Starting phenix.real_space_refine on Wed Mar 4 23:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iqw_9708/03_2026/6iqw_9708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iqw_9708/03_2026/6iqw_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 { model { file = "/net/cci-nas-00/data/ceres_data/6iqw_9708/03_2026/6iqw_9708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iqw_9708/03_2026/6iqw_9708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iqw_9708/03_2026/6iqw_9708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iqw_9708/03_2026/6iqw_9708.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4, 'TYR:plan': 1} 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: {'ARG:plan': 2, 'ASP:plan': 4, 'GLU:plan': 8} 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: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} 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: 3.44, per 1000 atoms: 0.20 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: 1.41 Conformation dependent library (CDL) restraints added in 746.1 milliseconds 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: 1.70 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: 2.52 Time building geometry restraints manager: 1.87 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.570 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 17380 Z= 0.328 Angle : 1.051 19.035 23617 Z= 0.594 Chirality : 0.059 0.298 2571 Planarity : 0.008 0.090 2941 Dihedral : 16.456 95.044 6622 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.21 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.014 0.001 ARG D 126 TYR 0.031 0.003 TYR E 272 PHE 0.038 0.003 PHE E 159 TRP 0.028 0.002 TRP A 131 HIS 0.009 0.002 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00683 (17379) covalent geometry : angle 1.05077 (23615) SS BOND : bond 0.00496 ( 1) SS BOND : angle 1.83450 ( 2) hydrogen bonds : bond 0.18302 ( 541) hydrogen bonds : angle 7.90657 ( 1515) *********************** 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 : 0.665 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: 0.8174 (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: 0.8775 (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: 0.1356 time to fit residues: 134.9469 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 : 0.591 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN C 22 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 205 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN E 36 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119947 restraints weight = 32536.874| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 4.07 r_work: 0.3454 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17380 Z= 0.144 Angle : 0.739 12.108 23617 Z= 0.382 Chirality : 0.048 0.323 2571 Planarity : 0.007 0.087 2941 Dihedral : 12.225 95.109 2704 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.88 % Favored : 89.02 % Rotamer: Outliers : 3.74 % Allowed : 18.87 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.16), residues: 2049 helix: -1.76 (0.16), residues: 744 sheet: -2.74 (0.34), residues: 195 loop : -3.16 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 73 TYR 0.032 0.002 TYR B 55 PHE 0.021 0.002 PHE A 325 TRP 0.017 0.002 TRP C 206 HIS 0.009 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00312 (17379) covalent geometry : angle 0.73907 (23615) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.76621 ( 2) hydrogen bonds : bond 0.04078 ( 541) hydrogen bonds : angle 5.76502 ( 1515) *********************** 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 604 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 540 time to evaluate : 0.567 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: 0.6382 (m-80) cc_final: 0.5635 (m-80) REVERT: A 71 MET cc_start: 0.8216 (tpt) cc_final: 0.7646 (tpt) REVERT: A 99 GLU cc_start: 0.9018 (tp30) cc_final: 0.8526 (tp30) REVERT: A 114 GLN cc_start: 0.8028 (pt0) cc_final: 0.7296 (mp10) REVERT: A 121 SER cc_start: 0.9144 (t) cc_final: 0.8719 (m) REVERT: A 169 LYS cc_start: 0.7179 (mtpp) cc_final: 0.6458 (mtmm) REVERT: A 181 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8715 (ptmm) REVERT: A 192 GLU cc_start: 0.8700 (tt0) cc_final: 0.8100 (pm20) REVERT: A 203 ARG cc_start: 0.9252 (ttm170) cc_final: 0.8904 (ptm-80) REVERT: A 237 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 253 LYS cc_start: 0.8921 (mmtp) cc_final: 0.8692 (mmmt) REVERT: A 272 ASP cc_start: 0.8789 (t0) cc_final: 0.8203 (t0) REVERT: A 287 ASN cc_start: 0.9229 (m110) cc_final: 0.9007 (m-40) REVERT: A 359 LEU cc_start: 0.9193 (tp) cc_final: 0.8182 (tp) REVERT: A 430 LEU cc_start: 0.7944 (mt) cc_final: 0.7588 (tp) REVERT: A 439 ASP cc_start: 0.8321 (m-30) cc_final: 0.8110 (m-30) REVERT: A 454 TYR cc_start: 0.8110 (t80) cc_final: 0.7286 (t80) REVERT: A 464 GLN cc_start: 0.8517 (mp10) cc_final: 0.7895 (mp10) REVERT: A 490 TYR cc_start: 0.8355 (t80) cc_final: 0.7583 (t80) REVERT: A 503 GLU cc_start: 0.8618 (tt0) cc_final: 0.8084 (mt-10) REVERT: A 513 ARG cc_start: 0.8695 (mtp85) cc_final: 0.8180 (ttm-80) REVERT: A 527 GLU cc_start: 0.8615 (tt0) cc_final: 0.7637 (tp30) REVERT: A 550 LYS cc_start: 0.8265 (mttt) cc_final: 0.8007 (mttm) REVERT: A 573 ASP cc_start: 0.8546 (m-30) cc_final: 0.8265 (p0) REVERT: A 629 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 638 ASP cc_start: 0.8711 (m-30) cc_final: 0.8053 (t0) REVERT: A 644 LEU cc_start: 0.9014 (tp) cc_final: 0.8764 (tt) REVERT: A 650 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7795 (mm-30) REVERT: A 725 TRP cc_start: 0.9091 (p-90) cc_final: 0.7548 (p-90) REVERT: A 745 LEU cc_start: 0.8208 (mt) cc_final: 0.7577 (mt) REVERT: A 755 ARG cc_start: 0.7903 (ptt180) cc_final: 0.7468 (ptt180) REVERT: B 96 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7288 (mtp180) REVERT: B 97 LYS cc_start: 0.8758 (tptp) cc_final: 0.8418 (mttm) REVERT: B 122 LYS cc_start: 0.9299 (ptpt) cc_final: 0.8390 (mmmm) REVERT: B 123 MET cc_start: 0.9328 (mtp) cc_final: 0.9030 (ttm) REVERT: B 133 LYS cc_start: 0.8535 (tptp) cc_final: 0.8158 (mtmt) REVERT: C 14 LYS cc_start: 0.8444 (ptpt) cc_final: 0.7966 (mtpp) REVERT: C 68 ASN cc_start: 0.8974 (t0) cc_final: 0.8766 (t0) REVERT: C 89 CYS cc_start: 0.8064 (m) cc_final: 0.7852 (m) REVERT: C 94 GLN cc_start: 0.7592 (mt0) cc_final: 0.7000 (mm-40) REVERT: C 95 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7802 (mp0) REVERT: C 106 ASN cc_start: 0.8331 (t0) cc_final: 0.7883 (t0) REVERT: C 133 LYS cc_start: 0.8945 (tptt) cc_final: 0.8305 (pttp) REVERT: C 156 TRP cc_start: 0.8510 (t60) cc_final: 0.7620 (t-100) REVERT: C 195 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8200 (tt0) REVERT: C 237 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8387 (ttpp) REVERT: C 244 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7536 (tp30) REVERT: D 70 ARG cc_start: 0.7680 (mmm160) cc_final: 0.7202 (mmt90) REVERT: D 267 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6225 (mtpp) REVERT: E 43 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7225 (mt-10) REVERT: E 58 PHE cc_start: 0.8188 (t80) cc_final: 0.7855 (t80) REVERT: E 63 ASP cc_start: 0.8682 (p0) cc_final: 0.8459 (p0) REVERT: E 86 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7795 (tp30) REVERT: E 89 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7577 (tmt-80) REVERT: E 105 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8186 (mtpp) REVERT: E 124 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.7059 (m-10) REVERT: E 148 GLU cc_start: 0.7610 (mp0) cc_final: 0.7374 (mt-10) REVERT: E 158 TYR cc_start: 0.8774 (p90) cc_final: 0.8317 (p90) REVERT: E 162 SER cc_start: 0.9112 (t) cc_final: 0.8749 (m) REVERT: E 200 HIS cc_start: 0.8260 (t-170) cc_final: 0.7771 (t70) REVERT: E 237 PHE cc_start: 0.8350 (m-80) cc_final: 0.7895 (m-80) REVERT: E 262 ARG cc_start: 0.6889 (mtt-85) cc_final: 0.6285 (mtt180) REVERT: E 264 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7392 (mm-30) REVERT: F 26 TYR cc_start: 0.7903 (t80) cc_final: 0.7492 (t80) REVERT: F 36 ASP cc_start: 0.8704 (t0) cc_final: 0.8479 (t0) REVERT: F 86 THR cc_start: 0.9126 (p) cc_final: 0.8877 (m) REVERT: F 99 GLN cc_start: 0.8404 (pm20) cc_final: 0.8175 (pm20) REVERT: F 127 TYR cc_start: 0.6706 (t80) cc_final: 0.6441 (t80) REVERT: F 131 LYS cc_start: 0.8346 (tttp) cc_final: 0.7618 (tppt) REVERT: F 183 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: F 204 ASP cc_start: 0.9062 (t0) cc_final: 0.8641 (t70) REVERT: F 220 LYS cc_start: 0.8428 (pttt) cc_final: 0.7784 (ttpt) REVERT: F 238 ILE cc_start: 0.7857 (tt) cc_final: 0.7593 (pt) REVERT: F 241 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8502 (mt-10) REVERT: F 263 ASN cc_start: 0.6203 (m-40) cc_final: 0.5258 (t0) REVERT: F 275 LEU cc_start: 0.8721 (mt) cc_final: 0.8449 (tt) REVERT: F 297 TYR cc_start: 0.7727 (m-80) cc_final: 0.7092 (m-80) REVERT: F 319 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8797 (mmt180) REVERT: F 385 LEU cc_start: 0.8431 (mt) cc_final: 0.7902 (tp) REVERT: F 389 MET cc_start: 0.7714 (mpp) cc_final: 0.7344 (mpp) outliers start: 64 outliers final: 33 residues processed: 574 average time/residue: 0.1331 time to fit residues: 112.5819 Evaluate side-chains 512 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 475 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 579 ASP 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 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 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 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 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 35 ILE Chi-restraints excluded: chain E residue 89 ARG 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 260 MET Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 28 ARG 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 127 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 187 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 194 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 212 ASN ** E 139 GLN ** 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 = 0.3852 r_free = 0.3852 target = 0.139924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115117 restraints weight = 33461.587| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 4.07 r_work: 0.3383 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17380 Z= 0.210 Angle : 0.750 11.131 23617 Z= 0.389 Chirality : 0.049 0.305 2571 Planarity : 0.006 0.094 2941 Dihedral : 11.973 91.433 2702 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.91 % Favored : 87.99 % Rotamer: Outliers : 4.67 % Allowed : 22.43 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.17), residues: 2049 helix: -1.20 (0.17), residues: 763 sheet: -2.40 (0.35), residues: 187 loop : -3.02 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 90 TYR 0.029 0.002 TYR F 303 PHE 0.042 0.002 PHE E 116 TRP 0.012 0.002 TRP C 156 HIS 0.007 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00475 (17379) covalent geometry : angle 0.74964 (23615) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.61239 ( 2) hydrogen bonds : bond 0.03838 ( 541) hydrogen bonds : angle 5.57598 ( 1515) *********************** 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 561 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 481 time to evaluate : 0.662 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: 0.6230 (m-80) cc_final: 0.5207 (m-80) REVERT: A 71 MET cc_start: 0.8190 (tpt) cc_final: 0.7648 (tpt) REVERT: A 99 GLU cc_start: 0.9019 (tp30) cc_final: 0.8632 (tp30) REVERT: A 114 GLN cc_start: 0.8360 (pt0) cc_final: 0.7483 (mp10) REVERT: A 121 SER cc_start: 0.9174 (t) cc_final: 0.8685 (m) REVERT: A 152 GLN cc_start: 0.8227 (pt0) cc_final: 0.7246 (tp40) REVERT: A 166 SER cc_start: 0.8489 (m) cc_final: 0.8142 (p) REVERT: A 169 LYS cc_start: 0.7272 (mtpp) cc_final: 0.6557 (mtmm) REVERT: A 192 GLU cc_start: 0.8769 (tt0) cc_final: 0.8297 (pm20) REVERT: A 203 ARG cc_start: 0.9307 (ttm170) cc_final: 0.8962 (ptm-80) REVERT: A 237 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7479 (mt-10) REVERT: A 253 LYS cc_start: 0.9020 (mmtp) cc_final: 0.8805 (mmmt) REVERT: A 272 ASP cc_start: 0.8816 (t0) cc_final: 0.8259 (t0) REVERT: A 276 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: A 342 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8406 (mp0) REVERT: A 359 LEU cc_start: 0.9266 (tp) cc_final: 0.8261 (tp) REVERT: A 391 VAL cc_start: 0.9103 (t) cc_final: 0.8813 (p) REVERT: A 430 LEU cc_start: 0.7980 (mt) cc_final: 0.7632 (tp) REVERT: A 454 TYR cc_start: 0.8172 (t80) cc_final: 0.7312 (t80) REVERT: A 464 GLN cc_start: 0.8595 (mp10) cc_final: 0.8006 (mp10) REVERT: A 490 TYR cc_start: 0.8511 (t80) cc_final: 0.7749 (t80) REVERT: A 513 ARG cc_start: 0.8691 (mtp85) cc_final: 0.8224 (ttm-80) REVERT: A 537 LYS cc_start: 0.8897 (mttt) cc_final: 0.8653 (mttm) REVERT: A 550 LYS cc_start: 0.8296 (mttt) cc_final: 0.8071 (mttm) REVERT: A 573 ASP cc_start: 0.8550 (m-30) cc_final: 0.8318 (p0) REVERT: A 629 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7121 (mt-10) REVERT: A 638 ASP cc_start: 0.8741 (m-30) cc_final: 0.8090 (t0) REVERT: A 648 LYS cc_start: 0.9267 (ttmm) cc_final: 0.9066 (mtpp) REVERT: A 650 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7870 (mm-30) REVERT: A 708 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8663 (mptt) REVERT: A 724 ARG cc_start: 0.8676 (mtp180) cc_final: 0.7446 (mmp-170) REVERT: A 725 TRP cc_start: 0.9132 (p-90) cc_final: 0.7541 (p-90) REVERT: A 745 LEU cc_start: 0.8388 (mt) cc_final: 0.7703 (mp) REVERT: A 762 TYR cc_start: 0.8633 (t80) cc_final: 0.8386 (t80) REVERT: B 96 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7111 (mtp180) REVERT: B 97 LYS cc_start: 0.8709 (tptp) cc_final: 0.8353 (mttm) REVERT: B 122 LYS cc_start: 0.9294 (ptpt) cc_final: 0.8510 (mmmt) REVERT: B 123 MET cc_start: 0.9295 (mtp) cc_final: 0.9048 (ttm) REVERT: B 133 LYS cc_start: 0.8706 (tptp) cc_final: 0.8256 (mtmt) REVERT: B 164 ASN cc_start: 0.8683 (t0) cc_final: 0.7996 (t0) REVERT: C 14 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8001 (mtpp) REVERT: C 58 ARG cc_start: 0.7847 (tpt170) cc_final: 0.7601 (tpt170) REVERT: C 85 SER cc_start: 0.9007 (m) cc_final: 0.8766 (p) REVERT: C 89 CYS cc_start: 0.8302 (m) cc_final: 0.8043 (m) REVERT: C 94 GLN cc_start: 0.7525 (mt0) cc_final: 0.7059 (mm-40) REVERT: C 95 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7825 (mp0) REVERT: C 106 ASN cc_start: 0.8410 (t0) cc_final: 0.7973 (t0) REVERT: C 133 LYS cc_start: 0.8817 (tptt) cc_final: 0.8256 (pttp) REVERT: C 142 ILE cc_start: 0.8989 (mt) cc_final: 0.8728 (mm) REVERT: C 195 GLU cc_start: 0.8740 (mt-10) cc_final: 0.7853 (tt0) REVERT: C 237 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8481 (ttpp) REVERT: C 244 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7609 (tp30) REVERT: D 70 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7295 (mmt90) REVERT: D 84 TYR cc_start: 0.8141 (m-80) cc_final: 0.7794 (m-80) REVERT: D 95 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7185 (tm-30) REVERT: D 115 ASP cc_start: 0.8341 (t0) cc_final: 0.7945 (t70) REVERT: D 180 PRO cc_start: 0.9126 (Cg_endo) cc_final: 0.8802 (Cg_exo) REVERT: D 198 TYR cc_start: 0.7940 (t80) cc_final: 0.7697 (t80) REVERT: D 201 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: E 43 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7333 (mt-10) REVERT: E 63 ASP cc_start: 0.8638 (p0) cc_final: 0.8393 (p0) REVERT: E 86 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7977 (tp30) REVERT: E 89 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (tpt170) REVERT: E 118 ILE cc_start: 0.9413 (tp) cc_final: 0.9112 (mt) REVERT: E 124 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.7041 (m-10) REVERT: E 148 GLU cc_start: 0.7644 (mp0) cc_final: 0.7401 (mt-10) REVERT: E 200 HIS cc_start: 0.8199 (t-170) cc_final: 0.7669 (t70) REVERT: E 262 ARG cc_start: 0.7171 (mtt-85) cc_final: 0.6907 (ttm170) REVERT: E 264 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7553 (mm-30) REVERT: F 26 TYR cc_start: 0.7851 (t80) cc_final: 0.7421 (t80) REVERT: F 36 ASP cc_start: 0.8784 (t0) cc_final: 0.8564 (t0) REVERT: F 86 THR cc_start: 0.9151 (p) cc_final: 0.8906 (m) REVERT: F 99 GLN cc_start: 0.8662 (pm20) cc_final: 0.8383 (pm20) REVERT: F 127 TYR cc_start: 0.6755 (t80) cc_final: 0.6512 (t80) REVERT: F 131 LYS cc_start: 0.8341 (tttp) cc_final: 0.7585 (tppt) REVERT: F 204 ASP cc_start: 0.9107 (t0) cc_final: 0.8647 (t70) REVERT: F 220 LYS cc_start: 0.8524 (pttt) cc_final: 0.7863 (ttpt) REVERT: F 238 ILE cc_start: 0.7675 (tt) cc_final: 0.7390 (pt) REVERT: F 241 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8553 (mt-10) REVERT: F 275 LEU cc_start: 0.8748 (mt) cc_final: 0.8402 (tt) REVERT: F 290 TRP cc_start: 0.8410 (m100) cc_final: 0.8072 (m100) REVERT: F 297 TYR cc_start: 0.7688 (m-80) cc_final: 0.7190 (m-80) REVERT: F 319 ARG cc_start: 0.9239 (ttp80) cc_final: 0.8813 (mmt180) REVERT: F 327 ASP cc_start: 0.6889 (t0) cc_final: 0.6382 (p0) outliers start: 80 outliers final: 57 residues processed: 520 average time/residue: 0.1352 time to fit residues: 104.3044 Evaluate side-chains 515 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 454 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 96 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 748 ILE 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 116 ILE 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 126 ARG Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 253 THR 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 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 35 ILE 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 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 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 114 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN E 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116882 restraints weight = 33333.858| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.07 r_work: 0.3396 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 17380 Z= 0.175 Angle : 0.708 11.622 23617 Z= 0.364 Chirality : 0.048 0.285 2571 Planarity : 0.006 0.091 2941 Dihedral : 11.849 96.232 2702 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.52 % Favored : 88.38 % Rotamer: Outliers : 5.14 % Allowed : 23.19 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.17), residues: 2049 helix: -0.78 (0.18), residues: 753 sheet: -2.59 (0.34), residues: 197 loop : -2.86 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 60 TYR 0.030 0.002 TYR F 303 PHE 0.035 0.002 PHE E 58 TRP 0.013 0.001 TRP C 152 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00406 (17379) covalent geometry : angle 0.70823 (23615) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.59079 ( 2) hydrogen bonds : bond 0.03568 ( 541) hydrogen bonds : angle 5.42673 ( 1515) *********************** 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 577 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 489 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7151 (mtt) cc_final: 0.6616 (mmm) REVERT: A 71 MET cc_start: 0.8087 (tpt) cc_final: 0.7547 (tpt) REVERT: A 99 GLU cc_start: 0.9031 (tp30) cc_final: 0.8644 (tp30) REVERT: A 114 GLN cc_start: 0.8240 (pt0) cc_final: 0.7476 (mp10) REVERT: A 121 SER cc_start: 0.9130 (t) cc_final: 0.8540 (m) REVERT: A 152 GLN cc_start: 0.8222 (pt0) cc_final: 0.7258 (tp40) REVERT: A 166 SER cc_start: 0.8371 (m) cc_final: 0.8004 (p) REVERT: A 169 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6461 (mtmm) REVERT: A 181 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8601 (tttt) REVERT: A 192 GLU cc_start: 0.8747 (tt0) cc_final: 0.8278 (pm20) REVERT: A 203 ARG cc_start: 0.9259 (ttm170) cc_final: 0.9023 (ptm-80) REVERT: A 237 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 253 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8814 (mmmt) REVERT: A 272 ASP cc_start: 0.8749 (t0) cc_final: 0.8245 (t0) REVERT: A 276 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: A 280 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8580 (ttm170) REVERT: A 289 VAL cc_start: 0.9720 (t) cc_final: 0.9456 (p) REVERT: A 342 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8426 (mp0) REVERT: A 359 LEU cc_start: 0.9238 (tp) cc_final: 0.8197 (tp) REVERT: A 430 LEU cc_start: 0.7966 (mt) cc_final: 0.7609 (tp) REVERT: A 454 TYR cc_start: 0.8095 (t80) cc_final: 0.7200 (t80) REVERT: A 464 GLN cc_start: 0.8626 (mp10) cc_final: 0.8085 (mp10) REVERT: A 490 TYR cc_start: 0.8450 (t80) cc_final: 0.7672 (t80) REVERT: A 492 LYS cc_start: 0.7950 (tppt) cc_final: 0.7659 (tppt) REVERT: A 513 ARG cc_start: 0.8688 (mtp85) cc_final: 0.8234 (ttm-80) REVERT: A 537 LYS cc_start: 0.8862 (mttt) cc_final: 0.8550 (mttp) REVERT: A 577 GLU cc_start: 0.7533 (tt0) cc_final: 0.7195 (tt0) REVERT: A 629 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 638 ASP cc_start: 0.8695 (m-30) cc_final: 0.8097 (t0) REVERT: A 650 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7959 (mm-30) REVERT: A 708 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8652 (mptt) REVERT: A 725 TRP cc_start: 0.9134 (p-90) cc_final: 0.7534 (p-90) REVERT: A 745 LEU cc_start: 0.8429 (mt) cc_final: 0.7743 (mp) REVERT: A 762 TYR cc_start: 0.8607 (t80) cc_final: 0.8358 (t80) REVERT: B 97 LYS cc_start: 0.8614 (tptp) cc_final: 0.8349 (mttm) REVERT: B 110 LYS cc_start: 0.8967 (tptp) cc_final: 0.8498 (mtmt) REVERT: B 133 LYS cc_start: 0.8725 (tptp) cc_final: 0.8449 (mtpt) REVERT: B 164 ASN cc_start: 0.8657 (t0) cc_final: 0.8006 (t0) REVERT: C 14 LYS cc_start: 0.8545 (ptpt) cc_final: 0.8033 (mtpp) REVERT: C 85 SER cc_start: 0.9010 (m) cc_final: 0.8775 (p) REVERT: C 89 CYS cc_start: 0.8176 (m) cc_final: 0.6635 (m) REVERT: C 92 ASP cc_start: 0.7077 (p0) cc_final: 0.6661 (p0) REVERT: C 94 GLN cc_start: 0.7511 (mt0) cc_final: 0.6834 (tp40) REVERT: C 95 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7741 (mp0) REVERT: C 106 ASN cc_start: 0.8464 (t0) cc_final: 0.8030 (t0) REVERT: C 109 TRP cc_start: 0.8432 (m100) cc_final: 0.6699 (m-10) REVERT: C 133 LYS cc_start: 0.8804 (tptt) cc_final: 0.8195 (pttp) REVERT: C 142 ILE cc_start: 0.8903 (mt) cc_final: 0.8647 (mm) REVERT: C 195 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8221 (tt0) REVERT: C 237 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8495 (ttpp) REVERT: D 70 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7383 (mpt-90) REVERT: D 115 ASP cc_start: 0.8314 (t0) cc_final: 0.8051 (t70) REVERT: D 201 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: D 224 TYR cc_start: 0.8695 (p90) cc_final: 0.8324 (p90) REVERT: E 43 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7385 (mt-10) REVERT: E 63 ASP cc_start: 0.8611 (p0) cc_final: 0.8370 (p0) REVERT: E 74 GLU cc_start: 0.8659 (mp0) cc_final: 0.8367 (mp0) REVERT: E 86 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7893 (tp30) REVERT: E 89 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8027 (tpt170) REVERT: E 95 ARG cc_start: 0.8439 (tpp80) cc_final: 0.8206 (tpp80) REVERT: E 118 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9187 (mt) REVERT: E 124 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6828 (m-10) REVERT: E 148 GLU cc_start: 0.7570 (mp0) cc_final: 0.7348 (mt-10) REVERT: E 200 HIS cc_start: 0.8314 (t-170) cc_final: 0.7728 (t70) REVERT: E 237 PHE cc_start: 0.8274 (m-80) cc_final: 0.7866 (m-10) REVERT: E 262 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.6760 (ttm170) REVERT: E 264 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7431 (mm-30) REVERT: F 23 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8217 (p) REVERT: F 36 ASP cc_start: 0.8829 (t0) cc_final: 0.8604 (t0) REVERT: F 45 MET cc_start: 0.6337 (mmm) cc_final: 0.5750 (mtm) REVERT: F 86 THR cc_start: 0.9112 (p) cc_final: 0.8873 (m) REVERT: F 99 GLN cc_start: 0.8659 (pm20) cc_final: 0.8410 (pm20) REVERT: F 131 LYS cc_start: 0.8462 (tttp) cc_final: 0.7795 (tppt) REVERT: F 204 ASP cc_start: 0.9082 (t0) cc_final: 0.8692 (t70) REVERT: F 220 LYS cc_start: 0.8562 (pttt) cc_final: 0.7937 (ttpt) REVERT: F 238 ILE cc_start: 0.7755 (tt) cc_final: 0.7224 (pt) REVERT: F 241 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8550 (mt-10) REVERT: F 275 LEU cc_start: 0.8715 (mt) cc_final: 0.8393 (tt) REVERT: F 290 TRP cc_start: 0.8493 (m100) cc_final: 0.8100 (m100) REVERT: F 297 TYR cc_start: 0.7777 (m-80) cc_final: 0.7212 (m-80) REVERT: F 327 ASP cc_start: 0.7049 (t0) cc_final: 0.6463 (p0) outliers start: 88 outliers final: 64 residues processed: 532 average time/residue: 0.1261 time to fit residues: 101.0214 Evaluate side-chains 521 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 450 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 180 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 ARG 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 718 ARG 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 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 118 THR Chi-restraints excluded: chain C residue 126 ARG 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 248 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 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 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 23 VAL 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 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 331 HIS 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 150 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 172 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS A 598 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 212 ASN F 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.141552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116807 restraints weight = 32978.447| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.03 r_work: 0.3405 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17380 Z= 0.160 Angle : 0.706 14.027 23617 Z= 0.360 Chirality : 0.048 0.267 2571 Planarity : 0.005 0.097 2941 Dihedral : 11.721 94.240 2702 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.42 % Favored : 88.48 % Rotamer: Outliers : 5.43 % Allowed : 24.88 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.18), residues: 2049 helix: -0.55 (0.18), residues: 748 sheet: -2.42 (0.35), residues: 192 loop : -2.69 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 74 TYR 0.040 0.002 TYR F 322 PHE 0.027 0.002 PHE E 116 TRP 0.017 0.002 TRP A 596 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00367 (17379) covalent geometry : angle 0.70581 (23615) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.59259 ( 2) hydrogen bonds : bond 0.03504 ( 541) hydrogen bonds : angle 5.39472 ( 1515) *********************** 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 582 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 489 time to evaluate : 0.651 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 65 MET cc_start: 0.7083 (mtt) cc_final: 0.6565 (mmm) REVERT: A 71 MET cc_start: 0.8134 (tpt) cc_final: 0.7666 (tpt) REVERT: A 74 ARG cc_start: 0.7396 (tpm170) cc_final: 0.7176 (tpm170) REVERT: A 99 GLU cc_start: 0.9062 (tp30) cc_final: 0.8608 (tp30) REVERT: A 114 GLN cc_start: 0.8200 (pt0) cc_final: 0.7489 (mp10) REVERT: A 121 SER cc_start: 0.9006 (t) cc_final: 0.8439 (m) REVERT: A 152 GLN cc_start: 0.8139 (pt0) cc_final: 0.7176 (tp40) REVERT: A 166 SER cc_start: 0.8385 (m) cc_final: 0.8015 (p) REVERT: A 169 LYS cc_start: 0.7135 (mtpp) cc_final: 0.6439 (mtmm) REVERT: A 181 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8663 (ptmm) REVERT: A 192 GLU cc_start: 0.8757 (tt0) cc_final: 0.8246 (pm20) REVERT: A 203 ARG cc_start: 0.9247 (ttm170) cc_final: 0.8994 (ptm-80) REVERT: A 237 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 253 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8818 (mmmt) REVERT: A 272 ASP cc_start: 0.8663 (t0) cc_final: 0.8200 (t0) REVERT: A 276 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: A 280 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8605 (ttm170) REVERT: A 283 LEU cc_start: 0.9422 (mt) cc_final: 0.9102 (mt) REVERT: A 289 VAL cc_start: 0.9724 (t) cc_final: 0.9495 (p) REVERT: A 342 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8429 (mp0) REVERT: A 359 LEU cc_start: 0.9217 (tp) cc_final: 0.8171 (tp) REVERT: A 403 PRO cc_start: 0.7971 (Cg_endo) cc_final: 0.7608 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7978 (mt) cc_final: 0.7624 (tp) REVERT: A 454 TYR cc_start: 0.8087 (t80) cc_final: 0.7193 (t80) REVERT: A 464 GLN cc_start: 0.8589 (mp10) cc_final: 0.8047 (mp10) REVERT: A 490 TYR cc_start: 0.8323 (t80) cc_final: 0.7582 (t80) REVERT: A 513 ARG cc_start: 0.8691 (mtp85) cc_final: 0.8270 (ttm-80) REVERT: A 537 LYS cc_start: 0.8907 (mttt) cc_final: 0.8578 (mttm) REVERT: A 629 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7150 (mt-10) REVERT: A 638 ASP cc_start: 0.8637 (m-30) cc_final: 0.8056 (t0) REVERT: A 708 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8640 (mptt) REVERT: A 724 ARG cc_start: 0.8627 (mtp180) cc_final: 0.7421 (mmp-170) REVERT: A 725 TRP cc_start: 0.9127 (p-90) cc_final: 0.7501 (p-90) REVERT: A 742 PHE cc_start: 0.9456 (m-80) cc_final: 0.9216 (m-80) REVERT: A 745 LEU cc_start: 0.8435 (mt) cc_final: 0.7734 (mt) REVERT: A 773 MET cc_start: 0.8449 (mtp) cc_final: 0.8132 (mtt) REVERT: B 97 LYS cc_start: 0.8623 (tptp) cc_final: 0.8300 (mttm) REVERT: B 164 ASN cc_start: 0.8661 (t0) cc_final: 0.7999 (t0) REVERT: C 14 LYS cc_start: 0.8489 (ptpt) cc_final: 0.8021 (mtpp) REVERT: C 85 SER cc_start: 0.8978 (m) cc_final: 0.8743 (p) REVERT: C 89 CYS cc_start: 0.8132 (m) cc_final: 0.6559 (m) REVERT: C 92 ASP cc_start: 0.7050 (p0) cc_final: 0.6604 (p0) REVERT: C 94 GLN cc_start: 0.7559 (mt0) cc_final: 0.6868 (tp40) REVERT: C 95 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7672 (mp0) REVERT: C 106 ASN cc_start: 0.8452 (t0) cc_final: 0.8018 (t0) REVERT: C 109 TRP cc_start: 0.8415 (m100) cc_final: 0.6716 (m-10) REVERT: C 133 LYS cc_start: 0.8835 (tptt) cc_final: 0.8263 (pttp) REVERT: C 141 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8568 (tt) REVERT: C 142 ILE cc_start: 0.8925 (mt) cc_final: 0.8678 (mm) REVERT: C 237 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8343 (ttpp) REVERT: C 259 ILE cc_start: 0.8147 (mp) cc_final: 0.7821 (mt) REVERT: D 70 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7434 (mpt-90) REVERT: D 115 ASP cc_start: 0.8260 (t0) cc_final: 0.8027 (t70) REVERT: D 131 SER cc_start: 0.8694 (p) cc_final: 0.8473 (p) REVERT: D 180 PRO cc_start: 0.9120 (Cg_endo) cc_final: 0.8856 (Cg_exo) REVERT: D 201 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: D 224 TYR cc_start: 0.8725 (p90) cc_final: 0.8463 (p90) REVERT: E 43 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7383 (mt-10) REVERT: E 63 ASP cc_start: 0.8599 (p0) cc_final: 0.8347 (p0) REVERT: E 74 GLU cc_start: 0.8694 (mp0) cc_final: 0.8391 (mp0) REVERT: E 86 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7792 (tp30) REVERT: E 124 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6963 (m-10) REVERT: E 148 GLU cc_start: 0.7649 (mp0) cc_final: 0.7413 (mt-10) REVERT: E 200 HIS cc_start: 0.8175 (t-170) cc_final: 0.7743 (t70) REVERT: E 237 PHE cc_start: 0.8241 (m-80) cc_final: 0.7840 (m-80) REVERT: E 262 ARG cc_start: 0.7133 (mtt-85) cc_final: 0.6606 (ttm170) REVERT: E 264 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7040 (mm-30) REVERT: F 23 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8255 (p) REVERT: F 26 TYR cc_start: 0.7859 (t80) cc_final: 0.7442 (t80) REVERT: F 36 ASP cc_start: 0.8838 (t0) cc_final: 0.8611 (t0) REVERT: F 45 MET cc_start: 0.6641 (mmm) cc_final: 0.6116 (mtm) REVERT: F 86 THR cc_start: 0.9107 (p) cc_final: 0.8877 (m) REVERT: F 99 GLN cc_start: 0.8698 (pm20) cc_final: 0.8483 (pm20) REVERT: F 131 LYS cc_start: 0.8451 (tttp) cc_final: 0.7433 (mptt) REVERT: F 189 MET cc_start: 0.7770 (mtm) cc_final: 0.7526 (tpp) REVERT: F 204 ASP cc_start: 0.9055 (t0) cc_final: 0.8704 (t70) REVERT: F 220 LYS cc_start: 0.8559 (pttt) cc_final: 0.7950 (ttpt) REVERT: F 238 ILE cc_start: 0.7689 (tt) cc_final: 0.7079 (pt) REVERT: F 241 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8531 (mt-10) REVERT: F 275 LEU cc_start: 0.8668 (mt) cc_final: 0.8371 (tt) REVERT: F 290 TRP cc_start: 0.8497 (m100) cc_final: 0.8073 (m100) REVERT: F 297 TYR cc_start: 0.7716 (m-80) cc_final: 0.7088 (m-80) REVERT: F 298 THR cc_start: 0.8540 (m) cc_final: 0.8327 (p) REVERT: F 327 ASP cc_start: 0.7073 (t0) cc_final: 0.6482 (p0) outliers start: 93 outliers final: 70 residues processed: 535 average time/residue: 0.1265 time to fit residues: 101.6228 Evaluate side-chains 533 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 457 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 718 ARG 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 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 126 ARG Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 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 245 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 333 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 162 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 13 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- 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 44 HIS C 205 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 212 ASN E 30 ASN E 200 HIS ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117591 restraints weight = 32960.212| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 4.02 r_work: 0.3419 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17380 Z= 0.154 Angle : 0.690 13.548 23617 Z= 0.354 Chirality : 0.048 0.246 2571 Planarity : 0.005 0.094 2941 Dihedral : 11.594 90.972 2698 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.37 % Favored : 88.53 % Rotamer: Outliers : 5.61 % Allowed : 25.93 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.18), residues: 2049 helix: -0.39 (0.18), residues: 751 sheet: -2.30 (0.34), residues: 198 loop : -2.62 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 74 TYR 0.047 0.002 TYR F 322 PHE 0.032 0.002 PHE E 58 TRP 0.019 0.001 TRP F 239 HIS 0.013 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00355 (17379) covalent geometry : angle 0.69043 (23615) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.57973 ( 2) hydrogen bonds : bond 0.03407 ( 541) hydrogen bonds : angle 5.33289 ( 1515) *********************** 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 585 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 489 time to evaluate : 0.638 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 71 MET cc_start: 0.8137 (tpt) cc_final: 0.7792 (tpt) REVERT: A 99 GLU cc_start: 0.9064 (tp30) cc_final: 0.8631 (tp30) REVERT: A 114 GLN cc_start: 0.8176 (pt0) cc_final: 0.7503 (mp10) REVERT: A 121 SER cc_start: 0.8994 (t) cc_final: 0.8421 (m) REVERT: A 152 GLN cc_start: 0.8183 (pt0) cc_final: 0.7216 (tp40) REVERT: A 166 SER cc_start: 0.8374 (m) cc_final: 0.8005 (p) REVERT: A 169 LYS cc_start: 0.7093 (mtpp) cc_final: 0.6411 (mtmm) REVERT: A 181 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8593 (ptmm) REVERT: A 192 GLU cc_start: 0.8734 (tt0) cc_final: 0.8229 (pm20) REVERT: A 203 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8991 (ptm-80) REVERT: A 237 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 253 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8828 (mmmt) REVERT: A 272 ASP cc_start: 0.8618 (t0) cc_final: 0.8165 (t0) REVERT: A 276 GLU cc_start: 0.8745 (tp30) cc_final: 0.8339 (tm-30) REVERT: A 280 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8676 (tpp80) REVERT: A 283 LEU cc_start: 0.9477 (mt) cc_final: 0.9140 (mt) REVERT: A 342 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8418 (mp0) REVERT: A 359 LEU cc_start: 0.9204 (tp) cc_final: 0.8143 (tp) REVERT: A 403 PRO cc_start: 0.7921 (Cg_endo) cc_final: 0.7547 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7954 (mt) cc_final: 0.7617 (tp) REVERT: A 454 TYR cc_start: 0.8058 (t80) cc_final: 0.7181 (t80) REVERT: A 464 GLN cc_start: 0.8603 (mp10) cc_final: 0.8045 (mp10) REVERT: A 490 TYR cc_start: 0.8345 (t80) cc_final: 0.7611 (t80) REVERT: A 492 LYS cc_start: 0.7971 (tppt) cc_final: 0.7752 (tppt) REVERT: A 513 ARG cc_start: 0.8739 (mtp85) cc_final: 0.8361 (ttm-80) REVERT: A 537 LYS cc_start: 0.8902 (mttt) cc_final: 0.8533 (mttm) REVERT: A 629 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7159 (mt-10) REVERT: A 638 ASP cc_start: 0.8644 (m-30) cc_final: 0.8092 (t0) REVERT: A 725 TRP cc_start: 0.9137 (p-90) cc_final: 0.7500 (p-90) REVERT: A 742 PHE cc_start: 0.9456 (m-80) cc_final: 0.9199 (m-80) REVERT: A 745 LEU cc_start: 0.8397 (mt) cc_final: 0.7715 (mt) REVERT: A 773 MET cc_start: 0.8519 (mtp) cc_final: 0.8177 (mtt) REVERT: B 66 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.5908 (t80) REVERT: B 97 LYS cc_start: 0.8604 (tptp) cc_final: 0.8335 (mttm) REVERT: B 143 ASP cc_start: 0.9293 (t70) cc_final: 0.8871 (p0) REVERT: B 162 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7666 (mtmt) REVERT: B 164 ASN cc_start: 0.8632 (t0) cc_final: 0.7989 (t0) REVERT: C 14 LYS cc_start: 0.8444 (ptpt) cc_final: 0.7961 (mtpp) REVERT: C 85 SER cc_start: 0.8964 (m) cc_final: 0.8724 (p) REVERT: C 89 CYS cc_start: 0.8010 (m) cc_final: 0.6012 (m) REVERT: C 92 ASP cc_start: 0.6988 (p0) cc_final: 0.6538 (p0) REVERT: C 94 GLN cc_start: 0.7501 (mt0) cc_final: 0.6743 (tp40) REVERT: C 102 ASN cc_start: 0.7050 (p0) cc_final: 0.5882 (m-40) REVERT: C 106 ASN cc_start: 0.8417 (t0) cc_final: 0.7989 (t0) REVERT: C 109 TRP cc_start: 0.8391 (m100) cc_final: 0.6747 (m-10) REVERT: C 133 LYS cc_start: 0.8817 (tptt) cc_final: 0.8242 (pttp) REVERT: C 141 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8570 (tt) REVERT: C 142 ILE cc_start: 0.8924 (mt) cc_final: 0.8692 (mm) REVERT: C 195 GLU cc_start: 0.8711 (tt0) cc_final: 0.7991 (tt0) REVERT: C 207 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7977 (ttt-90) REVERT: C 237 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8378 (ttpp) REVERT: C 244 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7572 (tp30) REVERT: C 259 ILE cc_start: 0.8197 (mp) cc_final: 0.7420 (mt) REVERT: D 55 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8625 (tt) REVERT: D 70 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7411 (mpt-90) REVERT: D 115 ASP cc_start: 0.8187 (t0) cc_final: 0.7907 (t70) REVERT: D 131 SER cc_start: 0.8639 (p) cc_final: 0.8400 (p) REVERT: D 180 PRO cc_start: 0.9142 (Cg_endo) cc_final: 0.8901 (Cg_exo) REVERT: D 201 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: E 43 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7376 (mt-10) REVERT: E 63 ASP cc_start: 0.8549 (p0) cc_final: 0.8304 (p0) REVERT: E 86 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7709 (tp30) REVERT: E 124 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6766 (m-10) REVERT: E 200 HIS cc_start: 0.8102 (t70) cc_final: 0.7897 (t-90) REVERT: E 237 PHE cc_start: 0.8366 (m-80) cc_final: 0.8011 (m-80) REVERT: E 262 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6182 (mtt180) REVERT: F 23 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8134 (p) REVERT: F 26 TYR cc_start: 0.7834 (t80) cc_final: 0.7424 (t80) REVERT: F 36 ASP cc_start: 0.8818 (t0) cc_final: 0.8566 (t0) REVERT: F 45 MET cc_start: 0.6713 (mmm) cc_final: 0.6326 (mtm) REVERT: F 86 THR cc_start: 0.9111 (p) cc_final: 0.8883 (m) REVERT: F 99 GLN cc_start: 0.8719 (pm20) cc_final: 0.8392 (pm20) REVERT: F 131 LYS cc_start: 0.8458 (tttp) cc_final: 0.7458 (mptt) REVERT: F 204 ASP cc_start: 0.9123 (t0) cc_final: 0.8748 (t70) REVERT: F 220 LYS cc_start: 0.8562 (pttt) cc_final: 0.7930 (ttpt) REVERT: F 241 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8448 (mt-10) REVERT: F 275 LEU cc_start: 0.8646 (mt) cc_final: 0.8378 (tt) REVERT: F 290 TRP cc_start: 0.8523 (m100) cc_final: 0.8038 (m100) REVERT: F 297 TYR cc_start: 0.7701 (m-80) cc_final: 0.6972 (m-80) REVERT: F 327 ASP cc_start: 0.7121 (t0) cc_final: 0.6514 (p0) outliers start: 96 outliers final: 77 residues processed: 539 average time/residue: 0.1344 time to fit residues: 108.3936 Evaluate side-chains 539 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 453 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 210 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 718 ARG 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 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 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 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 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 289 LEU 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 200 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 0.0770 chunk 117 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- 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** A 382 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 212 ASN D 183 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 = 0.3888 r_free = 0.3888 target = 0.143092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118380 restraints weight = 32679.336| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.01 r_work: 0.3441 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17380 Z= 0.147 Angle : 0.687 12.863 23617 Z= 0.353 Chirality : 0.048 0.239 2571 Planarity : 0.005 0.096 2941 Dihedral : 11.527 88.122 2698 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.83 % Favored : 89.07 % Rotamer: Outliers : 6.07 % Allowed : 26.29 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.18), residues: 2049 helix: -0.31 (0.19), residues: 754 sheet: -2.28 (0.35), residues: 198 loop : -2.57 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 152 TYR 0.031 0.002 TYR A 727 PHE 0.027 0.002 PHE E 58 TRP 0.015 0.001 TRP A 596 HIS 0.019 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00340 (17379) covalent geometry : angle 0.68724 (23615) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.56713 ( 2) hydrogen bonds : bond 0.03392 ( 541) hydrogen bonds : angle 5.27056 ( 1515) *********************** 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 585 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 481 time to evaluate : 0.600 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 65 MET cc_start: 0.7281 (mtt) cc_final: 0.6675 (mmm) REVERT: A 71 MET cc_start: 0.8158 (tpt) cc_final: 0.7740 (tpt) REVERT: A 99 GLU cc_start: 0.9092 (tp30) cc_final: 0.8704 (tp30) REVERT: A 114 GLN cc_start: 0.8244 (pt0) cc_final: 0.7600 (mp10) REVERT: A 121 SER cc_start: 0.9058 (t) cc_final: 0.8515 (m) REVERT: A 152 GLN cc_start: 0.8122 (pt0) cc_final: 0.7175 (tp40) REVERT: A 166 SER cc_start: 0.8388 (m) cc_final: 0.8042 (p) REVERT: A 169 LYS cc_start: 0.7053 (mtpp) cc_final: 0.6358 (mtmm) REVERT: A 181 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8625 (ptmm) REVERT: A 192 GLU cc_start: 0.8736 (tt0) cc_final: 0.8215 (pm20) REVERT: A 203 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8997 (ptm-80) REVERT: A 210 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8887 (tp) REVERT: A 237 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 253 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8801 (mmmt) REVERT: A 272 ASP cc_start: 0.8620 (t0) cc_final: 0.8175 (t0) REVERT: A 280 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8535 (ttm170) REVERT: A 283 LEU cc_start: 0.9511 (mt) cc_final: 0.9174 (mt) REVERT: A 301 GLN cc_start: 0.9040 (pm20) cc_final: 0.8769 (pm20) REVERT: A 342 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8419 (mp0) REVERT: A 359 LEU cc_start: 0.9195 (tp) cc_final: 0.8214 (tp) REVERT: A 391 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8769 (t) REVERT: A 403 PRO cc_start: 0.7894 (Cg_endo) cc_final: 0.7515 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7958 (mt) cc_final: 0.7624 (tp) REVERT: A 454 TYR cc_start: 0.8065 (t80) cc_final: 0.7203 (t80) REVERT: A 464 GLN cc_start: 0.8580 (mp10) cc_final: 0.8007 (mp10) REVERT: A 490 TYR cc_start: 0.8325 (t80) cc_final: 0.7594 (t80) REVERT: A 513 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8364 (ttm-80) REVERT: A 537 LYS cc_start: 0.8901 (mttt) cc_final: 0.8541 (mttm) REVERT: A 613 TYR cc_start: 0.8679 (t80) cc_final: 0.8454 (t80) REVERT: A 629 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 638 ASP cc_start: 0.8677 (m-30) cc_final: 0.8137 (t0) REVERT: A 724 ARG cc_start: 0.8519 (mtp180) cc_final: 0.7291 (mmp-170) REVERT: A 725 TRP cc_start: 0.9123 (p-90) cc_final: 0.7479 (p-90) REVERT: A 742 PHE cc_start: 0.9455 (m-80) cc_final: 0.9210 (m-80) REVERT: A 745 LEU cc_start: 0.8424 (mt) cc_final: 0.7754 (mt) REVERT: A 768 LEU cc_start: 0.8662 (mt) cc_final: 0.8377 (tp) REVERT: A 773 MET cc_start: 0.8534 (mtp) cc_final: 0.8178 (mtt) REVERT: B 66 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5990 (t80) REVERT: B 97 LYS cc_start: 0.8521 (tptp) cc_final: 0.8270 (mttm) REVERT: B 162 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7728 (mtmt) REVERT: B 164 ASN cc_start: 0.8627 (t0) cc_final: 0.8094 (t0) REVERT: C 14 LYS cc_start: 0.8433 (ptpt) cc_final: 0.7908 (mtpp) REVERT: C 58 ARG cc_start: 0.7900 (tpt170) cc_final: 0.7629 (tpt170) REVERT: C 85 SER cc_start: 0.8965 (m) cc_final: 0.8728 (p) REVERT: C 89 CYS cc_start: 0.7950 (m) cc_final: 0.5938 (m) REVERT: C 92 ASP cc_start: 0.6989 (p0) cc_final: 0.6549 (p0) REVERT: C 94 GLN cc_start: 0.7641 (mt0) cc_final: 0.6887 (tp40) REVERT: C 102 ASN cc_start: 0.6900 (p0) cc_final: 0.6407 (m-40) REVERT: C 106 ASN cc_start: 0.8415 (t0) cc_final: 0.7976 (t0) REVERT: C 109 TRP cc_start: 0.8387 (m100) cc_final: 0.6801 (m-10) REVERT: C 133 LYS cc_start: 0.8805 (tptt) cc_final: 0.8124 (ptpp) REVERT: C 134 GLU cc_start: 0.8617 (pp20) cc_final: 0.8227 (pp20) REVERT: C 142 ILE cc_start: 0.8931 (mt) cc_final: 0.8707 (mm) REVERT: C 195 GLU cc_start: 0.8720 (tt0) cc_final: 0.7981 (tt0) REVERT: C 207 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7994 (ttt-90) REVERT: C 237 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8331 (ttpp) REVERT: C 244 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7534 (tp30) REVERT: C 259 ILE cc_start: 0.8230 (mp) cc_final: 0.7469 (mt) REVERT: D 55 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8600 (tt) REVERT: D 70 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7457 (mpt-90) REVERT: D 96 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7314 (m-40) REVERT: D 115 ASP cc_start: 0.8158 (t0) cc_final: 0.7940 (t70) REVERT: D 131 SER cc_start: 0.8541 (p) cc_final: 0.8283 (p) REVERT: D 180 PRO cc_start: 0.9144 (Cg_endo) cc_final: 0.8919 (Cg_exo) REVERT: D 201 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: E 20 ARG cc_start: 0.8760 (mmp80) cc_final: 0.8339 (mmp80) REVERT: E 43 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7332 (mt-10) REVERT: E 58 PHE cc_start: 0.7949 (t80) cc_final: 0.7680 (t80) REVERT: E 63 ASP cc_start: 0.8551 (p0) cc_final: 0.8336 (p0) REVERT: E 86 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7710 (tp30) REVERT: E 109 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7640 (pp) REVERT: E 118 ILE cc_start: 0.9404 (tp) cc_final: 0.9109 (mt) REVERT: E 124 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: E 200 HIS cc_start: 0.8088 (t70) cc_final: 0.7877 (t-90) REVERT: E 237 PHE cc_start: 0.8295 (m-80) cc_final: 0.7968 (m-80) REVERT: E 249 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 264 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6758 (mm-30) REVERT: F 23 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8114 (p) REVERT: F 26 TYR cc_start: 0.7805 (t80) cc_final: 0.7412 (t80) REVERT: F 36 ASP cc_start: 0.8803 (t0) cc_final: 0.8559 (t0) REVERT: F 45 MET cc_start: 0.6791 (mmm) cc_final: 0.6449 (mtm) REVERT: F 86 THR cc_start: 0.9170 (p) cc_final: 0.8947 (m) REVERT: F 131 LYS cc_start: 0.8468 (tttp) cc_final: 0.7493 (mptt) REVERT: F 220 LYS cc_start: 0.8508 (pttt) cc_final: 0.7893 (ttpt) REVERT: F 241 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8441 (mt-10) REVERT: F 275 LEU cc_start: 0.8640 (mt) cc_final: 0.8382 (tt) REVERT: F 290 TRP cc_start: 0.8558 (m100) cc_final: 0.8067 (m100) REVERT: F 297 TYR cc_start: 0.7716 (m-80) cc_final: 0.6898 (m-80) REVERT: F 319 ARG cc_start: 0.9301 (ttp80) cc_final: 0.8742 (mmt180) REVERT: F 322 TYR cc_start: 0.7520 (m-80) cc_final: 0.7263 (m-80) REVERT: F 327 ASP cc_start: 0.7052 (t0) cc_final: 0.6468 (p0) outliers start: 104 outliers final: 77 residues processed: 535 average time/residue: 0.1307 time to fit residues: 104.9227 Evaluate side-chains 546 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 458 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 210 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 280 ARG 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 649 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 718 ARG 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 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 135 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 212 ASN 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 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 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 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 109 LEU 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 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 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 331 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 84 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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** B 179 HIS ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 106 ASN F 13 HIS F 18 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116087 restraints weight = 33310.277| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 4.01 r_work: 0.3409 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17380 Z= 0.193 Angle : 0.730 12.919 23617 Z= 0.373 Chirality : 0.049 0.255 2571 Planarity : 0.006 0.095 2941 Dihedral : 11.509 84.685 2698 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.10 % Favored : 87.80 % Rotamer: Outliers : 6.66 % Allowed : 25.76 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.18), residues: 2049 helix: -0.16 (0.19), residues: 744 sheet: -2.34 (0.35), residues: 196 loop : -2.52 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 74 TYR 0.029 0.002 TYR F 303 PHE 0.022 0.002 PHE A 549 TRP 0.014 0.002 TRP A 596 HIS 0.008 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00446 (17379) covalent geometry : angle 0.72999 (23615) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.64694 ( 2) hydrogen bonds : bond 0.03503 ( 541) hydrogen bonds : angle 5.35416 ( 1515) *********************** 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 574 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 460 time to evaluate : 0.561 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 65 MET cc_start: 0.7348 (mtt) cc_final: 0.6593 (mmm) REVERT: A 71 MET cc_start: 0.8085 (tpt) cc_final: 0.7635 (tpt) REVERT: A 99 GLU cc_start: 0.9113 (tp30) cc_final: 0.8779 (tp30) REVERT: A 114 GLN cc_start: 0.8295 (pt0) cc_final: 0.7647 (mp10) REVERT: A 121 SER cc_start: 0.9189 (t) cc_final: 0.8649 (m) REVERT: A 152 GLN cc_start: 0.8088 (pt0) cc_final: 0.7167 (tp40) REVERT: A 166 SER cc_start: 0.8398 (m) cc_final: 0.8019 (p) REVERT: A 169 LYS cc_start: 0.7147 (mtpp) cc_final: 0.6444 (mtmm) REVERT: A 181 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8605 (ptmm) REVERT: A 192 GLU cc_start: 0.8747 (tt0) cc_final: 0.8268 (pm20) REVERT: A 203 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.9009 (ptm-80) REVERT: A 210 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8992 (tp) REVERT: A 237 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7922 (mt-10) REVERT: A 253 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8876 (mmmt) REVERT: A 272 ASP cc_start: 0.8664 (t0) cc_final: 0.8203 (t0) REVERT: A 283 LEU cc_start: 0.9514 (mt) cc_final: 0.9186 (mt) REVERT: A 334 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 342 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8426 (mp0) REVERT: A 385 ARG cc_start: 0.7547 (mmm-85) cc_final: 0.7330 (mmp-170) REVERT: A 403 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7518 (Cg_exo) REVERT: A 430 LEU cc_start: 0.7966 (mt) cc_final: 0.7655 (tp) REVERT: A 454 TYR cc_start: 0.8093 (t80) cc_final: 0.7245 (t80) REVERT: A 464 GLN cc_start: 0.8600 (mp10) cc_final: 0.8048 (mp10) REVERT: A 490 TYR cc_start: 0.8370 (t80) cc_final: 0.7656 (t80) REVERT: A 513 ARG cc_start: 0.8776 (mtp85) cc_final: 0.8408 (ttm-80) REVERT: A 537 LYS cc_start: 0.8916 (mttt) cc_final: 0.8567 (mttm) REVERT: A 550 LYS cc_start: 0.8224 (mttm) cc_final: 0.7919 (mttm) REVERT: A 624 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8830 (mt) REVERT: A 629 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7117 (mt-10) REVERT: A 638 ASP cc_start: 0.8703 (m-30) cc_final: 0.8232 (t0) REVERT: A 707 TRP cc_start: 0.8546 (m100) cc_final: 0.8132 (m100) REVERT: A 724 ARG cc_start: 0.8553 (mtp180) cc_final: 0.7324 (mmp-170) REVERT: A 725 TRP cc_start: 0.9160 (p-90) cc_final: 0.7508 (p-90) REVERT: A 742 PHE cc_start: 0.9467 (m-80) cc_final: 0.9175 (m-80) REVERT: A 745 LEU cc_start: 0.8475 (mt) cc_final: 0.7802 (mt) REVERT: A 773 MET cc_start: 0.8539 (mtp) cc_final: 0.8198 (mtt) REVERT: B 66 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.5946 (t80) REVERT: B 97 LYS cc_start: 0.8547 (tptp) cc_final: 0.8271 (mttm) REVERT: B 162 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7837 (mtmt) REVERT: B 164 ASN cc_start: 0.8656 (t0) cc_final: 0.8090 (t0) REVERT: C 14 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8025 (mtpp) REVERT: C 59 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9029 (mp) REVERT: C 85 SER cc_start: 0.8984 (m) cc_final: 0.8738 (p) REVERT: C 89 CYS cc_start: 0.8006 (m) cc_final: 0.6411 (m) REVERT: C 92 ASP cc_start: 0.6869 (p0) cc_final: 0.6408 (p0) REVERT: C 94 GLN cc_start: 0.7556 (mt0) cc_final: 0.6947 (tp40) REVERT: C 106 ASN cc_start: 0.8398 (t0) cc_final: 0.7949 (t0) REVERT: C 109 TRP cc_start: 0.8446 (m100) cc_final: 0.6911 (m-10) REVERT: C 133 LYS cc_start: 0.8798 (tptt) cc_final: 0.8242 (pttp) REVERT: C 141 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8701 (tt) REVERT: C 142 ILE cc_start: 0.8935 (mt) cc_final: 0.8682 (mm) REVERT: C 195 GLU cc_start: 0.8708 (tt0) cc_final: 0.7964 (tt0) REVERT: C 207 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7945 (ttt-90) REVERT: C 237 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8415 (ttpp) REVERT: C 244 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7613 (tp30) REVERT: C 259 ILE cc_start: 0.8215 (mp) cc_final: 0.7499 (mt) REVERT: D 55 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8569 (tt) REVERT: D 70 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7462 (mpt-90) REVERT: D 93 ASN cc_start: 0.8885 (p0) cc_final: 0.8442 (p0) REVERT: D 96 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7347 (m-40) REVERT: D 115 ASP cc_start: 0.8344 (t0) cc_final: 0.8026 (t70) REVERT: D 131 SER cc_start: 0.8587 (p) cc_final: 0.8356 (p) REVERT: D 180 PRO cc_start: 0.9172 (Cg_endo) cc_final: 0.8951 (Cg_exo) REVERT: E 20 ARG cc_start: 0.8778 (mmp80) cc_final: 0.8480 (mmp80) REVERT: E 43 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7408 (mt-10) REVERT: E 63 ASP cc_start: 0.8611 (p0) cc_final: 0.8377 (p0) REVERT: E 86 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7698 (tp30) REVERT: E 109 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7718 (pp) REVERT: E 118 ILE cc_start: 0.9427 (tp) cc_final: 0.9087 (mt) REVERT: E 124 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: E 200 HIS cc_start: 0.8159 (t70) cc_final: 0.7948 (t-90) REVERT: E 231 ARG cc_start: 0.7667 (pmt-80) cc_final: 0.7397 (pmt-80) REVERT: E 237 PHE cc_start: 0.8364 (m-80) cc_final: 0.7714 (m-80) REVERT: E 262 ARG cc_start: 0.6792 (ttm170) cc_final: 0.5956 (mtt180) REVERT: E 264 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7203 (mm-30) REVERT: F 23 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8198 (p) REVERT: F 26 TYR cc_start: 0.7824 (t80) cc_final: 0.7360 (t80) REVERT: F 36 ASP cc_start: 0.8805 (t0) cc_final: 0.8479 (t0) REVERT: F 45 MET cc_start: 0.6929 (mmm) cc_final: 0.6593 (mtm) REVERT: F 86 THR cc_start: 0.9086 (p) cc_final: 0.8860 (m) REVERT: F 99 GLN cc_start: 0.8650 (pm20) cc_final: 0.8441 (pm20) REVERT: F 131 LYS cc_start: 0.8491 (tttp) cc_final: 0.7500 (mptt) REVERT: F 189 MET cc_start: 0.7980 (ttm) cc_final: 0.7750 (tpp) REVERT: F 204 ASP cc_start: 0.9072 (t0) cc_final: 0.8849 (t70) REVERT: F 220 LYS cc_start: 0.8535 (pttt) cc_final: 0.7920 (ttpt) REVERT: F 241 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8420 (mt-10) REVERT: F 275 LEU cc_start: 0.8680 (mt) cc_final: 0.8407 (tt) REVERT: F 290 TRP cc_start: 0.8580 (m100) cc_final: 0.8110 (m100) REVERT: F 297 TYR cc_start: 0.7767 (m-80) cc_final: 0.7136 (m-80) REVERT: F 319 ARG cc_start: 0.9311 (ttp80) cc_final: 0.8925 (mmt180) REVERT: F 327 ASP cc_start: 0.7075 (t0) cc_final: 0.6477 (p0) outliers start: 114 outliers final: 92 residues processed: 522 average time/residue: 0.1251 time to fit residues: 98.5112 Evaluate side-chains 555 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 452 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 210 LEU 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 391 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 624 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 718 ARG 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 116 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 141 ILE 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 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 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 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 17 ASP Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 109 LEU 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 149 ILE 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 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 13 HIS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 321 PHE 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 110 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 113 optimal weight: 0.0370 chunk 181 optimal weight: 0.5980 chunk 1 optimal weight: 0.0570 chunk 174 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5380 ------------------------------------------------------------------------------- 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 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 13 HIS ** 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 = 0.3910 r_free = 0.3910 target = 0.144861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119735 restraints weight = 32740.949| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 4.06 r_work: 0.3446 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17380 Z= 0.141 Angle : 0.716 13.727 23617 Z= 0.362 Chirality : 0.048 0.246 2571 Planarity : 0.006 0.097 2941 Dihedral : 11.413 83.250 2698 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.93 % Favored : 88.97 % Rotamer: Outliers : 5.32 % Allowed : 27.28 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.18), residues: 2049 helix: -0.10 (0.19), residues: 753 sheet: -2.31 (0.36), residues: 198 loop : -2.51 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 74 TYR 0.028 0.002 TYR A 552 PHE 0.053 0.002 PHE E 58 TRP 0.016 0.001 TRP A 596 HIS 0.017 0.002 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00329 (17379) covalent geometry : angle 0.71603 (23615) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.67316 ( 2) hydrogen bonds : bond 0.03335 ( 541) hydrogen bonds : angle 5.26931 ( 1515) *********************** 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 571 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 480 time to evaluate : 0.611 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: symmetry clash REVERT: A 65 MET cc_start: 0.7255 (mtt) cc_final: 0.6548 (mmm) REVERT: A 71 MET cc_start: 0.7994 (tpt) cc_final: 0.7604 (tpt) REVERT: A 99 GLU cc_start: 0.9032 (tp30) cc_final: 0.8694 (tp30) REVERT: A 114 GLN cc_start: 0.8231 (pt0) cc_final: 0.7607 (mp10) REVERT: A 121 SER cc_start: 0.9163 (t) cc_final: 0.8689 (m) REVERT: A 152 GLN cc_start: 0.8031 (pt0) cc_final: 0.7125 (tp40) REVERT: A 164 GLU cc_start: 0.7874 (tt0) cc_final: 0.7647 (tm-30) REVERT: A 166 SER cc_start: 0.8376 (m) cc_final: 0.8028 (p) REVERT: A 169 LYS cc_start: 0.7045 (mtpp) cc_final: 0.6348 (mtmm) REVERT: A 181 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8724 (ptmm) REVERT: A 192 GLU cc_start: 0.8689 (tt0) cc_final: 0.8143 (pm20) REVERT: A 196 ILE cc_start: 0.9296 (mp) cc_final: 0.9077 (mm) REVERT: A 203 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8895 (ptm-80) REVERT: A 210 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 237 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 241 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 253 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8804 (mmmt) REVERT: A 272 ASP cc_start: 0.8518 (t0) cc_final: 0.8046 (t0) REVERT: A 283 LEU cc_start: 0.9520 (mt) cc_final: 0.9219 (mt) REVERT: A 295 HIS cc_start: 0.7851 (t-90) cc_final: 0.7627 (t70) REVERT: A 301 GLN cc_start: 0.9013 (pm20) cc_final: 0.8749 (pm20) REVERT: A 334 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 342 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8430 (mp0) REVERT: A 359 LEU cc_start: 0.9176 (tp) cc_final: 0.8281 (tp) REVERT: A 403 PRO cc_start: 0.7869 (Cg_endo) cc_final: 0.7502 (Cg_exo) REVERT: A 464 GLN cc_start: 0.8564 (mp10) cc_final: 0.7921 (mp10) REVERT: A 490 TYR cc_start: 0.8286 (t80) cc_final: 0.7577 (t80) REVERT: A 537 LYS cc_start: 0.8898 (mttt) cc_final: 0.8532 (mttm) REVERT: A 550 LYS cc_start: 0.8186 (mttm) cc_final: 0.7840 (mttm) REVERT: A 638 ASP cc_start: 0.8661 (m-30) cc_final: 0.8192 (t0) REVERT: A 724 ARG cc_start: 0.8500 (mtp180) cc_final: 0.7266 (mmp-170) REVERT: A 725 TRP cc_start: 0.9124 (p-90) cc_final: 0.7512 (p-90) REVERT: A 742 PHE cc_start: 0.9444 (m-80) cc_final: 0.9198 (m-80) REVERT: A 745 LEU cc_start: 0.8427 (mt) cc_final: 0.7733 (mt) REVERT: A 768 LEU cc_start: 0.8651 (mt) cc_final: 0.8414 (tp) REVERT: A 773 MET cc_start: 0.8526 (mtp) cc_final: 0.8179 (mtt) REVERT: B 66 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5998 (t80) REVERT: B 97 LYS cc_start: 0.8517 (tptp) cc_final: 0.8245 (mttm) REVERT: B 164 ASN cc_start: 0.8621 (t0) cc_final: 0.8062 (t0) REVERT: C 14 LYS cc_start: 0.8502 (ptpt) cc_final: 0.8015 (mtpp) REVERT: C 70 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.8102 (tpt90) REVERT: C 85 SER cc_start: 0.8926 (m) cc_final: 0.8671 (p) REVERT: C 89 CYS cc_start: 0.7810 (m) cc_final: 0.5845 (m) REVERT: C 94 GLN cc_start: 0.7593 (mt0) cc_final: 0.7023 (tp40) REVERT: C 102 ASN cc_start: 0.7119 (p0) cc_final: 0.6329 (m-40) REVERT: C 106 ASN cc_start: 0.8378 (t0) cc_final: 0.7935 (t0) REVERT: C 109 TRP cc_start: 0.8282 (m100) cc_final: 0.6850 (m-10) REVERT: C 133 LYS cc_start: 0.8797 (tptt) cc_final: 0.8172 (pttp) REVERT: C 142 ILE cc_start: 0.8936 (mt) cc_final: 0.8710 (mm) REVERT: C 195 GLU cc_start: 0.8672 (tt0) cc_final: 0.8115 (tt0) REVERT: C 207 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7927 (ttt-90) REVERT: C 237 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8342 (ttpp) REVERT: C 244 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7537 (tp30) REVERT: C 259 ILE cc_start: 0.8254 (mp) cc_final: 0.7538 (mt) REVERT: D 55 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8586 (tt) REVERT: D 70 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7577 (mpt-90) REVERT: D 93 ASN cc_start: 0.8863 (p0) cc_final: 0.8535 (p0) REVERT: D 115 ASP cc_start: 0.8218 (t0) cc_final: 0.7913 (t70) REVERT: D 125 CYS cc_start: 0.9124 (m) cc_final: 0.8909 (m) REVERT: D 131 SER cc_start: 0.8510 (p) cc_final: 0.8245 (p) REVERT: D 180 PRO cc_start: 0.9153 (Cg_endo) cc_final: 0.8944 (Cg_exo) REVERT: D 205 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7813 (t70) REVERT: E 20 ARG cc_start: 0.8759 (mmp80) cc_final: 0.8415 (mmp80) REVERT: E 30 ASN cc_start: 0.9158 (m-40) cc_final: 0.8816 (m-40) REVERT: E 43 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7339 (mt-10) REVERT: E 86 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7511 (tp30) REVERT: E 109 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7682 (pp) REVERT: E 118 ILE cc_start: 0.9395 (tp) cc_final: 0.9034 (mt) REVERT: E 124 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6570 (m-10) REVERT: E 237 PHE cc_start: 0.8326 (m-80) cc_final: 0.7522 (m-80) REVERT: E 262 ARG cc_start: 0.6546 (ttm170) cc_final: 0.5838 (mtt180) REVERT: F 26 TYR cc_start: 0.7816 (t80) cc_final: 0.7406 (t80) REVERT: F 36 ASP cc_start: 0.8776 (t0) cc_final: 0.8486 (t0) REVERT: F 45 MET cc_start: 0.6817 (mmm) cc_final: 0.6449 (mtm) REVERT: F 86 THR cc_start: 0.9149 (p) cc_final: 0.8945 (m) REVERT: F 98 MET cc_start: 0.6308 (mpp) cc_final: 0.6065 (mpp) REVERT: F 131 LYS cc_start: 0.8483 (tttp) cc_final: 0.7492 (mptt) REVERT: F 204 ASP cc_start: 0.9099 (t0) cc_final: 0.8814 (t70) REVERT: F 220 LYS cc_start: 0.8524 (pttt) cc_final: 0.7922 (ttpt) REVERT: F 241 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8423 (mt-10) REVERT: F 275 LEU cc_start: 0.8647 (mt) cc_final: 0.8401 (tt) REVERT: F 290 TRP cc_start: 0.8571 (m100) cc_final: 0.8081 (m100) REVERT: F 297 TYR cc_start: 0.7703 (m-80) cc_final: 0.7063 (m-80) REVERT: F 319 ARG cc_start: 0.9224 (ttp80) cc_final: 0.8894 (mmt180) REVERT: F 327 ASP cc_start: 0.7094 (t0) cc_final: 0.6492 (p0) outliers start: 91 outliers final: 75 residues processed: 523 average time/residue: 0.1250 time to fit residues: 99.5886 Evaluate side-chains 540 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 457 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 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 718 ARG 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 116 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 135 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 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 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 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 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 39 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 109 LEU 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 134 LEU 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 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 331 HIS 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 114 optimal weight: 30.0000 chunk 87 optimal weight: 0.2980 chunk 133 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 204 optimal weight: 0.0470 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 173 optimal weight: 0.0000 chunk 128 optimal weight: 0.9980 overall best weight: 0.4082 ------------------------------------------------------------------------------- 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 44 HIS ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123736 restraints weight = 32612.104| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 4.10 r_work: 0.3497 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17380 Z= 0.132 Angle : 0.719 13.741 23617 Z= 0.362 Chirality : 0.048 0.247 2571 Planarity : 0.006 0.092 2941 Dihedral : 11.286 81.956 2698 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.44 % Favored : 89.51 % Rotamer: Outliers : 3.86 % Allowed : 28.86 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.18), residues: 2049 helix: -0.04 (0.19), residues: 739 sheet: -2.06 (0.35), residues: 200 loop : -2.47 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 152 TYR 0.030 0.002 TYR F 303 PHE 0.066 0.002 PHE E 58 TRP 0.021 0.001 TRP F 272 HIS 0.008 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00300 (17379) covalent geometry : angle 0.71925 (23615) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.79889 ( 2) hydrogen bonds : bond 0.03338 ( 541) hydrogen bonds : angle 5.15089 ( 1515) ********************** 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 566 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 500 time to evaluate : 0.652 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 65 MET cc_start: 0.7119 (mtt) cc_final: 0.6367 (mmm) REVERT: A 71 MET cc_start: 0.7781 (tpt) cc_final: 0.7438 (tpt) REVERT: A 99 GLU cc_start: 0.9015 (tp30) cc_final: 0.8663 (tp30) REVERT: A 114 GLN cc_start: 0.8192 (pt0) cc_final: 0.7573 (mp10) REVERT: A 138 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8198 (mtpt) REVERT: A 166 SER cc_start: 0.8374 (m) cc_final: 0.7987 (p) REVERT: A 169 LYS cc_start: 0.6977 (mtpp) cc_final: 0.6337 (mtmm) REVERT: A 181 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8587 (ptmm) REVERT: A 192 GLU cc_start: 0.8648 (tt0) cc_final: 0.8013 (pm20) REVERT: A 237 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 253 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8777 (mmmt) REVERT: A 272 ASP cc_start: 0.8280 (t0) cc_final: 0.7869 (t0) REVERT: A 283 LEU cc_start: 0.9536 (mt) cc_final: 0.9253 (mt) REVERT: A 342 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8417 (mp0) REVERT: A 359 LEU cc_start: 0.9162 (tp) cc_final: 0.8392 (tp) REVERT: A 403 PRO cc_start: 0.7816 (Cg_endo) cc_final: 0.7438 (Cg_exo) REVERT: A 464 GLN cc_start: 0.8536 (mp10) cc_final: 0.8215 (mm-40) REVERT: A 490 TYR cc_start: 0.8225 (t80) cc_final: 0.7495 (t80) REVERT: A 557 ILE cc_start: 0.9229 (mt) cc_final: 0.8962 (mt) REVERT: A 600 PHE cc_start: 0.8509 (t80) cc_final: 0.8105 (t80) REVERT: A 638 ASP cc_start: 0.8677 (m-30) cc_final: 0.8315 (t0) REVERT: A 650 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7617 (mm-30) REVERT: A 724 ARG cc_start: 0.8495 (mtp180) cc_final: 0.7321 (mmp-170) REVERT: A 725 TRP cc_start: 0.9093 (p-90) cc_final: 0.7515 (p-90) REVERT: A 742 PHE cc_start: 0.9425 (m-80) cc_final: 0.9168 (m-80) REVERT: A 745 LEU cc_start: 0.8392 (mt) cc_final: 0.7733 (mt) REVERT: A 773 MET cc_start: 0.8490 (mtp) cc_final: 0.8136 (mtt) REVERT: B 66 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.6138 (t80) REVERT: B 97 LYS cc_start: 0.8396 (tptp) cc_final: 0.8112 (mttm) REVERT: B 107 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 122 LYS cc_start: 0.8976 (ptmt) cc_final: 0.8253 (ptpp) REVERT: B 164 ASN cc_start: 0.8585 (t0) cc_final: 0.8057 (t0) REVERT: C 14 LYS cc_start: 0.8383 (ptpt) cc_final: 0.7791 (mtpp) REVERT: C 70 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7965 (tpt90) REVERT: C 89 CYS cc_start: 0.7413 (m) cc_final: 0.6658 (m) REVERT: C 94 GLN cc_start: 0.7632 (mt0) cc_final: 0.7230 (tp40) REVERT: C 102 ASN cc_start: 0.6946 (p0) cc_final: 0.6315 (m-40) REVERT: C 106 ASN cc_start: 0.8188 (t0) cc_final: 0.7794 (t0) REVERT: C 133 LYS cc_start: 0.8800 (tptt) cc_final: 0.8265 (pttm) REVERT: C 195 GLU cc_start: 0.8614 (tt0) cc_final: 0.7873 (tt0) REVERT: C 237 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8290 (ttpt) REVERT: C 244 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7394 (tp30) REVERT: C 259 ILE cc_start: 0.8228 (mp) cc_final: 0.7338 (mt) REVERT: D 55 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8498 (tt) REVERT: D 70 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7590 (mpt-90) REVERT: D 93 ASN cc_start: 0.8803 (p0) cc_final: 0.8438 (p0) REVERT: D 115 ASP cc_start: 0.8100 (t0) cc_final: 0.7762 (t70) REVERT: D 131 SER cc_start: 0.8596 (p) cc_final: 0.8283 (p) REVERT: D 205 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.7915 (t70) REVERT: E 20 ARG cc_start: 0.8717 (mmp80) cc_final: 0.8337 (mmp80) REVERT: E 43 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7270 (mt-10) REVERT: E 86 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7460 (tp30) REVERT: E 106 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8100 (t0) REVERT: E 118 ILE cc_start: 0.9388 (tp) cc_final: 0.9030 (mt) REVERT: E 124 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6358 (m-10) REVERT: E 152 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8357 (tpp80) REVERT: E 200 HIS cc_start: 0.7884 (t-90) cc_final: 0.7295 (t-170) REVERT: E 235 TRP cc_start: 0.7576 (m100) cc_final: 0.6336 (m100) REVERT: E 237 PHE cc_start: 0.8343 (m-80) cc_final: 0.7519 (m-80) REVERT: E 262 ARG cc_start: 0.6538 (ttm170) cc_final: 0.6069 (mtt180) REVERT: E 280 LEU cc_start: 0.8787 (tp) cc_final: 0.8571 (mp) REVERT: F 26 TYR cc_start: 0.7800 (t80) cc_final: 0.7409 (t80) REVERT: F 36 ASP cc_start: 0.8759 (t0) cc_final: 0.8536 (t0) REVERT: F 131 LYS cc_start: 0.8454 (tttp) cc_final: 0.7406 (mptt) REVERT: F 204 ASP cc_start: 0.9036 (t0) cc_final: 0.8804 (t70) REVERT: F 220 LYS cc_start: 0.8486 (pttt) cc_final: 0.7888 (ttpt) REVERT: F 275 LEU cc_start: 0.8642 (mt) cc_final: 0.8413 (tt) REVERT: F 290 TRP cc_start: 0.8515 (m100) cc_final: 0.8059 (m100) REVERT: F 297 TYR cc_start: 0.7736 (m-80) cc_final: 0.6901 (m-80) REVERT: F 319 ARG cc_start: 0.9197 (ttp80) cc_final: 0.8891 (mmt180) outliers start: 66 outliers final: 53 residues processed: 533 average time/residue: 0.1288 time to fit residues: 103.2103 Evaluate side-chains 521 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 462 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 718 ARG 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 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 128 PHE 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 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 55 LEU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 106 ASN 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 134 LEU 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 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain F residue 142 VAL 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 ************** Weight determination summary: number of chunks: 207 random chunks: chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125096 restraints weight = 32556.083| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 4.09 r_work: 0.3501 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 17380 Z= 0.235 Angle : 0.895 59.199 23617 Z= 0.499 Chirality : 0.051 0.918 2571 Planarity : 0.006 0.090 2941 Dihedral : 11.314 81.940 2698 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.44 % Favored : 89.46 % Rotamer: Outliers : 3.91 % Allowed : 29.79 % Favored : 66.30 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.18), residues: 2049 helix: -0.06 (0.19), residues: 739 sheet: -2.04 (0.35), residues: 200 loop : -2.46 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 140 TYR 0.029 0.002 TYR A 727 PHE 0.062 0.002 PHE E 58 TRP 0.018 0.001 TRP A 596 HIS 0.044 0.002 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00491 (17379) covalent geometry : angle 0.89467 (23615) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.77029 ( 2) hydrogen bonds : bond 0.03342 ( 541) hydrogen bonds : angle 5.15359 ( 1515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.30 seconds wall clock time: 70 minutes 36.64 seconds (4236.64 seconds total)