Starting phenix.real_space_refine on Wed Mar 4 12:53:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ye4_33763/03_2026/7ye4_33763.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ye4_33763/03_2026/7ye4_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ye4_33763/03_2026/7ye4_33763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ye4_33763/03_2026/7ye4_33763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ye4_33763/03_2026/7ye4_33763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ye4_33763/03_2026/7ye4_33763.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ARG%COO: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: 2.84, per 1000 atoms: 0.20 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: 0.96 Conformation dependent library (CDL) restraints added in 590.0 milliseconds 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: 0.62 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: 2.60 Time building geometry restraints manager: 1.36 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.140 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.001 0.000 ARG A 767 TYR 0.016 0.001 TYR A 686 PHE 0.023 0.001 PHE A 440 TRP 0.015 0.001 TRP A 776 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00278 (14179) covalent geometry : angle 0.67662 (19264) SS BOND : bond 0.00615 ( 3) SS BOND : angle 3.30428 ( 6) hydrogen bonds : bond 0.31079 ( 362) hydrogen bonds : angle 11.67091 ( 1119) *********************** 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 : 0.487 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: 0.1260 time to fit residues: 49.8969 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 34 GLN 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 = 0.4530 r_free = 0.4530 target = 0.223118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.176740 restraints weight = 14963.835| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.15 r_work: 0.3830 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14182 Z= 0.206 Angle : 0.617 7.898 19270 Z= 0.326 Chirality : 0.045 0.178 2100 Planarity : 0.005 0.051 2533 Dihedral : 4.448 30.887 1958 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.13 % Allowed : 15.02 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.17), residues: 1775 helix: -3.70 (0.17), residues: 287 sheet: -2.00 (0.21), residues: 531 loop : -3.17 (0.17), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 132 TYR 0.018 0.002 TYR A 465 PHE 0.026 0.002 PHE A 791 TRP 0.017 0.002 TRP A 776 HIS 0.009 0.002 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00464 (14179) covalent geometry : angle 0.61562 (19264) SS BOND : bond 0.01261 ( 3) SS BOND : angle 2.79116 ( 6) hydrogen bonds : bond 0.04448 ( 362) hydrogen bonds : angle 6.39094 ( 1119) *********************** 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 231 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.514 Fit side-chains REVERT: A 635 TRP cc_start: 0.7704 (t-100) cc_final: 0.7374 (t60) REVERT: A 646 MET cc_start: 0.7807 (tpt) cc_final: 0.6827 (tpt) REVERT: B 387 VAL cc_start: 0.7495 (m) cc_final: 0.7261 (t) REVERT: E 79 GLN cc_start: 0.8815 (pt0) cc_final: 0.8541 (mt0) REVERT: P 1154 GLU cc_start: 0.4791 (tm-30) cc_final: 0.4401 (tm-30) outliers start: 31 outliers final: 26 residues processed: 222 average time/residue: 0.1122 time to fit residues: 36.8598 Evaluate side-chains 197 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 302 THR 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 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 294 ASN 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 D residue 160 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 22 THR 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 120 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 156 optimal weight: 0.0050 chunk 76 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN B 230 GLN D 60 ASN D 69 GLN D 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.218663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.162776 restraints weight = 14999.853| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.06 r_work: 0.3778 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14182 Z= 0.196 Angle : 0.595 8.294 19270 Z= 0.313 Chirality : 0.044 0.175 2100 Planarity : 0.004 0.051 2533 Dihedral : 4.522 33.028 1958 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.16 % Allowed : 17.49 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.17), residues: 1775 helix: -2.66 (0.24), residues: 304 sheet: -1.79 (0.21), residues: 533 loop : -2.92 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 132 TYR 0.018 0.002 TYR B 345 PHE 0.024 0.002 PHE A 791 TRP 0.018 0.002 TRP B 317 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00446 (14179) covalent geometry : angle 0.59207 (19264) SS BOND : bond 0.01034 ( 3) SS BOND : angle 3.21156 ( 6) hydrogen bonds : bond 0.04264 ( 362) hydrogen bonds : angle 5.93038 ( 1119) *********************** 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 235 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.495 Fit side-chains REVERT: A 196 HIS cc_start: 0.7596 (m90) cc_final: 0.7377 (m90) REVERT: A 765 ASN cc_start: 0.7898 (p0) cc_final: 0.7562 (m-40) REVERT: B 170 GLN cc_start: 0.8663 (mp10) cc_final: 0.8437 (mp10) REVERT: B 304 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7225 (mtm110) REVERT: P 1072 GLU cc_start: 0.4269 (mm-30) cc_final: 0.1813 (tp30) REVERT: P 1264 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7252 (tp) outliers start: 46 outliers final: 29 residues processed: 224 average time/residue: 0.1153 time to fit residues: 38.1576 Evaluate side-chains 196 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 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 338 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 213 ASP 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 1129 ASP Chi-restraints excluded: chain P residue 1264 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 88 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.222908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.174550 restraints weight = 15020.360| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.29 r_work: 0.3819 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14182 Z= 0.106 Angle : 0.514 9.757 19270 Z= 0.268 Chirality : 0.042 0.170 2100 Planarity : 0.004 0.040 2533 Dihedral : 4.072 30.574 1958 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.67 % Allowed : 18.93 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.18), residues: 1775 helix: -1.77 (0.28), residues: 297 sheet: -1.40 (0.23), residues: 500 loop : -2.70 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 421 TYR 0.015 0.001 TYR B 345 PHE 0.018 0.001 PHE A 804 TRP 0.013 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00236 (14179) covalent geometry : angle 0.51014 (19264) SS BOND : bond 0.00599 ( 3) SS BOND : angle 3.41627 ( 6) hydrogen bonds : bond 0.03156 ( 362) hydrogen bonds : angle 5.34841 ( 1119) *********************** 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 216 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.510 Fit side-chains REVERT: A 196 HIS cc_start: 0.7565 (m90) cc_final: 0.7312 (m90) REVERT: B 304 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7110 (mtm110) REVERT: D 74 ASP cc_start: 0.7290 (t0) cc_final: 0.7069 (t0) REVERT: E 79 GLN cc_start: 0.8846 (pt0) cc_final: 0.8587 (mt0) REVERT: P 1011 PHE cc_start: 0.5965 (m-80) cc_final: 0.5690 (m-10) REVERT: P 1072 GLU cc_start: 0.3957 (mm-30) cc_final: 0.1459 (tp30) outliers start: 39 outliers final: 28 residues processed: 201 average time/residue: 0.1077 time to fit residues: 32.5055 Evaluate side-chains 197 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 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 310 ILE 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 B residue 379 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 85 optimal weight: 0.0270 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4516 r_free = 0.4516 target = 0.222051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.176144 restraints weight = 15035.486| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.11 r_work: 0.3835 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14182 Z= 0.112 Angle : 0.509 8.518 19270 Z= 0.265 Chirality : 0.042 0.160 2100 Planarity : 0.003 0.040 2533 Dihedral : 3.969 29.735 1958 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.70 % Allowed : 18.86 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.19), residues: 1775 helix: -1.29 (0.30), residues: 297 sheet: -1.31 (0.22), residues: 506 loop : -2.55 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 421 TYR 0.021 0.001 TYR A 585 PHE 0.033 0.001 PHE A 428 TRP 0.012 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00254 (14179) covalent geometry : angle 0.50608 (19264) SS BOND : bond 0.00302 ( 3) SS BOND : angle 2.96696 ( 6) hydrogen bonds : bond 0.03037 ( 362) hydrogen bonds : angle 5.12105 ( 1119) *********************** 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 234 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.411 Fit side-chains REVERT: A 716 LEU cc_start: 0.8829 (tt) cc_final: 0.8582 (mp) REVERT: A 765 ASN cc_start: 0.7933 (p0) cc_final: 0.7497 (m-40) REVERT: B 304 ARG cc_start: 0.7423 (mtm110) cc_final: 0.7203 (mtm110) REVERT: E 79 GLN cc_start: 0.8793 (pt0) cc_final: 0.8534 (mt0) REVERT: P 1011 PHE cc_start: 0.5833 (m-80) cc_final: 0.5605 (m-10) REVERT: P 1072 GLU cc_start: 0.4851 (mm-30) cc_final: 0.2898 (tp30) REVERT: P 1113 PHE cc_start: 0.3734 (OUTLIER) cc_final: 0.3349 (m-10) outliers start: 54 outliers final: 34 residues processed: 217 average time/residue: 0.1026 time to fit residues: 33.6038 Evaluate side-chains 206 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain 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 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 323 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1113 PHE Chi-restraints excluded: chain P residue 1129 ASP 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 151 optimal weight: 0.0770 chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN E 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.223190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.177703 restraints weight = 14884.211| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.11 r_work: 0.3843 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14182 Z= 0.100 Angle : 0.505 9.730 19270 Z= 0.261 Chirality : 0.042 0.157 2100 Planarity : 0.003 0.039 2533 Dihedral : 3.877 29.208 1958 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.50 % Allowed : 18.93 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.19), residues: 1775 helix: -0.91 (0.31), residues: 297 sheet: -1.27 (0.22), residues: 542 loop : -2.42 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.015 0.001 TYR A 585 PHE 0.022 0.001 PHE A 428 TRP 0.011 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00224 (14179) covalent geometry : angle 0.50060 (19264) SS BOND : bond 0.00441 ( 3) SS BOND : angle 3.62202 ( 6) hydrogen bonds : bond 0.02835 ( 362) hydrogen bonds : angle 4.95464 ( 1119) *********************** 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 226 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.478 Fit side-chains REVERT: A 307 ASP cc_start: 0.7899 (t70) cc_final: 0.7561 (t0) REVERT: A 765 ASN cc_start: 0.7906 (p0) cc_final: 0.7471 (m-40) REVERT: B 304 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7457 (mtm110) REVERT: E 79 GLN cc_start: 0.8775 (pt0) cc_final: 0.8544 (mt0) REVERT: P 1011 PHE cc_start: 0.5957 (m-80) cc_final: 0.5638 (m-10) REVERT: P 1072 GLU cc_start: 0.4603 (mm-30) cc_final: 0.2495 (tp30) REVERT: P 1113 PHE cc_start: 0.3679 (OUTLIER) cc_final: 0.3366 (m-10) outliers start: 51 outliers final: 42 residues processed: 208 average time/residue: 0.1103 time to fit residues: 34.4148 Evaluate side-chains 211 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 216 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 261 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 310 ILE 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 B residue 379 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1113 PHE Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 174 optimal weight: 6.9990 chunk 99 optimal weight: 0.0970 chunk 162 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.0030 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.8194 ------------------------------------------------------------------------------- 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 D 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.217772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.171557 restraints weight = 15123.018| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.16 r_work: 0.3775 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3948 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= 0.170 Angle : 0.570 9.336 19270 Z= 0.296 Chirality : 0.044 0.147 2100 Planarity : 0.004 0.039 2533 Dihedral : 4.283 30.409 1958 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.05 % Allowed : 19.20 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.19), residues: 1775 helix: -0.99 (0.30), residues: 299 sheet: -1.28 (0.22), residues: 517 loop : -2.42 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.019 0.001 TYR B 345 PHE 0.027 0.002 PHE A 428 TRP 0.012 0.001 TRP B 317 HIS 0.004 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00388 (14179) covalent geometry : angle 0.56619 (19264) SS BOND : bond 0.00761 ( 3) SS BOND : angle 3.80312 ( 6) hydrogen bonds : bond 0.03338 ( 362) hydrogen bonds : angle 5.15651 ( 1119) *********************** 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 237 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 646 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7181 (tpt) REVERT: A 765 ASN cc_start: 0.7979 (p0) cc_final: 0.7541 (m-40) REVERT: B 172 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: B 304 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7534 (mtm110) REVERT: D 75 LEU cc_start: 0.7822 (mt) cc_final: 0.7569 (mt) REVERT: D 225 MET cc_start: 0.7863 (mtt) cc_final: 0.7635 (mtt) REVERT: E 63 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8549 (mt) REVERT: P 1072 GLU cc_start: 0.5027 (mm-30) cc_final: 0.3015 (tp30) REVERT: P 1113 PHE cc_start: 0.3705 (OUTLIER) cc_final: 0.3355 (m-10) outliers start: 59 outliers final: 42 residues processed: 215 average time/residue: 0.1093 time to fit residues: 34.8880 Evaluate side-chains 211 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 567 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 67 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 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 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 B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU 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 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 1269 ARG Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.221624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.174828 restraints weight = 14971.535| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.23 r_work: 0.3821 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14182 Z= 0.101 Angle : 0.514 8.318 19270 Z= 0.265 Chirality : 0.042 0.150 2100 Planarity : 0.003 0.041 2533 Dihedral : 3.955 29.311 1958 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.02 % Allowed : 20.92 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.19), residues: 1775 helix: -0.69 (0.31), residues: 297 sheet: -1.18 (0.22), residues: 520 loop : -2.32 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.014 0.001 TYR B 345 PHE 0.018 0.001 PHE A 802 TRP 0.011 0.001 TRP B 228 HIS 0.004 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00226 (14179) covalent geometry : angle 0.51109 (19264) SS BOND : bond 0.00238 ( 3) SS BOND : angle 3.12055 ( 6) hydrogen bonds : bond 0.02840 ( 362) hydrogen bonds : angle 4.84746 ( 1119) *********************** 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 214 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.531 Fit side-chains REVERT: A 215 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7642 (mp10) REVERT: A 545 MET cc_start: 0.8415 (ttm) cc_final: 0.8013 (ttm) REVERT: A 646 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6824 (tpt) REVERT: A 765 ASN cc_start: 0.7938 (p0) cc_final: 0.7474 (m-40) REVERT: B 304 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7507 (mtm110) REVERT: D 75 LEU cc_start: 0.7739 (mt) cc_final: 0.7490 (mt) REVERT: D 111 MET cc_start: 0.8182 (mmm) cc_final: 0.7976 (mmm) REVERT: E 79 GLN cc_start: 0.8810 (pt0) cc_final: 0.8541 (mt0) REVERT: P 1072 GLU cc_start: 0.4877 (mm-30) cc_final: 0.2735 (tp30) REVERT: P 1113 PHE cc_start: 0.3819 (OUTLIER) cc_final: 0.3478 (m-10) REVERT: P 1154 GLU cc_start: 0.5547 (tm-30) cc_final: 0.5028 (tm-30) outliers start: 44 outliers final: 39 residues processed: 200 average time/residue: 0.1018 time to fit residues: 31.0964 Evaluate side-chains 208 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 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 524 SER Chi-restraints excluded: chain A residue 567 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 67 LEU Chi-restraints excluded: chain B residue 171 LEU 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 270 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 MET 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 B residue 379 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1019 LEU 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 1145 SER Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 124 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 67 optimal weight: 0.0030 chunk 6 optimal weight: 7.9990 chunk 117 optimal weight: 0.0970 chunk 158 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.220928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.174496 restraints weight = 14995.808| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.19 r_work: 0.3811 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14182 Z= 0.110 Angle : 0.525 10.423 19270 Z= 0.270 Chirality : 0.043 0.152 2100 Planarity : 0.003 0.040 2533 Dihedral : 3.947 28.874 1958 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.36 % Allowed : 20.64 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.19), residues: 1775 helix: -0.64 (0.31), residues: 298 sheet: -1.20 (0.21), residues: 557 loop : -2.30 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 83 TYR 0.015 0.001 TYR B 345 PHE 0.020 0.001 PHE A 802 TRP 0.011 0.001 TRP B 228 HIS 0.003 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00251 (14179) covalent geometry : angle 0.52052 (19264) SS BOND : bond 0.00538 ( 3) SS BOND : angle 4.05936 ( 6) hydrogen bonds : bond 0.02851 ( 362) hydrogen bonds : angle 4.77544 ( 1119) *********************** 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 213 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.319 Fit side-chains REVERT: A 215 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7634 (mp10) REVERT: A 383 ASP cc_start: 0.8250 (m-30) cc_final: 0.8037 (m-30) REVERT: A 545 MET cc_start: 0.8476 (ttm) cc_final: 0.8075 (ttm) REVERT: A 646 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6887 (tpt) REVERT: A 765 ASN cc_start: 0.7973 (p0) cc_final: 0.7523 (m-40) REVERT: B 304 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7469 (mtm110) REVERT: D 75 LEU cc_start: 0.7777 (mt) cc_final: 0.7511 (mt) REVERT: D 111 MET cc_start: 0.8199 (mmm) cc_final: 0.7983 (mmm) REVERT: E 79 GLN cc_start: 0.8794 (pt0) cc_final: 0.8541 (mt0) REVERT: P 1072 GLU cc_start: 0.5024 (mm-30) cc_final: 0.2866 (tp30) REVERT: P 1113 PHE cc_start: 0.3625 (OUTLIER) cc_final: 0.3212 (m-10) REVERT: P 1154 GLU cc_start: 0.5704 (tm-30) cc_final: 0.5386 (tm-30) REVERT: P 1175 TYR cc_start: 0.5287 (t80) cc_final: 0.5017 (t80) outliers start: 49 outliers final: 43 residues processed: 198 average time/residue: 0.1025 time to fit residues: 30.7143 Evaluate side-chains 207 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 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 524 SER Chi-restraints excluded: chain A residue 567 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 67 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 194 LEU 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 270 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 306 MET 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 B residue 379 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 58 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 128 optimal weight: 0.0050 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.223071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178531 restraints weight = 14893.529| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.12 r_work: 0.3850 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4052 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= 0.094 Angle : 0.507 8.490 19270 Z= 0.261 Chirality : 0.042 0.153 2100 Planarity : 0.003 0.041 2533 Dihedral : 3.812 28.298 1958 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.88 % Allowed : 21.12 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.20), residues: 1775 helix: -0.34 (0.32), residues: 289 sheet: -1.11 (0.22), residues: 556 loop : -2.26 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.014 0.001 TYR B 345 PHE 0.019 0.001 PHE A 802 TRP 0.010 0.001 TRP B 279 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00212 (14179) covalent geometry : angle 0.50324 (19264) SS BOND : bond 0.00506 ( 3) SS BOND : angle 3.67481 ( 6) hydrogen bonds : bond 0.02684 ( 362) hydrogen bonds : angle 4.63019 ( 1119) ********************** 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: 42 poor density : 168 time to evaluate : 0.472 Fit side-chains REVERT: A 215 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7634 (mp10) REVERT: A 224 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 545 MET cc_start: 0.8379 (ttm) cc_final: 0.8011 (ttm) REVERT: A 646 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.6864 (tpt) REVERT: A 765 ASN cc_start: 0.7909 (p0) cc_final: 0.7473 (m-40) REVERT: B 304 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7451 (mtm110) REVERT: D 75 LEU cc_start: 0.7760 (mt) cc_final: 0.7510 (mt) REVERT: E 79 GLN cc_start: 0.8794 (pt0) cc_final: 0.8578 (mt0) REVERT: P 1019 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6016 (mt) REVERT: P 1072 GLU cc_start: 0.5127 (mm-30) cc_final: 0.2859 (tp30) REVERT: P 1113 PHE cc_start: 0.3762 (OUTLIER) cc_final: 0.3347 (m-10) REVERT: P 1154 GLU cc_start: 0.5884 (tm-30) cc_final: 0.5670 (tm-30) REVERT: P 1175 TYR cc_start: 0.5272 (t80) cc_final: 0.4976 (t80) outliers start: 42 outliers final: 39 residues processed: 197 average time/residue: 0.1043 time to fit residues: 31.1584 Evaluate side-chains 207 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 567 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 67 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 194 LEU 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 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 B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU 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 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 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 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 159 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 1 optimal weight: 0.0020 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.218674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.169227 restraints weight = 14958.012| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.13 r_work: 0.3789 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4231 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= 0.151 Angle : 0.556 10.067 19270 Z= 0.286 Chirality : 0.043 0.148 2100 Planarity : 0.003 0.045 2533 Dihedral : 4.096 28.745 1958 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.22 % Allowed : 20.85 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.19), residues: 1775 helix: -0.57 (0.31), residues: 293 sheet: -1.16 (0.21), residues: 557 loop : -2.32 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.017 0.001 TYR B 345 PHE 0.020 0.001 PHE A 802 TRP 0.011 0.001 TRP B 228 HIS 0.004 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00346 (14179) covalent geometry : angle 0.55158 (19264) SS BOND : bond 0.00608 ( 3) SS BOND : angle 4.06603 ( 6) hydrogen bonds : bond 0.03089 ( 362) hydrogen bonds : angle 4.82769 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.77 seconds wall clock time: 72 minutes 10.87 seconds (4330.87 seconds total)