Starting phenix.real_space_refine on Fri May 16 00:04:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ye4_33763/05_2025/7ye4_33763.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ye4_33763/05_2025/7ye4_33763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ye4_33763/05_2025/7ye4_33763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ye4_33763/05_2025/7ye4_33763.map" model { file = "/net/cci-nas-00/data/ceres_data/7ye4_33763/05_2025/7ye4_33763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ye4_33763/05_2025/7ye4_33763.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8749 2.51 5 N 2363 2.21 5 O 2723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13877 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6211 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2713 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 377 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 7, 'TRANS': 46} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "P" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2142 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 278} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 7.59, per 1000 atoms: 0.55 Number of scatterers: 13877 At special positions: 0 Unit cell: (125.736, 133.848, 140.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2723 8.00 N 2363 7.00 C 8749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS P1293 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS P1043 " distance=2.03 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: 2.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 23 sheets defined 16.8% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.658A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 removed outlier: 4.607A pdb=" N ASN A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.614A pdb=" N VAL A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 4.026A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 195' Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.994A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 removed outlier: 3.584A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.859A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 542 through 552 removed outlier: 4.573A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.935A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 4.035A pdb=" N LEU B 322 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 323' Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.604A pdb=" N TYR D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 removed outlier: 4.212A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 49 through 54' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.615A pdb=" N LEU D 58 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 3.890A pdb=" N ILE D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.677A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 93 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.519A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 113 " --> pdb=" O MET D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.587A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 143 Processing helix chain 'D' and resid 144 through 154 removed outlier: 3.843A pdb=" N LYS D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.540A pdb=" N VAL D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.578A pdb=" N ARG D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 removed outlier: 4.076A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.531A pdb=" N TYR D 222 " --> pdb=" O MET D 218 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.620A pdb=" N GLU D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.558A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 1003 through 1012 removed outlier: 3.944A pdb=" N ALA P1009 " --> pdb=" O ARG P1005 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU P1010 " --> pdb=" O ASN P1006 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE P1011 " --> pdb=" O ALA P1007 " (cutoff:3.500A) Processing helix chain 'P' and resid 1013 through 1022 removed outlier: 3.878A pdb=" N LEU P1019 " --> pdb=" O TYR P1015 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL P1022 " --> pdb=" O PHE P1018 " (cutoff:3.500A) Processing helix chain 'P' and resid 1135 through 1139 removed outlier: 4.276A pdb=" N GLY P1138 " --> pdb=" O THR P1135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 99 removed outlier: 7.779A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 166 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 154 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 168 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS A 152 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 183 removed outlier: 4.453A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 183 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.856A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 337 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 336 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.574A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA6, first strand: chain 'A' and resid 440 through 446 removed outlier: 3.536A pdb=" N THR A 514 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 440 through 446 removed outlier: 3.536A pdb=" N THR A 514 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 785 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.563A pdb=" N VAL B 81 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.769A pdb=" N HIS B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 131 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.782A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 185 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB4, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 291 removed outlier: 3.968A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 297 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB7, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.692A pdb=" N ILE B 380 " --> pdb=" O TYR B 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.085A pdb=" N THR E 72 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AC1, first strand: chain 'P' and resid 1044 through 1047 removed outlier: 3.975A pdb=" N ARG P1044 " --> pdb=" O GLN P1064 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN P1064 " --> pdb=" O ARG P1044 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 1057 through 1058 Processing sheet with id=AC3, first strand: chain 'P' and resid 1081 through 1089 removed outlier: 4.087A pdb=" N GLY P1081 " --> pdb=" O TYR P1108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR P1108 " --> pdb=" O GLY P1081 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR P1132 " --> pdb=" O ARG P1142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 1081 through 1089 removed outlier: 4.087A pdb=" N GLY P1081 " --> pdb=" O TYR P1108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR P1108 " --> pdb=" O GLY P1081 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P1124 " --> pdb=" O TYR P1150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR P1146 " --> pdb=" O HIS P1128 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG P1205 " --> pdb=" O GLU P1172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR P1206 " --> pdb=" O TYR P1229 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY P1228 " --> pdb=" O LEU P1259 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG P1257 " --> pdb=" O GLN P1230 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET P1260 " --> pdb=" O LYS P1280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 1165 through 1167 removed outlier: 3.695A pdb=" N VAL P1221 " --> pdb=" O PHE P1214 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS P1220 " --> pdb=" O GLU P1267 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA P1266 " --> pdb=" O ARG P1273 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG P1273 " --> pdb=" O ALA P1266 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4632 1.35 - 1.46: 3431 1.46 - 1.58: 6038 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 14179 Sorted by residual: bond pdb=" C VAL A 155 " pdb=" N THR A 156 " ideal model delta sigma weight residual 1.331 1.387 -0.056 2.83e-02 1.25e+03 3.91e+00 bond pdb=" N THR B 315 " pdb=" CA THR B 315 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.94e+00 bond pdb=" N ASP A 562 " pdb=" CA ASP A 562 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.42e-02 4.96e+03 2.62e+00 bond pdb=" CA ASP A 562 " pdb=" CB ASP A 562 " ideal model delta sigma weight residual 1.527 1.551 -0.024 1.61e-02 3.86e+03 2.29e+00 bond pdb=" CA THR B 315 " pdb=" CB THR B 315 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.28e+00 ... (remaining 14174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 18961 2.29 - 4.58: 247 4.58 - 6.87: 40 6.87 - 9.15: 14 9.15 - 11.44: 2 Bond angle restraints: 19264 Sorted by residual: angle pdb=" N VAL D 192 " pdb=" CA VAL D 192 " pdb=" C VAL D 192 " ideal model delta sigma weight residual 112.96 107.40 5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" C GLN A 561 " pdb=" N ASP A 562 " pdb=" CA ASP A 562 " ideal model delta sigma weight residual 122.82 130.48 -7.66 1.42e+00 4.96e-01 2.91e+01 angle pdb=" C ALA B 374 " pdb=" N ASP B 375 " pdb=" CA ASP B 375 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C LYS A 728 " pdb=" N TYR A 729 " pdb=" CA TYR A 729 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" C ASN A 161 " pdb=" N ARG A 162 " pdb=" CA ARG A 162 " ideal model delta sigma weight residual 122.82 129.13 -6.31 1.42e+00 4.96e-01 1.98e+01 ... (remaining 19259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7560 17.94 - 35.87: 641 35.87 - 53.81: 105 53.81 - 71.74: 14 71.74 - 89.68: 14 Dihedral angle restraints: 8334 sinusoidal: 3199 harmonic: 5135 Sorted by residual: dihedral pdb=" CA TYR A 729 " pdb=" C TYR A 729 " pdb=" N ALA A 730 " pdb=" CA ALA A 730 " ideal model delta harmonic sigma weight residual 180.00 148.63 31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS P1293 " pdb=" CB CYS P1293 " ideal model delta sinusoidal sigma weight residual -86.00 -37.14 -48.86 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA GLU B 282 " pdb=" C GLU B 282 " pdb=" N LEU B 283 " pdb=" CA LEU B 283 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 8331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1617 0.049 - 0.097: 364 0.097 - 0.146: 101 0.146 - 0.194: 10 0.194 - 0.242: 8 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA ASP A 562 " pdb=" N ASP A 562 " pdb=" C ASP A 562 " pdb=" CB ASP A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA THR B 315 " pdb=" N THR B 315 " pdb=" C THR B 315 " pdb=" CB THR B 315 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR B 315 " pdb=" CA THR B 315 " pdb=" OG1 THR B 315 " pdb=" CG2 THR B 315 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2097 not shown) Planarity restraints: 2533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 370 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 371 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 158 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 159 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 720 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 721 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 721 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 721 " -0.032 5.00e-02 4.00e+02 ... (remaining 2530 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4757 2.86 - 3.37: 11217 3.37 - 3.88: 21840 3.88 - 4.39: 23743 4.39 - 4.90: 42244 Nonbonded interactions: 103801 Sorted by model distance: nonbonded pdb=" OH TYR A 608 " pdb=" OE1 GLU A 650 " model vdw 2.352 3.040 nonbonded pdb=" O SER P1012 " pdb=" OG SER P1012 " model vdw 2.356 3.040 nonbonded pdb=" OE2 GLU A 305 " pdb=" OG SER A 324 " model vdw 2.356 3.040 nonbonded pdb=" OG SER P1092 " pdb=" O PHE P1096 " model vdw 2.357 3.040 nonbonded pdb=" OH TYR D 110 " pdb=" OD2 ASP D 162 " model vdw 2.360 3.040 ... (remaining 103796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.810 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14182 Z= 0.145 Angle : 0.679 11.444 19270 Z= 0.372 Chirality : 0.047 0.242 2100 Planarity : 0.004 0.063 2533 Dihedral : 13.680 89.677 5065 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.07 % Allowed : 7.68 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.15), residues: 1775 helix: -5.11 (0.06), residues: 269 sheet: -2.49 (0.20), residues: 532 loop : -3.51 (0.15), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 776 HIS 0.002 0.000 HIS A 533 PHE 0.023 0.001 PHE A 440 TYR 0.016 0.001 TYR A 686 ARG 0.001 0.000 ARG A 767 Details of bonding type rmsd hydrogen bonds : bond 0.31079 ( 362) hydrogen bonds : angle 11.67091 ( 1119) SS BOND : bond 0.00615 ( 3) SS BOND : angle 3.30428 ( 6) covalent geometry : bond 0.00278 (14179) covalent geometry : angle 0.67662 (19264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 1.424 Fit side-chains REVERT: A 646 MET cc_start: 0.6353 (tpt) cc_final: 0.5578 (tpt) REVERT: B 146 LYS cc_start: 0.8146 (tptp) cc_final: 0.7906 (tptp) REVERT: B 192 LEU cc_start: 0.7650 (tp) cc_final: 0.7386 (tt) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.2865 time to fit residues: 113.0716 Evaluate side-chains 190 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 20.0000 chunk 134 optimal weight: 0.0070 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 523 ASN A 534 ASN A 677 HIS A 775 GLN A 789 GLN B 175 ASN B 302 ASN C 71 ASN D 40 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN D 228 ASN P1026 ASN P1170 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.226984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.171481 restraints weight = 14777.676| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.03 r_work: 0.3871 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14182 Z= 0.167 Angle : 0.571 8.032 19270 Z= 0.302 Chirality : 0.044 0.174 2100 Planarity : 0.004 0.050 2533 Dihedral : 4.189 29.793 1958 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.85 % Allowed : 14.06 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.17), residues: 1775 helix: -3.65 (0.18), residues: 284 sheet: -1.99 (0.21), residues: 528 loop : -3.16 (0.17), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 776 HIS 0.007 0.001 HIS E 83 PHE 0.021 0.002 PHE A 791 TYR 0.017 0.002 TYR A 296 ARG 0.006 0.001 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 362) hydrogen bonds : angle 6.35488 ( 1119) SS BOND : bond 0.01874 ( 3) SS BOND : angle 2.82664 ( 6) covalent geometry : bond 0.00369 (14179) covalent geometry : angle 0.56911 (19264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.354 Fit side-chains REVERT: A 224 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 646 MET cc_start: 0.7556 (tpt) cc_final: 0.6564 (tpt) REVERT: B 379 LEU cc_start: 0.8377 (mm) cc_final: 0.8170 (mp) REVERT: E 79 GLN cc_start: 0.8800 (pt0) cc_final: 0.8575 (mt0) REVERT: P 1154 GLU cc_start: 0.4566 (tm-30) cc_final: 0.4151 (tm-30) outliers start: 27 outliers final: 24 residues processed: 219 average time/residue: 0.2416 time to fit residues: 77.9905 Evaluate side-chains 201 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 121 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 259 ASN A 748 ASN D 69 GLN D 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.224680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.175385 restraints weight = 14772.860| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.13 r_work: 0.3858 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14182 Z= 0.130 Angle : 0.520 8.498 19270 Z= 0.273 Chirality : 0.042 0.177 2100 Planarity : 0.004 0.042 2533 Dihedral : 4.007 30.904 1958 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.33 % Allowed : 17.01 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.18), residues: 1775 helix: -2.35 (0.25), residues: 291 sheet: -1.67 (0.22), residues: 505 loop : -2.81 (0.17), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.005 0.001 HIS E 83 PHE 0.015 0.001 PHE A 791 TYR 0.015 0.001 TYR A 686 ARG 0.007 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 362) hydrogen bonds : angle 5.72484 ( 1119) SS BOND : bond 0.00656 ( 3) SS BOND : angle 2.59688 ( 6) covalent geometry : bond 0.00293 (14179) covalent geometry : angle 0.51793 (19264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.349 Fit side-chains REVERT: A 224 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 646 MET cc_start: 0.7741 (tpt) cc_final: 0.7291 (tpt) REVERT: B 226 MET cc_start: 0.6051 (tpt) cc_final: 0.5819 (mmp) REVERT: B 304 ARG cc_start: 0.7481 (mtm110) cc_final: 0.7138 (mtm110) REVERT: E 79 GLN cc_start: 0.8808 (pt0) cc_final: 0.8596 (mt0) REVERT: P 1154 GLU cc_start: 0.4822 (tm-30) cc_final: 0.4577 (tm-30) outliers start: 34 outliers final: 21 residues processed: 214 average time/residue: 0.2323 time to fit residues: 73.7247 Evaluate side-chains 195 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 161 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 chunk 138 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.227931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.179364 restraints weight = 14754.583| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.16 r_work: 0.3890 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14182 Z= 0.089 Angle : 0.480 9.805 19270 Z= 0.251 Chirality : 0.042 0.171 2100 Planarity : 0.003 0.039 2533 Dihedral : 3.774 29.335 1958 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.67 % Allowed : 17.90 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.18), residues: 1775 helix: -1.53 (0.29), residues: 292 sheet: -1.50 (0.22), residues: 534 loop : -2.60 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 PHE 0.013 0.001 PHE A 802 TYR 0.014 0.001 TYR B 345 ARG 0.005 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 362) hydrogen bonds : angle 5.22243 ( 1119) SS BOND : bond 0.00445 ( 3) SS BOND : angle 2.87426 ( 6) covalent geometry : bond 0.00198 (14179) covalent geometry : angle 0.47714 (19264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 1.450 Fit side-chains REVERT: A 646 MET cc_start: 0.7558 (tpt) cc_final: 0.7138 (tpt) REVERT: P 1113 PHE cc_start: 0.3555 (OUTLIER) cc_final: 0.3172 (m-10) REVERT: P 1120 ASP cc_start: 0.3056 (m-30) cc_final: 0.2840 (m-30) REVERT: P 1131 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5985 (mp0) REVERT: P 1264 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7022 (tp) outliers start: 39 outliers final: 23 residues processed: 212 average time/residue: 0.2372 time to fit residues: 74.5272 Evaluate side-chains 197 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1113 PHE Chi-restraints excluded: chain P residue 1131 GLU Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 25 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 0.0070 chunk 11 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.220437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.172921 restraints weight = 15032.806| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.07 r_work: 0.3809 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14182 Z= 0.167 Angle : 0.560 11.038 19270 Z= 0.292 Chirality : 0.044 0.176 2100 Planarity : 0.004 0.041 2533 Dihedral : 4.221 30.545 1958 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.36 % Allowed : 17.83 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.19), residues: 1775 helix: -1.29 (0.29), residues: 297 sheet: -1.40 (0.22), residues: 513 loop : -2.53 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.004 0.001 HIS P1062 PHE 0.022 0.002 PHE A 791 TYR 0.018 0.002 TYR B 345 ARG 0.006 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 362) hydrogen bonds : angle 5.28452 ( 1119) SS BOND : bond 0.01195 ( 3) SS BOND : angle 3.91943 ( 6) covalent geometry : bond 0.00382 (14179) covalent geometry : angle 0.55615 (19264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 1.652 Fit side-chains revert: symmetry clash REVERT: A 445 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7726 (tp40) REVERT: A 646 MET cc_start: 0.8091 (tpt) cc_final: 0.7529 (tpt) REVERT: A 765 ASN cc_start: 0.7895 (p0) cc_final: 0.7597 (m-40) REVERT: A 785 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7950 (p90) REVERT: A 802 PHE cc_start: 0.8805 (t80) cc_final: 0.8549 (t80) REVERT: B 304 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7311 (mtm110) REVERT: B 379 LEU cc_start: 0.8425 (mm) cc_final: 0.8137 (mt) REVERT: P 1011 PHE cc_start: 0.5302 (m-80) cc_final: 0.5062 (m-10) REVERT: P 1072 GLU cc_start: 0.5164 (mm-30) cc_final: 0.3055 (tp30) REVERT: P 1131 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: P 1264 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7255 (tp) outliers start: 49 outliers final: 35 residues processed: 217 average time/residue: 0.2447 time to fit residues: 78.7467 Evaluate side-chains 214 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1113 PHE Chi-restraints excluded: chain P residue 1131 GLU Chi-restraints excluded: chain P residue 1208 VAL Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 107 optimal weight: 0.0030 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN P1160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.220435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.173553 restraints weight = 14973.316| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.04 r_work: 0.3812 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14182 Z= 0.143 Angle : 0.535 9.980 19270 Z= 0.278 Chirality : 0.043 0.164 2100 Planarity : 0.004 0.040 2533 Dihedral : 4.149 30.378 1958 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.43 % Allowed : 19.34 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1775 helix: -1.05 (0.30), residues: 297 sheet: -1.30 (0.22), residues: 518 loop : -2.46 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 228 HIS 0.005 0.001 HIS P1062 PHE 0.036 0.002 PHE A 428 TYR 0.014 0.001 TYR A 686 ARG 0.004 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 362) hydrogen bonds : angle 5.09292 ( 1119) SS BOND : bond 0.00441 ( 3) SS BOND : angle 3.18657 ( 6) covalent geometry : bond 0.00328 (14179) covalent geometry : angle 0.53252 (19264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 1.325 Fit side-chains REVERT: A 765 ASN cc_start: 0.7977 (p0) cc_final: 0.7535 (m-40) REVERT: A 802 PHE cc_start: 0.8771 (t80) cc_final: 0.8455 (t80) REVERT: B 223 GLN cc_start: 0.6491 (pp30) cc_final: 0.6285 (pp30) REVERT: B 304 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7330 (mtm110) REVERT: B 379 LEU cc_start: 0.8463 (mm) cc_final: 0.8193 (mt) REVERT: C 83 ARG cc_start: 0.7231 (ptm160) cc_final: 0.7002 (ptm-80) REVERT: D 111 MET cc_start: 0.8185 (mmm) cc_final: 0.7962 (mmm) REVERT: P 1011 PHE cc_start: 0.5367 (m-80) cc_final: 0.5147 (m-10) REVERT: P 1072 GLU cc_start: 0.5263 (mm-30) cc_final: 0.2952 (tp30) REVERT: P 1113 PHE cc_start: 0.3850 (OUTLIER) cc_final: 0.3578 (m-10) REVERT: P 1131 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: P 1264 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.6502 (mt) outliers start: 50 outliers final: 36 residues processed: 212 average time/residue: 0.2381 time to fit residues: 75.8669 Evaluate side-chains 209 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1113 PHE Chi-restraints excluded: chain P residue 1131 GLU Chi-restraints excluded: chain P residue 1145 SER Chi-restraints excluded: chain P residue 1208 VAL Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 86 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 47 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** B 266 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 = 0.4544 r_free = 0.4544 target = 0.225591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.180579 restraints weight = 14894.881| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.07 r_work: 0.3871 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14182 Z= 0.088 Angle : 0.492 8.679 19270 Z= 0.254 Chirality : 0.042 0.160 2100 Planarity : 0.003 0.039 2533 Dihedral : 3.780 28.300 1958 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.74 % Allowed : 20.30 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.19), residues: 1775 helix: -0.62 (0.31), residues: 298 sheet: -1.22 (0.22), residues: 558 loop : -2.30 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.004 0.000 HIS P1062 PHE 0.019 0.001 PHE A 428 TYR 0.013 0.001 TYR C 41 ARG 0.004 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.02653 ( 362) hydrogen bonds : angle 4.71959 ( 1119) SS BOND : bond 0.00244 ( 3) SS BOND : angle 3.68499 ( 6) covalent geometry : bond 0.00195 (14179) covalent geometry : angle 0.48786 (19264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.398 Fit side-chains REVERT: A 467 THR cc_start: 0.8210 (m) cc_final: 0.7965 (m) REVERT: A 618 TYR cc_start: 0.8987 (m-80) cc_final: 0.8767 (m-80) REVERT: A 765 ASN cc_start: 0.7840 (p0) cc_final: 0.7426 (m-40) REVERT: B 379 LEU cc_start: 0.8372 (mm) cc_final: 0.8122 (mt) REVERT: D 111 MET cc_start: 0.8168 (mmm) cc_final: 0.7964 (mmm) REVERT: P 1072 GLU cc_start: 0.5063 (mm-30) cc_final: 0.2746 (tp30) REVERT: P 1131 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6402 (mp0) outliers start: 40 outliers final: 29 residues processed: 215 average time/residue: 0.2454 time to fit residues: 79.3013 Evaluate side-chains 208 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1131 GLU Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 2 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 0.0570 chunk 97 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.222703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.174400 restraints weight = 14803.667| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.17 r_work: 0.3829 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14182 Z= 0.111 Angle : 0.509 9.936 19270 Z= 0.263 Chirality : 0.042 0.153 2100 Planarity : 0.003 0.040 2533 Dihedral : 3.848 28.532 1958 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.81 % Allowed : 20.16 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1775 helix: -0.57 (0.31), residues: 296 sheet: -1.19 (0.22), residues: 558 loop : -2.27 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 228 HIS 0.004 0.001 HIS P1062 PHE 0.031 0.001 PHE P1113 TYR 0.013 0.001 TYR A 686 ARG 0.008 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.02785 ( 362) hydrogen bonds : angle 4.74064 ( 1119) SS BOND : bond 0.00445 ( 3) SS BOND : angle 3.70417 ( 6) covalent geometry : bond 0.00252 (14179) covalent geometry : angle 0.50468 (19264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.361 Fit side-chains REVERT: A 321 ARG cc_start: 0.7463 (ttm110) cc_final: 0.6872 (ttp80) REVERT: A 765 ASN cc_start: 0.7954 (p0) cc_final: 0.7482 (m-40) REVERT: B 379 LEU cc_start: 0.8413 (mm) cc_final: 0.8181 (mt) REVERT: D 111 MET cc_start: 0.8166 (mmm) cc_final: 0.7944 (mmm) REVERT: P 1131 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6279 (mp0) outliers start: 41 outliers final: 34 residues processed: 198 average time/residue: 0.2384 time to fit residues: 70.2424 Evaluate side-chains 200 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1129 ASP Chi-restraints excluded: chain P residue 1131 GLU Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.0010 chunk 83 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.221735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.173091 restraints weight = 14831.981| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.18 r_work: 0.3826 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14182 Z= 0.117 Angle : 0.518 10.424 19270 Z= 0.267 Chirality : 0.042 0.150 2100 Planarity : 0.003 0.061 2533 Dihedral : 3.889 28.785 1958 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.74 % Allowed : 20.37 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.20), residues: 1775 helix: -0.51 (0.31), residues: 296 sheet: -1.20 (0.21), residues: 559 loop : -2.25 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS P1062 PHE 0.018 0.001 PHE A 802 TYR 0.013 0.001 TYR A 686 ARG 0.011 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 362) hydrogen bonds : angle 4.72849 ( 1119) SS BOND : bond 0.00404 ( 3) SS BOND : angle 3.59966 ( 6) covalent geometry : bond 0.00266 (14179) covalent geometry : angle 0.51389 (19264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 765 ASN cc_start: 0.7975 (p0) cc_final: 0.7511 (m-40) REVERT: B 223 GLN cc_start: 0.6472 (pp30) cc_final: 0.6234 (pp30) REVERT: B 317 TRP cc_start: 0.7769 (p-90) cc_final: 0.7508 (p-90) REVERT: B 379 LEU cc_start: 0.8430 (mm) cc_final: 0.8194 (mt) REVERT: D 75 LEU cc_start: 0.7740 (mt) cc_final: 0.7507 (mt) REVERT: D 111 MET cc_start: 0.8189 (mmm) cc_final: 0.7936 (mmm) REVERT: P 1011 PHE cc_start: 0.6095 (m-10) cc_final: 0.5761 (m-80) REVERT: P 1072 GLU cc_start: 0.5073 (mm-30) cc_final: 0.2841 (tp30) REVERT: P 1131 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: P 1175 TYR cc_start: 0.5372 (t80) cc_final: 0.4992 (t80) outliers start: 40 outliers final: 35 residues processed: 196 average time/residue: 0.2504 time to fit residues: 73.4736 Evaluate side-chains 205 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1129 ASP Chi-restraints excluded: chain P residue 1131 GLU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 0.0570 chunk 115 optimal weight: 4.9990 chunk 70 optimal weight: 0.0670 chunk 26 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.222735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.176800 restraints weight = 14848.568| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.19 r_work: 0.3829 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14182 Z= 0.104 Angle : 0.513 11.631 19270 Z= 0.264 Chirality : 0.042 0.152 2100 Planarity : 0.003 0.053 2533 Dihedral : 3.828 28.008 1958 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.61 % Allowed : 20.99 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.20), residues: 1775 helix: -0.45 (0.31), residues: 296 sheet: -1.12 (0.22), residues: 559 loop : -2.24 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 PHE 0.019 0.001 PHE A 802 TYR 0.013 0.001 TYR A 686 ARG 0.013 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 362) hydrogen bonds : angle 4.64245 ( 1119) SS BOND : bond 0.00305 ( 3) SS BOND : angle 3.46637 ( 6) covalent geometry : bond 0.00237 (14179) covalent geometry : angle 0.50990 (19264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 ASN cc_start: 0.7907 (p0) cc_final: 0.7457 (m-40) REVERT: B 223 GLN cc_start: 0.6501 (pp30) cc_final: 0.6262 (pp30) REVERT: B 379 LEU cc_start: 0.8446 (mm) cc_final: 0.8204 (mt) REVERT: D 75 LEU cc_start: 0.7715 (mt) cc_final: 0.7493 (mt) REVERT: P 1011 PHE cc_start: 0.6112 (m-10) cc_final: 0.5782 (m-80) REVERT: P 1072 GLU cc_start: 0.5169 (mm-30) cc_final: 0.2752 (tp30) REVERT: P 1131 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: P 1175 TYR cc_start: 0.5369 (t80) cc_final: 0.4983 (t80) outliers start: 38 outliers final: 34 residues processed: 189 average time/residue: 0.2610 time to fit residues: 74.5509 Evaluate side-chains 202 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1129 ASP Chi-restraints excluded: chain P residue 1131 GLU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.0000 chunk 123 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.224165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.177651 restraints weight = 14841.302| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.18 r_work: 0.3855 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14182 Z= 0.092 Angle : 0.501 12.528 19270 Z= 0.257 Chirality : 0.042 0.150 2100 Planarity : 0.003 0.057 2533 Dihedral : 3.702 27.351 1958 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.54 % Allowed : 21.26 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.20), residues: 1775 helix: -0.29 (0.32), residues: 297 sheet: -1.02 (0.22), residues: 557 loop : -2.20 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 228 HIS 0.003 0.000 HIS P1062 PHE 0.021 0.001 PHE A 802 TYR 0.013 0.001 TYR A 618 ARG 0.014 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.02566 ( 362) hydrogen bonds : angle 4.51862 ( 1119) SS BOND : bond 0.00179 ( 3) SS BOND : angle 3.24994 ( 6) covalent geometry : bond 0.00208 (14179) covalent geometry : angle 0.49800 (19264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8651.37 seconds wall clock time: 149 minutes 53.62 seconds (8993.62 seconds total)