT: A 537 LYS cc_start: 0.8973 (mttt) cc_final: 0.8647 (mttm) REVERT: A 629 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7112 (mt-10) REVERT: A 638 ASP cc_start: 0.8754 (m-30) cc_final: 0.8244 (t0) REVERT: A 707 TRP cc_start: 0.8555 (m100) cc_final: 0.8155 (m100) REVERT: A 708 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8674 (mptt) REVERT: A 724 ARG cc_start: 0.8622 (mtp180) cc_final: 0.7432 (mmp-170) REVERT: A 725 TRP cc_start: 0.9197 (p-90) cc_final: 0.7536 (p-90) REVERT: A 742 PHE cc_start: 0.9493 (m-80) cc_final: 0.9203 (m-80) REVERT: A 745 LEU cc_start: 0.8570 (mt) cc_final: 0.7886 (mt) REVERT: B 66 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.5813 (t80) REVERT: B 96 ARG cc_start: 0.7559 (ttm110) cc_final: 0.6630 (tpt170) REVERT: B 97 LYS cc_start: 0.8666 (tptp) cc_final: 0.8295 (mttm) REVERT: B 117 LYS cc_start: 0.7730 (ptpp) cc_final: 0.7382 (mmmt) REVERT: B 133 LYS cc_start: 0.8688 (tptp) cc_final: 0.8382 (ptpt) REVERT: C 14 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8054 (mtpp) REVERT: C 85 SER cc_start: 0.9064 (m) cc_final: 0.8824 (p) REVERT: C 89 CYS cc_start: 0.8174 (m) cc_final: 0.6866 (m) REVERT: C 94 GLN cc_start: 0.7611 (mt0) cc_final: 0.6904 (tp40) REVERT: C 95 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7825 (mp0) REVERT: C 106 ASN cc_start: 0.8523 (t0) cc_final: 0.8115 (t0) REVERT: C 109 TRP cc_start: 0.8632 (m100) cc_final: 0.7026 (m-10) REVERT: C 142 ILE cc_start: 0.8970 (mt) cc_final: 0.8727 (mm) REVERT: C 195 GLU cc_start: 0.8812 (tt0) cc_final: 0.8203 (tt0) REVERT: C 207 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7973 (ttt-90) REVERT: C 237 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8357 (ttpp) REVERT: C 244 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7670 (tp30) REVERT: C 259 ILE cc_start: 0.8144 (mp) cc_final: 0.7385 (mt) REVERT: D 55 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8758 (tt) REVERT: D 70 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7477 (mpt-90) REVERT: D 115 ASP cc_start: 0.8374 (t0) cc_final: 0.8130 (t70) REVERT: D 224 TYR cc_start: 0.8772 (p90) cc_final: 0.8536 (p90) REVERT: E 43 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7495 (mt-10) REVERT: E 63 ASP cc_start: 0.8600 (p0) cc_final: 0.8324 (p0) REVERT: E 86 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7734 (tp30) REVERT: E 89 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8097 (tpt170) REVERT: E 118 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9126 (mt) REVERT: E 124 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.7069 (m-10) REVERT: E 200 HIS cc_start: 0.8078 (t70) cc_final: 0.7691 (t70) REVERT: E 237 PHE cc_start: 0.8330 (m-80) cc_final: 0.7872 (m-10) REVERT: E 262 ARG cc_start: 0.6914 (ttm170) cc_final: 0.6295 (ttm170) REVERT: E 264 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7593 (mm-30) REVERT: F 23 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8346 (p) REVERT: F 36 ASP cc_start: 0.8846 (t0) cc_final: 0.8598 (t0) REVERT: F 45 MET cc_start: 0.6822 (mmm) cc_final: 0.6253 (mtm) REVERT: F 86 THR cc_start: 0.9133 (p) cc_final: 0.8887 (m) REVERT: F 99 GLN cc_start: 0.8822 (pm20) cc_final: 0.8478 (pm20) REVERT: F 163 TYR cc_start: 0.8137 (t80) cc_final: 0.7521 (t80) REVERT: F 189 MET cc_start: 0.7830 (ttm) cc_final: 0.7319 (mmm) REVERT: F 220 LYS cc_start: 0.8554 (pttt) cc_final: 0.7919 (ttpt) REVERT: F 241 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8455 (mt-10) REVERT: F 275 LEU cc_start: 0.8682 (mt) cc_final: 0.8364 (tt) REVERT: F 290 TRP cc_start: 0.8580 (m100) cc_final: 0.8148 (m100) REVERT: F 297 TYR cc_start: 0.7688 (m-80) cc_final: 0.7054 (m-80) REVERT: F 298 THR cc_start: 0.8513 (m) cc_final: 0.8301 (p) REVERT: F 327 ASP cc_start: 0.7075 (t0) cc_final: 0.6502 (p0) REVERT: F 390 PRO cc_start: 0.8441 (Cg_exo) cc_final: 0.8229 (Cg_endo) outliers start: 123 outliers final: 101 residues processed: 525 average time/residue: 0.3066 time to fit residues: 238.5178 Evaluate side-chains 543 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 434 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 203 ARG Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 336 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 733 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 765 ASP 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 39 VAL Chi-restraints excluded: chain C residue 40 ILE 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 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 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 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 197 ILE 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 225 LEU Chi-restraints excluded: chain D residue 230 SER 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 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 140 ASP 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 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 104 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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** D 96 ASN D 183 ASN ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115803 restraints weight = 33346.401| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.04 r_work: 0.3386 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17379 Z= 0.261 Angle : 0.732 13.298 23615 Z= 0.374 Chirality : 0.049 0.250 2571 Planarity : 0.006 0.099 2941 Dihedral : 11.785 86.193 2702 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.66 % Favored : 88.24 % Rotamer: Outliers : 6.48 % Allowed : 26.52 % Favored : 67.00 % 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: -2.57 (0.18), residues: 2049 helix: -0.47 (0.18), residues: 755 sheet: -2.26 (0.36), residues: 193 loop : -2.58 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 152 HIS 0.008 0.001 HIS A 60 PHE 0.027 0.002 PHE E 58 TYR 0.036 0.002 TYR F 322 ARG 0.008 0.001 ARG B 74 *********************** 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 581 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 470 time to evaluate : 1.569 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 26 TYR cc_start: 0.6702 (m-80) cc_final: 0.6338 (m-80) REVERT: A 65 MET cc_start: 0.7170 (mtt) cc_final: 0.6835 (mtt) REVERT: A 71 MET cc_start: 0.8121 (tpt) cc_final: 0.7781 (tpt) REVERT: A 99 GLU cc_start: 0.9097 (tp30) cc_final: 0.8702 (tp30) REVERT: A 114 GLN cc_start: 0.8295 (pt0) cc_final: 0.7623 (mp10) REVERT: A 121 SER cc_start: 0.9051 (t) cc_final: 0.8453 (m) REVERT: A 152 GLN cc_start: 0.8122 (pt0) cc_final: 0.7188 (tp40) REVERT: A 166 SER cc_start: 0.8433 (m) cc_final: 0.8080 (p) REVERT: A 169 LYS cc_start: 0.7076 (mtpp) cc_final: 0.6404 (mtmm) REVERT: A 180 GLU cc_start: 0.9211 (tt0) cc_final: 0.8958 (mm-30) REVERT: A 181 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8617 (ptmm) REVERT: A 192 GLU cc_start: 0.8796 (tt0) cc_final: 0.8284 (pm20) REVERT: A 194 ASN cc_start: 0.8512 (t0) cc_final: 0.7991 (t0) REVERT: A 203 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8868 (ptm-80) REVERT: A 237 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 245 ASP cc_start: 0.9209 (m-30) cc_final: 0.8413 (t0) REVERT: A 253 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8853 (mmmt) REVERT: A 272 ASP cc_start: 0.8737 (t0) cc_final: 0.8210 (t0) REVERT: A 276 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: A 334 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 342 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8478 (mp0) REVERT: A 359 LEU cc_start: 0.9218 (tp) cc_final: 0.8437 (tp) REVERT: A 391 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8828 (t) REVERT: A 430 LEU cc_start: 0.7908 (mt) cc_final: 0.7572 (tp) REVERT: A 454 TYR cc_start: 0.8150 (t80) cc_final: 0.7173 (t80) REVERT: A 464 GLN cc_start: 0.8637 (mp10) cc_final: 0.7955 (mp10) REVERT: A 490 TYR cc_start: 0.8452 (t80) cc_final: 0.7670 (t80) REVERT: A 513 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8250 (ttm-80) REVERT: A 537 LYS cc_start: 0.8955 (mttt) cc_final: 0.8610 (mttm) REVERT: A 629 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 638 ASP cc_start: 0.8698 (m-30) cc_final: 0.8218 (t0) REVERT: A 707 TRP cc_start: 0.8533 (m100) cc_final: 0.8277 (m100) REVERT: A 708 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8636 (mptt) REVERT: A 724 ARG cc_start: 0.8531 (mtp180) cc_final: 0.7265 (mmp-170) REVERT: A 725 TRP cc_start: 0.9169 (p-90) cc_final: 0.7513 (p-90) REVERT: A 745 LEU cc_start: 0.8551 (mt) cc_final: 0.7899 (mt) REVERT: B 66 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.5817 (t80) REVERT: B 96 ARG cc_start: 0.7470 (ttm110) cc_final: 0.6413 (tpt170) REVERT: B 97 LYS cc_start: 0.8667 (tptp) cc_final: 0.8344 (mttm) REVERT: B 117 LYS cc_start: 0.7718 (ptpp) cc_final: 0.7342 (mmmt) REVERT: B 133 LYS cc_start: 0.8636 (tptp) cc_final: 0.8246 (mtmt) REVERT: C 14 LYS cc_start: 0.8471 (ptpt) cc_final: 0.7933 (mtpp) REVERT: C 85 SER cc_start: 0.9031 (m) cc_final: 0.8783 (p) REVERT: C 89 CYS cc_start: 0.8131 (m) cc_final: 0.6578 (m) REVERT: C 94 GLN cc_start: 0.7640 (mt0) cc_final: 0.7048 (tp40) REVERT: C 95 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7730 (mp0) REVERT: C 106 ASN cc_start: 0.8470 (t0) cc_final: 0.8109 (t0) REVERT: C 109 TRP cc_start: 0.8523 (m100) cc_final: 0.6850 (m-10) REVERT: C 142 ILE cc_start: 0.8947 (mt) cc_final: 0.8667 (mm) REVERT: C 195 GLU cc_start: 0.8664 (tt0) cc_final: 0.8101 (tt0) REVERT: C 207 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7993 (ttt-90) REVERT: C 237 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8363 (ttpp) REVERT: C 259 ILE cc_start: 0.8141 (mp) cc_final: 0.7834 (mt) REVERT: D 55 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8710 (tt) REVERT: D 70 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7472 (mpt-90) REVERT: D 96 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7289 (m-40) REVERT: D 115 ASP cc_start: 0.8313 (t0) cc_final: 0.8098 (t70) REVERT: E 20 ARG cc_start: 0.8766 (mmp80) cc_final: 0.8547 (mmp80) REVERT: E 43 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7537 (mt-10) REVERT: E 63 ASP cc_start: 0.8571 (p0) cc_final: 0.8318 (p0) REVERT: E 86 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7702 (tp30) REVERT: E 89 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.8004 (tpt170) REVERT: E 118 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9162 (mt) REVERT: E 200 HIS cc_start: 0.8103 (t70) cc_final: 0.7888 (t-90) REVERT: E 237 PHE cc_start: 0.8326 (m-80) cc_final: 0.7872 (m-80) REVERT: E 262 ARG cc_start: 0.6773 (ttm170) cc_final: 0.5918 (mtt180) REVERT: E 264 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7131 (mm-30) REVERT: F 23 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8346 (p) REVERT: F 36 ASP cc_start: 0.8833 (t0) cc_final: 0.8577 (t0) REVERT: F 45 MET cc_start: 0.6884 (mmm) cc_final: 0.6373 (mtm) REVERT: F 86 THR cc_start: 0.9117 (p) cc_final: 0.8872 (m) REVERT: F 99 GLN cc_start: 0.8784 (pm20) cc_final: 0.8433 (pm20) REVERT: F 189 MET cc_start: 0.7863 (ttm) cc_final: 0.7095 (tpp) REVERT: F 200 GLU cc_start: 0.7564 (tp30) cc_final: 0.7298 (tp30) REVERT: F 220 LYS cc_start: 0.8538 (pttt) cc_final: 0.7910 (ttpt) REVERT: F 241 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8444 (mt-10) REVERT: F 275 LEU cc_start: 0.8667 (mt) cc_final: 0.8394 (tt) REVERT: F 290 TRP cc_start: 0.8574 (m100) cc_final: 0.8132 (m100) REVERT: F 297 TYR cc_start: 0.7707 (m-80) cc_final: 0.7068 (m-80) REVERT: F 327 ASP cc_start: 0.7059 (t0) cc_final: 0.6520 (p0) REVERT: F 390 PRO cc_start: 0.8359 (Cg_exo) cc_final: 0.8155 (Cg_endo) outliers start: 111 outliers final: 90 residues processed: 534 average time/residue: 0.3047 time to fit residues: 240.7232 Evaluate side-chains 536 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 437 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 20 VAL 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 187 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU 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 391 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 606 VAL 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 733 LEU 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 40 ILE 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 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 258 ASP 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 55 LEU 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 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR 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 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 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 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 276 LEU Chi-restraints excluded: chain F residue 23 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 24 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 263 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116667 restraints weight = 33209.093| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.05 r_work: 0.3382 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17379 Z= 0.254 Angle : 0.726 13.644 23615 Z= 0.371 Chirality : 0.049 0.239 2571 Planarity : 0.006 0.095 2941 Dihedral : 11.721 84.331 2702 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.91 % Favored : 87.99 % Rotamer: Outliers : 6.66 % Allowed : 27.04 % Favored : 66.30 % 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: -2.50 (0.18), residues: 2049 helix: -0.40 (0.19), residues: 757 sheet: -2.23 (0.36), residues: 191 loop : -2.55 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 272 HIS 0.008 0.001 HIS A 60 PHE 0.046 0.002 PHE E 58 TYR 0.032 0.002 TYR F 303 ARG 0.008 0.001 ARG B 74 *********************** 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 584 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 470 time to evaluate : 1.905 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: A 26 TYR cc_start: 0.6652 (m-80) cc_final: 0.6442 (m-80) REVERT: A 65 MET cc_start: 0.7092 (mtt) cc_final: 0.6765 (mtt) REVERT: A 71 MET cc_start: 0.8160 (tpt) cc_final: 0.7728 (tpt) REVERT: A 99 GLU cc_start: 0.9089 (tp30) cc_final: 0.8705 (tp30) REVERT: A 114 GLN cc_start: 0.8272 (pt0) cc_final: 0.7642 (mp10) REVERT: A 121 SER cc_start: 0.9065 (t) cc_final: 0.8498 (m) REVERT: A 152 GLN cc_start: 0.8073 (pt0) cc_final: 0.7152 (tp40) REVERT: A 166 SER cc_start: 0.8460 (m) cc_final: 0.8116 (p) REVERT: A 169 LYS cc_start: 0.7076 (mtpp) cc_final: 0.6381 (mtmm) REVERT: A 180 GLU cc_start: 0.9199 (tt0) cc_final: 0.8877 (mm-30) REVERT: A 181 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8618 (ptmm) REVERT: A 192 GLU cc_start: 0.8812 (tt0) cc_final: 0.8278 (pm20) REVERT: A 194 ASN cc_start: 0.8535 (t0) cc_final: 0.7999 (t0) REVERT: A 199 TYR cc_start: 0.9037 (t80) cc_final: 0.8646 (t80) REVERT: A 200 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8729 (t0) REVERT: A 203 ARG cc_start: 0.9289 (ttm170) cc_final: 0.8882 (ptm-80) REVERT: A 237 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7574 (mt-10) REVERT: A 253 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8856 (mmmt) REVERT: A 272 ASP cc_start: 0.8682 (t0) cc_final: 0.8188 (t0) REVERT: A 276 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: A 334 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 342 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8422 (mp0) REVERT: A 359 LEU cc_start: 0.9207 (tp) cc_final: 0.8386 (tp) REVERT: A 373 GLU cc_start: 0.8814 (mp0) cc_final: 0.8606 (pm20) REVERT: A 385 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7351 (mmp-170) REVERT: A 391 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8836 (t) REVERT: A 430 LEU cc_start: 0.7922 (mt) cc_final: 0.7556 (tp) REVERT: A 454 TYR cc_start: 0.8163 (t80) cc_final: 0.7191 (t80) REVERT: A 464 GLN cc_start: 0.8635 (mp10) cc_final: 0.7947 (mp10) REVERT: A 490 TYR cc_start: 0.8448 (t80) cc_final: 0.7888 (t80) REVERT: A 513 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8270 (ttm-80) REVERT: A 537 LYS cc_start: 0.8933 (mttt) cc_final: 0.8567 (mttp) REVERT: A 558 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 600 PHE cc_start: 0.8941 (t80) cc_final: 0.8258 (t80) REVERT: A 629 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7098 (mt-10) REVERT: A 638 ASP cc_start: 0.8677 (m-30) cc_final: 0.8200 (t0) REVERT: A 707 TRP cc_start: 0.8577 (m100) cc_final: 0.8321 (m100) REVERT: A 708 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8633 (mptt) REVERT: A 724 ARG cc_start: 0.8523 (mtp180) cc_final: 0.7101 (tpm170) REVERT: A 725 TRP cc_start: 0.9169 (p-90) cc_final: 0.7484 (p-90) REVERT: A 745 LEU cc_start: 0.8506 (mt) cc_final: 0.7890 (mp) REVERT: B 66 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.5822 (t80) REVERT: B 96 ARG cc_start: 0.7370 (ttm110) cc_final: 0.6325 (tpt170) REVERT: B 97 LYS cc_start: 0.8630 (tptp) cc_final: 0.8323 (mttm) REVERT: B 117 LYS cc_start: 0.7717 (ptpp) cc_final: 0.7344 (mmmt) REVERT: B 162 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7804 (mtmt) REVERT: C 14 LYS cc_start: 0.8510 (ptpt) cc_final: 0.7981 (mtpp) REVERT: C 85 SER cc_start: 0.9031 (m) cc_final: 0.8783 (p) REVERT: C 89 CYS cc_start: 0.8086 (m) cc_final: 0.6037 (m) REVERT: C 92 ASP cc_start: 0.6963 (p0) cc_final: 0.6443 (p0) REVERT: C 94 GLN cc_start: 0.7660 (mt0) cc_final: 0.7068 (tp40) REVERT: C 95 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7834 (mp0) REVERT: C 102 ASN cc_start: 0.7166 (p0) cc_final: 0.6317 (m-40) REVERT: C 106 ASN cc_start: 0.8472 (t0) cc_final: 0.8089 (t0) REVERT: C 109 TRP cc_start: 0.8480 (m100) cc_final: 0.6869 (m-10) REVERT: C 142 ILE cc_start: 0.8930 (mt) cc_final: 0.8691 (mm) REVERT: C 195 GLU cc_start: 0.8691 (tt0) cc_final: 0.8151 (tt0) REVERT: C 207 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7991 (ttt-90) REVERT: C 237 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8335 (ttpp) REVERT: C 259 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7886 (mt) REVERT: D 55 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8680 (tt) REVERT: D 70 ARG cc_start: 0.7935 (mmm160) cc_final: 0.7413 (mpt-90) REVERT: D 96 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7466 (m110) REVERT: D 115 ASP cc_start: 0.8263 (t0) cc_final: 0.8060 (t70) REVERT: D 131 SER cc_start: 0.8729 (p) cc_final: 0.8499 (p) REVERT: E 43 GLU cc_start: 0.8569 (tm-30) cc_final: 0.7427 (mt-10) REVERT: E 63 ASP cc_start: 0.8566 (p0) cc_final: 0.8299 (p0) REVERT: E 86 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7651 (tp30) REVERT: E 89 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7993 (tpt170) REVERT: E 118 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9110 (mt) REVERT: E 124 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: E 202 MET cc_start: 0.7568 (tpp) cc_final: 0.7263 (ttt) REVERT: E 237 PHE cc_start: 0.8311 (m-80) cc_final: 0.7897 (m-80) REVERT: E 262 ARG cc_start: 0.6732 (ttm170) cc_final: 0.6023 (mtt180) REVERT: F 23 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8278 (p) REVERT: F 36 ASP cc_start: 0.8820 (t0) cc_final: 0.8578 (t0) REVERT: F 45 MET cc_start: 0.6937 (mmm) cc_final: 0.6521 (mtm) REVERT: F 86 THR cc_start: 0.9131 (p) cc_final: 0.8888 (m) REVERT: F 99 GLN cc_start: 0.8794 (pm20) cc_final: 0.8456 (pm20) REVERT: F 189 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7007 (tpp) REVERT: F 200 GLU cc_start: 0.7476 (tp30) cc_final: 0.7195 (tp30) REVERT: F 204 ASP cc_start: 0.9097 (t0) cc_final: 0.8625 (t70) REVERT: F 220 LYS cc_start: 0.8521 (pttt) cc_final: 0.7913 (ttpt) REVERT: F 241 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8433 (mt-10) REVERT: F 275 LEU cc_start: 0.8669 (mt) cc_final: 0.8423 (tt) REVERT: F 290 TRP cc_start: 0.8578 (m100) cc_final: 0.8123 (m100) REVERT: F 297 TYR cc_start: 0.7718 (m-80) cc_final: 0.6831 (m-80) REVERT: F 327 ASP cc_start: 0.7101 (t0) cc_final: 0.6620 (p0) REVERT: F 390 PRO cc_start: 0.8327 (Cg_exo) cc_final: 0.8126 (Cg_endo) outliers start: 114 outliers final: 90 residues processed: 529 average time/residue: 0.3084 time to fit residues: 241.9812 Evaluate side-chains 547 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 445 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 20 VAL 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 187 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU 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 391 VAL 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 606 VAL 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 40 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 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 C residue 253 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 259 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 55 LEU 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 139 SER Chi-restraints excluded: chain D residue 175 THR 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 225 LEU Chi-restraints excluded: chain D residue 230 SER 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 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 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 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 104 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 189 MET 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 277 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 172 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- 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 C 212 ASN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN E 106 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 = 0.3903 r_free = 0.3903 target = 0.144445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119246 restraints weight = 33066.968| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.07 r_work: 0.3438 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17379 Z= 0.206 Angle : 0.709 13.284 23615 Z= 0.362 Chirality : 0.048 0.215 2571 Planarity : 0.006 0.096 2941 Dihedral : 11.607 82.429 2702 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.30 % Favored : 89.60 % Rotamer: Outliers : 5.26 % Allowed : 28.50 % Favored : 66.24 % 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: -2.41 (0.18), residues: 2049 helix: -0.28 (0.19), residues: 756 sheet: -2.14 (0.35), residues: 198 loop : -2.55 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 272 HIS 0.011 0.001 HIS C 205 PHE 0.043 0.002 PHE E 58 TYR 0.033 0.002 TYR C 250 ARG 0.009 0.001 ARG B 74 *********************** 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 582 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 492 time to evaluate : 2.216 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 26 TYR cc_start: 0.6617 (m-80) cc_final: 0.6408 (m-80) REVERT: A 65 MET cc_start: 0.6984 (mtt) cc_final: 0.6665 (mtt) REVERT: A 71 MET cc_start: 0.7954 (tpt) cc_final: 0.7672 (tpt) REVERT: A 99 GLU cc_start: 0.9086 (tp30) cc_final: 0.8747 (tp30) REVERT: A 114 GLN cc_start: 0.8230 (pt0) cc_final: 0.7614 (mp10) REVERT: A 152 GLN cc_start: 0.8022 (pt0) cc_final: 0.7142 (tp40) REVERT: A 166 SER cc_start: 0.8466 (m) cc_final: 0.8148 (p) REVERT: A 169 LYS cc_start: 0.7034 (mtpp) cc_final: 0.6346 (mtmm) REVERT: A 180 GLU cc_start: 0.9151 (tt0) cc_final: 0.8838 (mm-30) REVERT: A 181 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8591 (ptmm) REVERT: A 192 GLU cc_start: 0.8726 (tt0) cc_final: 0.8190 (pm20) REVERT: A 194 ASN cc_start: 0.8389 (t0) cc_final: 0.7831 (t0) REVERT: A 199 TYR cc_start: 0.8949 (t80) cc_final: 0.8500 (t80) REVERT: A 200 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 203 ARG cc_start: 0.9259 (ttm170) cc_final: 0.8900 (ptm-80) REVERT: A 237 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 253 LYS cc_start: 0.9046 (mmtp) cc_final: 0.8816 (mmmt) REVERT: A 272 ASP cc_start: 0.8500 (t0) cc_final: 0.8040 (t0) REVERT: A 276 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: A 342 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8411 (mp0) REVERT: A 359 LEU cc_start: 0.9170 (tp) cc_final: 0.8407 (tp) REVERT: A 385 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7329 (mmp-170) REVERT: A 391 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8787 (t) REVERT: A 403 PRO cc_start: 0.7946 (Cg_endo) cc_final: 0.7600 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7888 (mt) cc_final: 0.7541 (tp) REVERT: A 454 TYR cc_start: 0.8129 (t80) cc_final: 0.7150 (t80) REVERT: A 464 GLN cc_start: 0.8609 (mp10) cc_final: 0.7903 (mp10) REVERT: A 490 TYR cc_start: 0.8297 (t80) cc_final: 0.7502 (t80) REVERT: A 513 ARG cc_start: 0.8734 (mtp85) cc_final: 0.8383 (ttm-80) REVERT: A 537 LYS cc_start: 0.8949 (mttt) cc_final: 0.8555 (mttp) REVERT: A 558 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 577 GLU cc_start: 0.7685 (tt0) cc_final: 0.6953 (pp20) REVERT: A 600 PHE cc_start: 0.8763 (t80) cc_final: 0.8391 (t80) REVERT: A 629 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 638 ASP cc_start: 0.8650 (m-30) cc_final: 0.8270 (t0) REVERT: A 656 PHE cc_start: 0.8665 (t80) cc_final: 0.8276 (t80) REVERT: A 724 ARG cc_start: 0.8511 (mtp180) cc_final: 0.7123 (tpm170) REVERT: A 725 TRP cc_start: 0.9141 (p-90) cc_final: 0.7547 (p-90) REVERT: A 745 LEU cc_start: 0.8429 (mt) cc_final: 0.7852 (mp) REVERT: A 768 LEU cc_start: 0.8662 (mt) cc_final: 0.8413 (tp) REVERT: B 66 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5921 (t80) REVERT: B 96 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6237 (tpt170) REVERT: B 97 LYS cc_start: 0.8539 (tptp) cc_final: 0.8253 (mttm) REVERT: B 117 LYS cc_start: 0.7727 (ptpp) cc_final: 0.7298 (mmmt) REVERT: C 14 LYS cc_start: 0.8444 (ptpt) cc_final: 0.7938 (mtpp) REVERT: C 85 SER cc_start: 0.8964 (m) cc_final: 0.8712 (p) REVERT: C 89 CYS cc_start: 0.7826 (m) cc_final: 0.6899 (m) REVERT: C 92 ASP cc_start: 0.6787 (p0) cc_final: 0.6564 (p0) REVERT: C 94 GLN cc_start: 0.7625 (mt0) cc_final: 0.7096 (tp40) REVERT: C 102 ASN cc_start: 0.6990 (p0) cc_final: 0.5999 (m-40) REVERT: C 106 ASN cc_start: 0.8424 (t0) cc_final: 0.7996 (t0) REVERT: C 133 LYS cc_start: 0.8782 (tptt) cc_final: 0.8228 (pttp) REVERT: C 195 GLU cc_start: 0.8579 (tt0) cc_final: 0.8041 (tt0) REVERT: C 207 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7953 (ttt-90) REVERT: C 212 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8595 (t0) REVERT: C 237 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8272 (ttpt) REVERT: C 244 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7511 (tp30) REVERT: C 259 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7370 (mt) REVERT: D 55 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8583 (tt) REVERT: D 70 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7547 (mpt-90) REVERT: D 96 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7693 (m-40) REVERT: D 115 ASP cc_start: 0.8219 (t0) cc_final: 0.7978 (t70) REVERT: E 20 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8495 (mmp80) REVERT: E 43 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7399 (mt-10) REVERT: E 63 ASP cc_start: 0.8507 (p0) cc_final: 0.8284 (p0) REVERT: E 86 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7645 (tp30) REVERT: E 118 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9059 (mt) REVERT: E 124 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6647 (m-10) REVERT: E 200 HIS cc_start: 0.7845 (t-90) cc_final: 0.7472 (t70) REVERT: E 202 MET cc_start: 0.7515 (tpp) cc_final: 0.7204 (ttt) REVERT: E 262 ARG cc_start: 0.6678 (ttm170) cc_final: 0.6172 (ttt180) REVERT: F 23 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8159 (p) REVERT: F 26 TYR cc_start: 0.7871 (t80) cc_final: 0.7448 (t80) REVERT: F 36 ASP cc_start: 0.8788 (t0) cc_final: 0.8503 (t0) REVERT: F 45 MET cc_start: 0.6989 (mmm) cc_final: 0.6612 (mtm) REVERT: F 86 THR cc_start: 0.9154 (p) cc_final: 0.8939 (m) REVERT: F 189 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6944 (tpp) REVERT: F 200 GLU cc_start: 0.7531 (tp30) cc_final: 0.7266 (tp30) REVERT: F 204 ASP cc_start: 0.9046 (t0) cc_final: 0.8627 (t70) REVERT: F 220 LYS cc_start: 0.8503 (pttt) cc_final: 0.7901 (ttpt) REVERT: F 241 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8428 (mt-10) REVERT: F 275 LEU cc_start: 0.8657 (mt) cc_final: 0.8438 (tt) REVERT: F 290 TRP cc_start: 0.8581 (m100) cc_final: 0.8070 (m100) REVERT: F 297 TYR cc_start: 0.7725 (m-80) cc_final: 0.6692 (m-80) REVERT: F 327 ASP cc_start: 0.6947 (t0) cc_final: 0.6425 (p0) outliers start: 90 outliers final: 63 residues processed: 535 average time/residue: 0.2995 time to fit residues: 239.0187 Evaluate side-chains 535 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 459 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 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 200 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 699 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 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 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 212 ASN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 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 55 LEU 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 204 THR 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 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 35 ILE 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 140 ASP Chi-restraints excluded: chain E residue 194 LEU 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 253 VAL 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 160 VAL Chi-restraints excluded: chain F residue 189 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 58 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 212 ASN E 106 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118894 restraints weight = 33268.796| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 4.08 r_work: 0.3429 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17379 Z= 0.227 Angle : 0.731 14.029 23615 Z= 0.372 Chirality : 0.049 0.268 2571 Planarity : 0.006 0.093 2941 Dihedral : 11.472 81.134 2698 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.93 % Favored : 88.92 % Rotamer: Outliers : 4.50 % Allowed : 29.73 % Favored : 65.77 % 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: -2.28 (0.18), residues: 2049 helix: -0.19 (0.19), residues: 747 sheet: -2.02 (0.36), residues: 198 loop : -2.44 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 290 HIS 0.026 0.002 HIS C 205 PHE 0.064 0.002 PHE E 58 TYR 0.035 0.002 TYR C 250 ARG 0.009 0.000 ARG B 74 ********************** REFINEMENT MACRO_CYCLE 10 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 548 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 471 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.6631 (m-80) cc_final: 0.6415 (m-80) REVERT: A 65 MET cc_start: 0.6985 (mtt) cc_final: 0.6663 (mtt) REVERT: A 71 MET cc_start: 0.7908 (tpt) cc_final: 0.7522 (tpt) REVERT: A 99 GLU cc_start: 0.9095 (tp30) cc_final: 0.8715 (tp30) REVERT: A 114 GLN cc_start: 0.8236 (pt0) cc_final: 0.7608 (mp10) REVERT: A 152 GLN cc_start: 0.8011 (pt0) cc_final: 0.7111 (tp40) REVERT: A 166 SER cc_start: 0.8462 (m) cc_final: 0.8140 (p) REVERT: A 169 LYS cc_start: 0.7079 (mtpp) cc_final: 0.6428 (mtmm) REVERT: A 180 GLU cc_start: 0.9156 (tt0) cc_final: 0.8815 (mm-30) REVERT: A 181 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8582 (ptmm) REVERT: A 192 GLU cc_start: 0.8722 (tt0) cc_final: 0.8186 (pm20) REVERT: A 199 TYR cc_start: 0.8978 (t80) cc_final: 0.8532 (t80) REVERT: A 200 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8713 (t0) REVERT: A 203 ARG cc_start: 0.9255 (ttm170) cc_final: 0.8925 (ptm-80) REVERT: A 237 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7601 (mt-10) REVERT: A 253 LYS cc_start: 0.9061 (mmtp) cc_final: 0.8839 (mmmt) REVERT: A 272 ASP cc_start: 0.8487 (t0) cc_final: 0.7919 (t0) REVERT: A 276 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: A 342 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8244 (mp0) REVERT: A 359 LEU cc_start: 0.9188 (tp) cc_final: 0.8391 (tp) REVERT: A 385 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.7270 (mmp-170) REVERT: A 391 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8785 (t) REVERT: A 403 PRO cc_start: 0.7905 (Cg_endo) cc_final: 0.7528 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7931 (mt) cc_final: 0.7567 (tp) REVERT: A 454 TYR cc_start: 0.8134 (t80) cc_final: 0.7175 (t80) REVERT: A 464 GLN cc_start: 0.8613 (mp10) cc_final: 0.8214 (mm-40) REVERT: A 490 TYR cc_start: 0.8357 (t80) cc_final: 0.7834 (t80) REVERT: A 513 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8454 (ttm-80) REVERT: A 537 LYS cc_start: 0.8938 (mttt) cc_final: 0.8580 (mttm) REVERT: A 558 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 577 GLU cc_start: 0.7743 (tt0) cc_final: 0.6955 (pp20) REVERT: A 600 PHE cc_start: 0.8814 (t80) cc_final: 0.8404 (t80) REVERT: A 629 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 638 ASP cc_start: 0.8665 (m-30) cc_final: 0.8320 (t0) REVERT: A 724 ARG cc_start: 0.8480 (mtp180) cc_final: 0.7107 (tpm170) REVERT: A 725 TRP cc_start: 0.9142 (p-90) cc_final: 0.7564 (p-90) REVERT: A 745 LEU cc_start: 0.8529 (mt) cc_final: 0.7940 (mp) REVERT: A 768 LEU cc_start: 0.8645 (mt) cc_final: 0.8386 (tp) REVERT: B 66 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6020 (t80) REVERT: B 96 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6107 (tpt170) REVERT: B 97 LYS cc_start: 0.8530 (tptp) cc_final: 0.8252 (mttm) REVERT: B 117 LYS cc_start: 0.7604 (ptpp) cc_final: 0.7178 (mmmt) REVERT: C 14 LYS cc_start: 0.8424 (ptpt) cc_final: 0.7973 (mtpp) REVERT: C 85 SER cc_start: 0.8940 (m) cc_final: 0.8691 (p) REVERT: C 89 CYS cc_start: 0.7875 (m) cc_final: 0.7019 (m) REVERT: C 92 ASP cc_start: 0.6882 (p0) cc_final: 0.6664 (p0) REVERT: C 94 GLN cc_start: 0.7764 (mt0) cc_final: 0.7180 (tp40) REVERT: C 102 ASN cc_start: 0.6816 (p0) cc_final: 0.6502 (m-40) REVERT: C 106 ASN cc_start: 0.8436 (t0) cc_final: 0.8041 (t0) REVERT: C 133 LYS cc_start: 0.8796 (tptt) cc_final: 0.8252 (pttp) REVERT: C 195 GLU cc_start: 0.8613 (tt0) cc_final: 0.8069 (tt0) REVERT: C 237 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8342 (ttpp) REVERT: C 244 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7444 (tp30) REVERT: C 259 ILE cc_start: 0.8226 (mp) cc_final: 0.7334 (mt) REVERT: D 55 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8546 (tt) REVERT: D 70 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7598 (mpt-90) REVERT: D 97 CYS cc_start: 0.6443 (p) cc_final: 0.6010 (m) REVERT: D 115 ASP cc_start: 0.8253 (t0) cc_final: 0.7941 (t70) REVERT: E 43 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7429 (mt-10) REVERT: E 63 ASP cc_start: 0.8482 (p0) cc_final: 0.8271 (p0) REVERT: E 86 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7476 (tp30) REVERT: E 124 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: E 152 ARG cc_start: 0.8950 (mmm160) cc_final: 0.8594 (tpp80) REVERT: E 200 HIS cc_start: 0.7804 (t-90) cc_final: 0.7408 (t70) REVERT: E 202 MET cc_start: 0.7505 (tpp) cc_final: 0.7256 (ttt) REVERT: E 237 PHE cc_start: 0.8325 (m-80) cc_final: 0.7934 (m-80) REVERT: E 262 ARG cc_start: 0.6808 (ttm170) cc_final: 0.6167 (mtt180) REVERT: F 23 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8145 (p) REVERT: F 26 TYR cc_start: 0.7845 (t80) cc_final: 0.7424 (t80) REVERT: F 36 ASP cc_start: 0.8773 (t0) cc_final: 0.8520 (t0) REVERT: F 45 MET cc_start: 0.6995 (mmm) cc_final: 0.6613 (mtm) REVERT: F 86 THR cc_start: 0.9149 (p) cc_final: 0.8933 (m) REVERT: F 189 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7069 (tpp) REVERT: F 204 ASP cc_start: 0.9045 (t0) cc_final: 0.8652 (t70) REVERT: F 220 LYS cc_start: 0.8503 (pttt) cc_final: 0.7902 (ttpt) REVERT: F 241 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8430 (mt-10) REVERT: F 275 LEU cc_start: 0.8692 (mt) cc_final: 0.8459 (tt) REVERT: F 290 TRP cc_start: 0.8617 (m100) cc_final: 0.8257 (m100) REVERT: F 297 TYR cc_start: 0.7681 (m-80) cc_final: 0.6717 (m-80) REVERT: F 327 ASP cc_start: 0.6826 (t0) cc_final: 0.6309 (p0) outliers start: 77 outliers final: 60 residues processed: 510 average time/residue: 0.2846 time to fit residues: 218.9405 Evaluate side-chains 527 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 459 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 699 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 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 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 C residue 253 THR 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 55 LEU Chi-restraints excluded: chain D residue 67 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 204 THR 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 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 111 LEU 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 140 ASP Chi-restraints excluded: chain E residue 194 LEU 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 253 VAL 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 160 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 277 GLU 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-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.5278 > 50: distance: 32 - 52: 23.802 distance: 36 - 59: 4.449 distance: 42 - 70: 28.081 distance: 46 - 52: 25.287 distance: 52 - 53: 36.907 distance: 53 - 54: 26.834 distance: 53 - 56: 24.954 distance: 54 - 55: 28.513 distance: 54 - 59: 25.506 distance: 56 - 57: 4.259 distance: 56 - 58: 18.060 distance: 59 - 60: 17.201 distance: 60 - 61: 36.087 distance: 60 - 63: 24.762 distance: 61 - 62: 47.489 distance: 61 - 70: 44.857 distance: 63 - 64: 31.751 distance: 64 - 65: 22.330 distance: 64 - 66: 20.855 distance: 65 - 67: 7.422 distance: 66 - 68: 7.139 distance: 68 - 69: 6.168 distance: 70 - 71: 42.149 distance: 71 - 72: 24.637 distance: 72 - 73: 43.739 distance: 72 - 74: 29.747 distance: 74 - 75: 26.263 distance: 75 - 76: 28.473 distance: 75 - 78: 10.013 distance: 76 - 77: 29.397 distance: 76 - 82: 25.034 distance: 78 - 79: 9.466 distance: 80 - 81: 5.243 distance: 82 - 83: 47.060 distance: 83 - 84: 41.400 distance: 83 - 86: 57.561 distance: 84 - 85: 38.570 distance: 84 - 91: 23.804 distance: 86 - 87: 45.274 distance: 87 - 88: 38.971 distance: 88 - 89: 40.018 distance: 88 - 90: 30.539 distance: 91 - 92: 6.737 distance: 91 - 97: 28.091 distance: 92 - 93: 46.039 distance: 92 - 95: 25.438 distance: 93 - 94: 42.130 distance: 93 - 98: 42.972 distance: 95 - 96: 14.570 distance: 96 - 97: 13.282 distance: 98 - 99: 41.028 distance: 99 - 100: 59.433 distance: 99 - 102: 13.796 distance: 100 - 101: 48.998 distance: 100 - 106: 36.638 distance: 102 - 103: 16.085 distance: 103 - 104: 6.918 distance: 103 - 105: 12.883 distance: 106 - 107: 17.158 distance: 107 - 108: 18.648 distance: 107 - 110: 12.069 distance: 108 - 109: 27.073 distance: 108 - 117: 27.577 distance: 110 - 111: 8.040 distance: 111 - 112: 11.605 distance: 112 - 113: 22.421 distance: 113 - 114: 11.283 distance: 114 - 115: 5.454 distance: 114 - 116: 10.814 distance: 117 - 118: 34.776 distance: 118 - 119: 23.896 distance: 118 - 121: 22.207 distance: 119 - 120: 10.662 distance: 119 - 128: 19.399 distance: 121 - 122: 13.878 distance: 122 - 123: 16.984 distance: 123 - 124: 25.223 distance: 124 - 125: 5.673 distance: 125 - 127: 4.852 distance: 128 - 129: 28.067 distance: 129 - 130: 14.036 distance: 129 - 132: 14.377 distance: 130 - 131: 17.594 distance: 130 - 134: 8.935 distance: 132 - 133: 9.336