Starting phenix.real_space_refine on Thu Jul 31 19:22:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ye4_33763/07_2025/7ye4_33763.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ye4_33763/07_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_33763/07_2025/7ye4_33763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ye4_33763/07_2025/7ye4_33763.map" model { file = "/net/cci-nas-00/data/ceres_data/7ye4_33763/07_2025/7ye4_33763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ye4_33763/07_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.89, per 1000 atoms: 0.57 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: 2.85 Conformation dependent library (CDL) restraints added in 1.7 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: 1.69 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: 4.92 Time building geometry restraints manager: 3.48 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: 0.790 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.020 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- 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 : 1.548 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: 0.2889 time to fit residues: 113.8214 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 : 1.478 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.171464 restraints weight = 14777.677| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.03 r_work: 0.3870 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.01873 ( 3) SS BOND : angle 2.82659 ( 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 : 1.516 Fit side-chains REVERT: A 224 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 646 MET cc_start: 0.7560 (tpt) cc_final: 0.6567 (tpt) REVERT: B 379 LEU cc_start: 0.8375 (mm) cc_final: 0.8169 (mp) REVERT: E 79 GLN cc_start: 0.8800 (pt0) cc_final: 0.8575 (mt0) REVERT: P 1154 GLU cc_start: 0.4555 (tm-30) cc_final: 0.4134 (tm-30) outliers start: 27 outliers final: 24 residues processed: 219 average time/residue: 0.2510 time to fit residues: 81.1710 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 : 1.357 ------------------------------------------------------------------------------- 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: 0.0870 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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 ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4547 r_free = 0.4547 target = 0.225454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.178106 restraints weight = 14858.728| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.08 r_work: 0.3857 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2674 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= 0.124 Angle : 0.514 8.423 19270 Z= 0.270 Chirality : 0.042 0.176 2100 Planarity : 0.004 0.042 2533 Dihedral : 3.964 30.732 1958 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.33 % Allowed : 16.74 % Favored : 80.93 % 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: -3.53 (0.18), residues: 1775 helix: -2.32 (0.25), residues: 291 sheet: -1.65 (0.23), residues: 505 loop : -2.80 (0.17), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 PHE 0.015 0.001 PHE A 440 TYR 0.015 0.001 TYR A 686 ARG 0.007 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 362) hydrogen bonds : angle 5.69050 ( 1119) SS BOND : bond 0.00837 ( 3) SS BOND : angle 2.68961 ( 6) covalent geometry : bond 0.00278 (14179) covalent geometry : angle 0.51163 (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 227 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.373 Fit side-chains REVERT: A 224 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 646 MET cc_start: 0.7674 (tpt) cc_final: 0.7249 (tpt) REVERT: B 226 MET cc_start: 0.6175 (tpt) cc_final: 0.5935 (mmp) REVERT: B 297 TYR cc_start: 0.8074 (m-80) cc_final: 0.7871 (m-80) REVERT: B 304 ARG cc_start: 0.7475 (mtm110) cc_final: 0.7128 (mtm110) REVERT: E 79 GLN cc_start: 0.8788 (pt0) cc_final: 0.8587 (mt0) REVERT: P 1154 GLU cc_start: 0.4720 (tm-30) cc_final: 0.4484 (tm-30) outliers start: 34 outliers final: 20 residues processed: 216 average time/residue: 0.2513 time to fit residues: 80.8371 Evaluate side-chains 197 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 163 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.0010 chunk 168 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.225655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.176537 restraints weight = 14792.409| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.14 r_work: 0.3866 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14182 Z= 0.109 Angle : 0.496 9.605 19270 Z= 0.259 Chirality : 0.042 0.172 2100 Planarity : 0.003 0.039 2533 Dihedral : 3.887 29.943 1958 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.81 % Allowed : 17.63 % Favored : 79.56 % 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: -3.14 (0.18), residues: 1775 helix: -1.63 (0.28), residues: 294 sheet: -1.53 (0.22), residues: 535 loop : -2.61 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 PHE 0.014 0.001 PHE A 440 TYR 0.015 0.001 TYR B 345 ARG 0.004 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 362) hydrogen bonds : angle 5.32053 ( 1119) SS BOND : bond 0.00712 ( 3) SS BOND : angle 3.05391 ( 6) covalent geometry : bond 0.00246 (14179) covalent geometry : angle 0.49281 (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 227 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.464 Fit side-chains REVERT: A 646 MET cc_start: 0.7738 (tpt) cc_final: 0.7235 (tpt) REVERT: A 716 LEU cc_start: 0.8828 (tt) cc_final: 0.8562 (mp) REVERT: B 304 ARG cc_start: 0.7445 (mtm110) cc_final: 0.7207 (mtm110) REVERT: E 79 GLN cc_start: 0.8760 (pt0) cc_final: 0.8538 (mt0) REVERT: P 1113 PHE cc_start: 0.3685 (OUTLIER) cc_final: 0.3181 (m-10) REVERT: P 1264 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.6345 (mt) outliers start: 41 outliers final: 29 residues processed: 213 average time/residue: 0.2712 time to fit residues: 86.1621 Evaluate side-chains 203 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 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 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 213 ASP Chi-restraints excluded: chain E residue 22 THR 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 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: 9.9990 chunk 123 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 34 GLN P1160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.217775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.170569 restraints weight = 15127.190| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.06 r_work: 0.3785 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14182 Z= 0.210 Angle : 0.603 11.127 19270 Z= 0.317 Chirality : 0.045 0.171 2100 Planarity : 0.004 0.060 2533 Dihedral : 4.548 32.022 1958 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 3.84 % Allowed : 18.24 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.10 (0.19), residues: 1775 helix: -1.52 (0.29), residues: 299 sheet: -1.54 (0.22), residues: 529 loop : -2.59 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 776 HIS 0.005 0.001 HIS P1062 PHE 0.028 0.002 PHE A 791 TYR 0.018 0.002 TYR B 345 ARG 0.005 0.001 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 362) hydrogen bonds : angle 5.49801 ( 1119) SS BOND : bond 0.01739 ( 3) SS BOND : angle 3.85720 ( 6) covalent geometry : bond 0.00480 (14179) covalent geometry : angle 0.59944 (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 249 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 1.594 Fit side-chains REVERT: A 285 GLU cc_start: 0.8113 (mp0) cc_final: 0.7892 (mp0) REVERT: A 545 MET cc_start: 0.8374 (ttm) cc_final: 0.8081 (ttm) REVERT: A 765 ASN cc_start: 0.7910 (p0) cc_final: 0.7560 (m-40) REVERT: A 802 PHE cc_start: 0.8835 (t80) cc_final: 0.8549 (t80) REVERT: B 280 LYS cc_start: 0.6243 (pptt) cc_final: 0.6010 (ptmm) REVERT: B 304 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7336 (mtm110) REVERT: B 379 LEU cc_start: 0.8545 (mm) cc_final: 0.8277 (mt) REVERT: P 1011 PHE cc_start: 0.5404 (m-80) cc_final: 0.5146 (m-10) REVERT: P 1072 GLU cc_start: 0.5168 (mm-30) cc_final: 0.2983 (tp30) REVERT: P 1113 PHE cc_start: 0.3858 (OUTLIER) cc_final: 0.3461 (m-10) REVERT: P 1264 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.6581 (mt) outliers start: 56 outliers final: 38 residues processed: 228 average time/residue: 0.2558 time to fit residues: 85.5393 Evaluate side-chains 208 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 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 160 THR 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 22 THR 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 1129 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 107 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN B 172 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.218321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.171266 restraints weight = 15211.984| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.18 r_work: 0.3773 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14182 Z= 0.169 Angle : 0.572 10.018 19270 Z= 0.299 Chirality : 0.044 0.170 2100 Planarity : 0.004 0.042 2533 Dihedral : 4.397 31.544 1958 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.91 % Allowed : 19.07 % Favored : 77.02 % 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: -2.94 (0.19), residues: 1775 helix: -1.28 (0.29), residues: 299 sheet: -1.39 (0.22), residues: 517 loop : -2.55 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 228 HIS 0.005 0.001 HIS P1062 PHE 0.033 0.002 PHE A 428 TYR 0.017 0.001 TYR B 345 ARG 0.006 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 362) hydrogen bonds : angle 5.28456 ( 1119) SS BOND : bond 0.01037 ( 3) SS BOND : angle 4.25790 ( 6) covalent geometry : bond 0.00386 (14179) covalent geometry : angle 0.56761 (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: 57 poor density : 173 time to evaluate : 1.383 Fit side-chains REVERT: A 765 ASN cc_start: 0.8007 (p0) cc_final: 0.7566 (m-40) REVERT: B 379 LEU cc_start: 0.8506 (mm) cc_final: 0.8272 (mt) REVERT: C 83 ARG cc_start: 0.7226 (ptm160) cc_final: 0.7008 (ptm-80) REVERT: D 111 MET cc_start: 0.8220 (mmm) cc_final: 0.7988 (mmm) REVERT: P 1011 PHE cc_start: 0.5451 (m-80) cc_final: 0.5246 (m-10) REVERT: P 1072 GLU cc_start: 0.5300 (mm-30) cc_final: 0.2984 (tp30) REVERT: P 1113 PHE cc_start: 0.4070 (OUTLIER) cc_final: 0.3674 (m-10) REVERT: P 1264 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.6638 (mt) outliers start: 57 outliers final: 38 residues processed: 215 average time/residue: 0.2248 time to fit residues: 73.3644 Evaluate side-chains 198 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 514 THR 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 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 1145 SER Chi-restraints excluded: chain P residue 1208 VAL Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 86 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 72 optimal weight: 0.0050 chunk 63 optimal weight: 0.0050 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 69 optimal weight: 0.0770 chunk 47 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN ** E 34 GLN ** 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 = 0.4529 r_free = 0.4529 target = 0.223871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.177835 restraints weight = 15000.554| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.17 r_work: 0.3847 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14182 Z= 0.091 Angle : 0.508 9.772 19270 Z= 0.263 Chirality : 0.042 0.197 2100 Planarity : 0.003 0.042 2533 Dihedral : 3.902 29.005 1958 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.33 % Allowed : 21.06 % Favored : 76.61 % 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: -2.60 (0.19), residues: 1775 helix: -0.77 (0.31), residues: 297 sheet: -1.20 (0.22), residues: 524 loop : -2.40 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.004 0.000 HIS P1062 PHE 0.017 0.001 PHE A 802 TYR 0.016 0.001 TYR A 585 ARG 0.005 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.02733 ( 362) hydrogen bonds : angle 4.85199 ( 1119) SS BOND : bond 0.00393 ( 3) SS BOND : angle 3.28261 ( 6) covalent geometry : bond 0.00201 (14179) covalent geometry : angle 0.50448 (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 214 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 467 THR cc_start: 0.8197 (m) cc_final: 0.7963 (m) REVERT: A 618 TYR cc_start: 0.9038 (m-80) cc_final: 0.8812 (m-80) REVERT: A 765 ASN cc_start: 0.7885 (p0) cc_final: 0.7429 (m-40) REVERT: B 379 LEU cc_start: 0.8379 (mm) cc_final: 0.8123 (mt) REVERT: D 111 MET cc_start: 0.8162 (mmm) cc_final: 0.7936 (mmm) REVERT: E 79 GLN cc_start: 0.8795 (pt0) cc_final: 0.8557 (mt0) REVERT: P 1011 PHE cc_start: 0.5385 (m-80) cc_final: 0.5180 (m-10) REVERT: P 1072 GLU cc_start: 0.5125 (mm-30) cc_final: 0.2841 (tp30) REVERT: P 1113 PHE cc_start: 0.3674 (OUTLIER) cc_final: 0.3428 (m-10) outliers start: 34 outliers final: 28 residues processed: 200 average time/residue: 0.2339 time to fit residues: 69.8551 Evaluate side-chains 200 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 397 THR 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 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 741 MET 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 213 ASP Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1113 PHE Chi-restraints excluded: chain P residue 1145 SER 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: 10.0000 chunk 147 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 47 optimal weight: 0.0020 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.0010 chunk 97 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.218137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.171429 restraints weight = 15046.012| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.11 r_work: 0.3785 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14182 Z= 0.175 Angle : 0.568 9.973 19270 Z= 0.295 Chirality : 0.044 0.152 2100 Planarity : 0.004 0.060 2533 Dihedral : 4.238 30.306 1958 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.16 % Allowed : 20.37 % Favored : 76.47 % 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: -2.66 (0.19), residues: 1775 helix: -0.86 (0.31), residues: 299 sheet: -1.27 (0.22), residues: 527 loop : -2.40 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 PHE 0.023 0.002 PHE A 802 TYR 0.017 0.001 TYR A 585 ARG 0.009 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 362) hydrogen bonds : angle 5.04520 ( 1119) SS BOND : bond 0.00612 ( 3) SS BOND : angle 3.82238 ( 6) covalent geometry : bond 0.00401 (14179) covalent geometry : angle 0.56449 (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 210 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 765 ASN cc_start: 0.8041 (p0) cc_final: 0.7575 (m-40) REVERT: B 215 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6793 (ttp-170) REVERT: B 379 LEU cc_start: 0.8528 (mm) cc_final: 0.8190 (mt) REVERT: D 75 LEU cc_start: 0.7862 (mt) cc_final: 0.7589 (mt) REVERT: D 111 MET cc_start: 0.8199 (mmm) cc_final: 0.7951 (mmm) REVERT: P 1072 GLU cc_start: 0.5160 (mm-30) cc_final: 0.2866 (tp30) REVERT: P 1113 PHE cc_start: 0.3773 (OUTLIER) cc_final: 0.3402 (m-10) REVERT: P 1154 GLU cc_start: 0.5902 (tm-30) cc_final: 0.5199 (tm-30) REVERT: P 1175 TYR cc_start: 0.5459 (t80) cc_final: 0.5158 (t80) outliers start: 46 outliers final: 35 residues processed: 194 average time/residue: 0.2345 time to fit residues: 69.0960 Evaluate side-chains 195 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL 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 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 215 ARG 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 E residue 26 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1113 PHE Chi-restraints excluded: chain P residue 1145 SER Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE 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: 4.9990 chunk 83 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.218110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.171765 restraints weight = 15067.595| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.11 r_work: 0.3785 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14182 Z= 0.150 Angle : 0.557 8.406 19270 Z= 0.289 Chirality : 0.043 0.148 2100 Planarity : 0.004 0.051 2533 Dihedral : 4.249 30.350 1958 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.22 % Allowed : 20.99 % Favored : 75.79 % 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: -2.64 (0.19), residues: 1775 helix: -0.82 (0.31), residues: 299 sheet: -1.31 (0.22), residues: 543 loop : -2.37 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 317 HIS 0.004 0.001 HIS P1062 PHE 0.019 0.001 PHE A 802 TYR 0.016 0.001 TYR A 585 ARG 0.012 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 362) hydrogen bonds : angle 4.98135 ( 1119) SS BOND : bond 0.00411 ( 3) SS BOND : angle 3.63417 ( 6) covalent geometry : bond 0.00342 (14179) covalent geometry : angle 0.55294 (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 211 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 1.516 Fit side-chains REVERT: A 765 ASN cc_start: 0.8025 (p0) cc_final: 0.7565 (m-40) REVERT: B 170 GLN cc_start: 0.8630 (mp10) cc_final: 0.8304 (mp10) REVERT: B 379 LEU cc_start: 0.8534 (mm) cc_final: 0.8220 (mt) REVERT: D 111 MET cc_start: 0.8205 (mmm) cc_final: 0.7955 (mmm) REVERT: P 1072 GLU cc_start: 0.5222 (mm-30) cc_final: 0.3034 (tp30) REVERT: P 1113 PHE cc_start: 0.3788 (OUTLIER) cc_final: 0.3461 (m-10) outliers start: 47 outliers final: 36 residues processed: 194 average time/residue: 0.2388 time to fit residues: 70.4297 Evaluate side-chains 192 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL 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 646 MET 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 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 D residue 237 ILE Chi-restraints excluded: chain E residue 26 VAL 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 1145 SER Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN B 230 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.212943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.165117 restraints weight = 15196.045| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.11 r_work: 0.3726 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14182 Z= 0.239 Angle : 0.666 11.015 19270 Z= 0.347 Chirality : 0.046 0.162 2100 Planarity : 0.004 0.059 2533 Dihedral : 4.880 32.255 1958 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 3.02 % Allowed : 21.67 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.91 (0.19), residues: 1775 helix: -0.98 (0.30), residues: 292 sheet: -1.46 (0.21), residues: 531 loop : -2.57 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 48 HIS 0.005 0.001 HIS E 83 PHE 0.026 0.002 PHE A 791 TYR 0.019 0.002 TYR B 345 ARG 0.013 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 362) hydrogen bonds : angle 5.38486 ( 1119) SS BOND : bond 0.00835 ( 3) SS BOND : angle 4.18805 ( 6) covalent geometry : bond 0.00548 (14179) covalent geometry : angle 0.66170 (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 210 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 1.432 Fit side-chains REVERT: A 765 ASN cc_start: 0.8048 (p0) cc_final: 0.7612 (m-40) REVERT: B 168 ASN cc_start: 0.8414 (m-40) cc_final: 0.8173 (m-40) REVERT: B 379 LEU cc_start: 0.8633 (mm) cc_final: 0.8395 (mt) REVERT: P 1072 GLU cc_start: 0.5309 (mm-30) cc_final: 0.3414 (tp30) outliers start: 44 outliers final: 35 residues processed: 195 average time/residue: 0.2742 time to fit residues: 81.6854 Evaluate side-chains 191 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 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 646 MET 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 185 VAL Chi-restraints excluded: chain B residue 209 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 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 205 TYR 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 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1145 SER Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 141 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** E 34 GLN ** 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 = 0.4491 r_free = 0.4491 target = 0.219696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.171854 restraints weight = 15055.797| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.21 r_work: 0.3800 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14182 Z= 0.106 Angle : 0.554 9.590 19270 Z= 0.288 Chirality : 0.043 0.170 2100 Planarity : 0.004 0.049 2533 Dihedral : 4.271 34.549 1958 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.92 % Allowed : 22.70 % Favored : 75.38 % 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: -2.64 (0.19), residues: 1775 helix: -0.69 (0.31), residues: 296 sheet: -1.22 (0.22), residues: 540 loop : -2.48 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 228 HIS 0.005 0.001 HIS P1062 PHE 0.024 0.001 PHE A 428 TYR 0.017 0.001 TYR D 154 ARG 0.014 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.02887 ( 362) hydrogen bonds : angle 4.90525 ( 1119) SS BOND : bond 0.00803 ( 3) SS BOND : angle 4.10776 ( 6) covalent geometry : bond 0.00238 (14179) covalent geometry : angle 0.54953 (19264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9636.44 seconds wall clock time: 167 minutes 31.22 seconds (10051.22 seconds total)