Starting phenix.real_space_refine on Sat Feb 17 18:03:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2x_26321/02_2024/7u2x_26321_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2x_26321/02_2024/7u2x_26321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2x_26321/02_2024/7u2x_26321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2x_26321/02_2024/7u2x_26321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2x_26321/02_2024/7u2x_26321_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2x_26321/02_2024/7u2x_26321_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 76 5.16 5 C 12633 2.51 5 N 3345 2.21 5 O 3409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19480 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2381 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 221 Chain: "E" Number of atoms: 9709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 9709 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PTRANS': 48, 'TRANS': 1378} Chain breaks: 6 Unresolved non-hydrogen bonds: 1596 Unresolved non-hydrogen angles: 1992 Unresolved non-hydrogen dihedrals: 1277 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'GLN:plan1': 28, 'ASP:plan': 40, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 21, 'GLU:plan': 46, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 807 Chain: "B" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2277 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 185 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2282 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 182 Chain: "D" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2296 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 178 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 132 Unusual residues: {'POV': 1, 'PTY': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 231 Unusual residues: {'ATP': 1, 'NAG': 1, 'POV': 1, 'PTY': 3} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 11.03, per 1000 atoms: 0.57 Number of scatterers: 19480 At special positions: 0 Unit cell: (165.87, 109.44, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 17 15.00 O 3409 8.00 N 3345 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 8.15 Conformation dependent library (CDL) restraints added in 3.9 seconds 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 21 sheets defined 48.2% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 176 removed outlier: 4.222A pdb=" N HIS A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 removed outlier: 3.847A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'E' and resid 9 through 11 No H-bonds generated for 'chain 'E' and resid 9 through 11' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 25 through 48 removed outlier: 3.747A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 72 through 96 Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 129 Processing helix chain 'E' and resid 133 through 159 removed outlier: 5.201A pdb=" N ILE E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 149 " --> pdb=" O ALA E 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS E 156 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.702A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 185 " --> pdb=" O MET E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.514A pdb=" N LYS E 238 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 259 through 275 Processing helix chain 'E' and resid 284 through 327 removed outlier: 6.118A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 348 through 351 No H-bonds generated for 'chain 'E' and resid 348 through 351' Processing helix chain 'E' and resid 355 through 400 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 414 through 456 Proline residue: E 436 - end of helix Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 459 through 504 removed outlier: 3.509A pdb=" N ALA E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Proline residue: E 472 - end of helix Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 515 through 564 removed outlier: 3.953A pdb=" N SER E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 573 through 615 removed outlier: 3.723A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 4.786A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 727 removed outlier: 3.858A pdb=" N LEU E 723 " --> pdb=" O LYS E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 805 Processing helix chain 'E' and resid 809 through 814 Processing helix chain 'E' and resid 832 through 846 Processing helix chain 'E' and resid 864 through 879 removed outlier: 3.698A pdb=" N GLU E 875 " --> pdb=" O GLY E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 917 through 919 No H-bonds generated for 'chain 'E' and resid 917 through 919' Processing helix chain 'E' and resid 921 through 930 Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 997 through 1008 removed outlier: 3.739A pdb=" N THR E1002 " --> pdb=" O TRP E 998 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS E1003 " --> pdb=" O ARG E 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1042 Processing helix chain 'E' and resid 1065 through 1107 removed outlier: 3.591A pdb=" N ARG E1099 " --> pdb=" O LYS E1095 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E1100 " --> pdb=" O ARG E1096 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E1107 " --> pdb=" O ASN E1103 " (cutoff:3.500A) Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1134 removed outlier: 4.653A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 removed outlier: 4.119A pdb=" N ILE E1157 " --> pdb=" O ALA E1153 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1209 removed outlier: 4.195A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.981A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1211 through 1216 Processing helix chain 'E' and resid 1220 through 1272 removed outlier: 3.645A pdb=" N ALA E1237 " --> pdb=" O SER E1233 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1320 removed outlier: 3.625A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY E1310 " --> pdb=" O GLU E1306 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E1318 " --> pdb=" O ARG E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1387 through 1393 removed outlier: 4.965A pdb=" N PHE E1393 " --> pdb=" O SER E1389 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1421 removed outlier: 4.488A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1449 through 1458 Processing helix chain 'E' and resid 1461 through 1466 Processing helix chain 'E' and resid 1477 through 1479 No H-bonds generated for 'chain 'E' and resid 1477 through 1479' Processing helix chain 'E' and resid 1485 through 1498 Processing helix chain 'E' and resid 1513 through 1529 removed outlier: 3.906A pdb=" N ASN E1518 " --> pdb=" O MET E1514 " (cutoff:3.500A) Processing helix chain 'E' and resid 1540 through 1544 Processing helix chain 'E' and resid 1563 through 1565 No H-bonds generated for 'chain 'E' and resid 1563 through 1565' Processing helix chain 'E' and resid 1573 through 1577 Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 176 removed outlier: 4.132A pdb=" N ARG B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 175 removed outlier: 3.827A pdb=" N HIS C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.082A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 176 removed outlier: 4.200A pdb=" N HIS D 175 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 removed outlier: 4.257A pdb=" N ASP D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 269' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 355 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.202A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.297A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= F, first strand: chain 'E' and resid 679 through 681 Processing sheet with id= G, first strand: chain 'E' and resid 850 through 854 removed outlier: 5.904A pdb=" N THR E 883 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU E 853 " --> pdb=" O THR E 883 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL E 885 " --> pdb=" O LEU E 853 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 1345 through 1347 Processing sheet with id= I, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.073A pdb=" N THR E 687 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS E 732 " --> pdb=" O THR E 687 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.511A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.260A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 289 through 291 removed outlier: 3.837A pdb=" N ILE B 296 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.949A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.511A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 214 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= R, first strand: chain 'D' and resid 188 through 192 Processing sheet with id= S, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.213A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= U, first strand: chain 'D' and resid 319 through 321 1058 hydrogen bonds defined for protein. 2958 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: 7.20 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3170 1.32 - 1.44: 5196 1.44 - 1.57: 11369 1.57 - 1.69: 33 1.69 - 1.81: 116 Bond restraints: 19884 Sorted by residual: bond pdb=" C VAL C 252 " pdb=" N ALA C 253 " ideal model delta sigma weight residual 1.333 1.260 0.073 2.74e-02 1.33e+03 7.06e+00 bond pdb=" C LEU E 894 " pdb=" N PRO E 895 " ideal model delta sigma weight residual 1.331 1.346 -0.014 7.90e-03 1.60e+04 3.15e+00 bond pdb=" C GLY B 289 " pdb=" N VAL B 290 " ideal model delta sigma weight residual 1.334 1.312 0.022 1.29e-02 6.01e+03 2.80e+00 bond pdb=" CA GLY E 818 " pdb=" C GLY E 818 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.58e+00 bond pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.46e+00 ... (remaining 19879 not shown) Histogram of bond angle deviations from ideal: 92.08 - 101.56: 53 101.56 - 111.05: 8779 111.05 - 120.53: 10966 120.53 - 130.01: 7279 130.01 - 139.49: 157 Bond angle restraints: 27234 Sorted by residual: angle pdb=" N GLY E 818 " pdb=" CA GLY E 818 " pdb=" C GLY E 818 " ideal model delta sigma weight residual 111.67 115.31 -3.64 9.20e-01 1.18e+00 1.56e+01 angle pdb=" N ILE E1475 " pdb=" CA ILE E1475 " pdb=" C ILE E1475 " ideal model delta sigma weight residual 106.21 110.10 -3.89 1.07e+00 8.73e-01 1.32e+01 angle pdb=" C ILE E 550 " pdb=" CA ILE E 550 " pdb=" CB ILE E 550 " ideal model delta sigma weight residual 114.35 110.94 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" N VAL B 244 " pdb=" CA VAL B 244 " pdb=" C VAL B 244 " ideal model delta sigma weight residual 112.98 108.96 4.02 1.25e+00 6.40e-01 1.03e+01 angle pdb=" C LEU E 174 " pdb=" N LEU E 175 " pdb=" CA LEU E 175 " ideal model delta sigma weight residual 121.58 115.73 5.85 1.95e+00 2.63e-01 9.01e+00 ... (remaining 27229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.17: 11130 24.17 - 48.33: 442 48.33 - 72.50: 58 72.50 - 96.66: 12 96.66 - 120.83: 4 Dihedral angle restraints: 11646 sinusoidal: 3664 harmonic: 7982 Sorted by residual: dihedral pdb=" C3 PTY E1602 " pdb=" O11 PTY E1602 " pdb=" P1 PTY E1602 " pdb=" O12 PTY E1602 " ideal model delta sinusoidal sigma weight residual -59.77 61.06 -120.83 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA GLY E 706 " pdb=" C GLY E 706 " pdb=" N GLN E 707 " pdb=" CA GLN E 707 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C31 P5S E1604 " pdb=" C32 P5S E1604 " pdb=" C33 P5S E1604 " pdb=" C34 P5S E1604 " ideal model delta sinusoidal sigma weight residual 179.95 65.56 114.39 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 11643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2236 0.039 - 0.078: 788 0.078 - 0.116: 270 0.116 - 0.155: 45 0.155 - 0.194: 3 Chirality restraints: 3342 Sorted by residual: chirality pdb=" CG LEU E1227 " pdb=" CB LEU E1227 " pdb=" CD1 LEU E1227 " pdb=" CD2 LEU E1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA VAL A 339 " pdb=" N VAL A 339 " pdb=" C VAL A 339 " pdb=" CB VAL A 339 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 3339 not shown) Planarity restraints: 3400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 44 " -0.047 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO E 45 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 339 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO A 340 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 316 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO E 317 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 317 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 317 " -0.036 5.00e-02 4.00e+02 ... (remaining 3397 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 284 2.67 - 3.23: 19706 3.23 - 3.79: 29796 3.79 - 4.34: 35084 4.34 - 4.90: 59273 Nonbonded interactions: 144143 Sorted by model distance: nonbonded pdb=" O SER C 116 " pdb=" OG SER C 119 " model vdw 2.118 2.440 nonbonded pdb=" OG SER E1423 " pdb=" O ILE E1502 " model vdw 2.174 2.440 nonbonded pdb=" O SER A 116 " pdb=" OG SER A 119 " model vdw 2.180 2.440 nonbonded pdb=" OD1 ASP A 329 " pdb=" OG SER A 331 " model vdw 2.210 2.440 nonbonded pdb=" O ILE E1512 " pdb=" N THR E1516 " model vdw 2.222 2.520 ... (remaining 144138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 or (resid 43 through 45 and ( \ name N or name CA or name C or name O or name CB )) or resid 46 through 48 or (r \ esid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thr \ ough 53 or (resid 54 through 59 and (name N or name CA or name C or name O or na \ me CB )) or resid 60 through 63 or (resid 64 through 67 and (name N or name CA o \ r name C or name O or name CB )) or resid 68 through 72 or (resid 73 through 74 \ and (name N or name CA or name C or name O or name CB )) or resid 75 through 80 \ or (resid 81 through 82 and (name N or name CA or name C or name O or name CB )) \ or resid 83 through 91 or (resid 92 through 94 and (name N or name CA or name C \ or name O or name CB )) or resid 95 through 117 or (resid 118 and (name N or na \ me CA or name C or name O or name CB )) or resid 119 through 147 or (resid 148 a \ nd (name N or name CA or name C or name O or name CB )) or resid 149 through 151 \ or (resid 152 and (name N or name CA or name C or name O or name CB )) or resid \ 153 through 179 or (resid 180 and (name N or name CA or name C or name O or nam \ e CB )) or resid 181 through 187 or (resid 188 through 189 and (name N or name C \ A or name C or name O or name CB )) or resid 190 through 192 or (resid 193 and ( \ name N or name CA or name C or name O or name CB )) or resid 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 204 \ or (resid 205 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 209 or (resid 210 through 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 221 or (resid 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 through 237 or (res \ id 238 and (name N or name CA or name C or name O or name CB )) or resid 239 thr \ ough 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ or resid 256 through 272 or (resid 273 through 276 and (name N or name CA or nam \ e C or name O or name CB )) or resid 277 or (resid 278 through 282 and (name N o \ r name CA or name C or name O or name CB )) or resid 283 through 309 or (resid 3 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 311 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 through 326 or (resid 327 through 330 and (name N or name CA or name C \ or name O or name CB )) or resid 331 through 344 or (resid 345 through 356 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 43 or (resid 44 throug \ h 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throug \ h 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name \ CB )) or resid 50 through 54 or (resid 55 through 59 and (name N or name CA or n \ ame C or name O or name CB )) or resid 60 through 63 or (resid 64 through 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 70 or \ (resid 71 and (name N or name CA or name C or name O or name CB )) or resid 72 t \ hrough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 80 or (resid 81 through 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 91 or (resid 92 through 94 and (name \ N or name CA or name C or name O or name CB )) or resid 95 through 99 or (resid \ 100 through 101 and (name N or name CA or name C or name O or name CB )) or res \ id 102 through 147 or (resid 148 and (name N or name CA or name C or name O or n \ ame CB )) or resid 149 through 153 or (resid 154 and (name N or name CA or name \ C or name O or name CB )) or resid 155 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 187 or (resid 188 \ through 189 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 90 through 191 or (resid 192 through 193 and (name N or name CA or name C or nam \ e O or name CB )) or resid 194 or (resid 195 and (name N or name CA or name C or \ name O or name CB )) or resid 196 through 205 or (resid 206 through 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 209 or (r \ esid 210 through 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 220 or (resid 221 through 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 250 or (resid 251 and (name N or \ name CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 \ and (name N or name CA or name C or name O or name CB )) or resid 260 through 2 \ 64 or (resid 265 and (name N or name CA or name C or name O or name CB )) or res \ id 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) or \ resid 268 or (resid 269 through 271 and (name N or name CA or name C or name O \ or name CB )) or resid 272 through 277 or (resid 278 through 282 and (name N or \ name CA or name C or name O or name CB )) or resid 283 through 292 or (resid 293 \ and (name N or name CA or name C or name O or name CB )) or resid 294 through 3 \ 17 or (resid 318 and (name N or name CA or name C or name O or name CB )) or res \ id 319 through 327 or (resid 328 through 330 and (name N or name CA or name C or \ name O or name CB )) or resid 331 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB )) or resid 339 through 340 or (resid 341 and \ (name N or name CA or name C or name O or name CB )) or resid 342 or (resid 343 \ through 356 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 31 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 43 or (resid 44 throu \ gh 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throu \ gh 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name \ CB )) or resid 50 through 63 or (resid 64 through 67 and (name N or name CA or \ name C or name O or name CB )) or resid 68 through 70 or (resid 71 and (name N o \ r name CA or name C or name O or name CB )) or resid 72 or (resid 73 through 74 \ and (name N or name CA or name C or name O or name CB )) or resid 75 through 76 \ or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 8 through 80 or (resid 81 through 82 and (name N or name CA or name C or name O \ or name CB )) or resid 83 through 99 or (resid 100 through 101 and (name N or na \ me CA or name C or name O or name CB )) or resid 102 through 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 188 \ or (resid 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 191 or (resid 192 through 193 and (name N or name CA or name C or n \ ame O or name CB )) or resid 194 or (resid 195 and (name N or name CA or name C \ or name O or name CB )) or resid 196 through 205 or (resid 206 through 207 and ( \ name N or name CA or name C or name O or name CB )) or resid 208 through 209 or \ (resid 210 through 211 and (name N or name CA or name C or name O or name CB )) \ or resid 212 through 220 or (resid 221 through 222 and (name N or name CA or nam \ e C or name O or name CB )) or resid 223 through 237 or (resid 238 and (name N o \ r name CA or name C or name O or name CB )) or resid 239 through 250 or (resid 2 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 252 through \ 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) or r \ esid 256 through 262 or (resid 263 and (name N or name CA or name C or name O or \ name CB )) or resid 264 or (resid 265 and (name N or name CA or name C or name \ O or name CB )) or resid 266 or (resid 267 and (name N or name CA or name C or n \ ame O or name CB )) or resid 268 through 272 or (resid 273 through 276 and (name \ N or name CA or name C or name O or name CB )) or resid 277 or (resid 278 throu \ gh 282 and (name N or name CA or name C or name O or name CB )) or resid 283 thr \ ough 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) \ or resid 294 through 317 or (resid 318 and (name N or name CA or name C or name \ O or name CB )) or resid 319 through 327 or (resid 328 through 330 and (name N o \ r name CA or name C or name O or name CB )) or resid 331 through 337 or (resid 3 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 339 through \ 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) or r \ esid 342 through 343 or (resid 344 through 356 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'D' and (resid 31 through 36 or (resid 37 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 or (resid 43 through 45 and ( \ name N or name CA or name C or name O or name CB )) or resid 46 through 55 or (r \ esid 56 through 59 and (name N or name CA or name C or name O or name CB )) or r \ esid 60 through 76 or (resid 77 and (name N or name CA or name C or name O or na \ me CB )) or resid 78 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 91 or (resid 92 through 94 and (name N \ or name CA or name C or name O or name CB )) or resid 95 through 99 or (resid 1 \ 00 through 101 and (name N or name CA or name C or name O or name CB )) or resid \ 102 through 139 or (resid 140 through 141 and (name N or name CA or name C or n \ ame O or name CB )) or resid 142 through 147 or (resid 148 and (name N or name C \ A or name C or name O or name CB )) or resid 149 through 151 or (resid 152 and ( \ name N or name CA or name C or name O or name CB )) or resid 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 179 \ or (resid 180 and (name N or name CA or name C or name O or name CB )) or resid \ 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) or r \ esid 183 through 188 or (resid 189 and (name N or name CA or name C or name O or \ name CB )) or resid 190 through 192 or (resid 193 and (name N or name CA or nam \ e C or name O or name CB )) or resid 194 through 198 or (resid 199 through 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 through 204 \ or (resid 205 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 210 or (resid 211 and (name N or name CA or name C or n \ ame O or name CB )) or resid 212 through 220 or (resid 221 through 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 through 237 or (res \ id 238 and (name N or name CA or name C or name O or name CB )) or resid 239 thr \ ough 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 254 or (resid 255 and (name N or name CA or name C or name \ O or name CB )) or resid 256 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 through 264 or (resid 265 and (name \ N or name CA or name C or name O or name CB )) or resid 266 or (resid 267 and ( \ name N or name CA or name C or name O or name CB )) or resid 268 through 269 or \ (resid 270 through 271 and (name N or name CA or name C or name O or name CB )) \ or resid 272 or (resid 273 through 276 and (name N or name CA or name C or name \ O or name CB )) or resid 277 through 280 or (resid 281 through 282 and (name N o \ r name CA or name C or name O or name CB )) or resid 283 through 287 or (resid 2 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 289 through \ 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or r \ esid 294 through 295 or (resid 296 and (name N or name CA or name C or name O or \ name CB )) or resid 297 through 324 or (resid 325 and (name N or name CA or nam \ e C or name O or name CB )) or resid 326 or (resid 327 through 330 and (name N o \ r name CA or name C or name O or name CB )) or resid 331 or (resid 332 and (name \ N or name CA or name C or name O or name CB )) or resid 333 through 337 or (res \ id 338 and (name N or name CA or name C or name O or name CB )) or resid 339 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 or (resid 343 through 356 and (name N or name CA or name C or name \ O or name CB )))) } 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 group one per residue 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.280 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 54.660 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.005 0.073 19884 Z= 0.335 Angle : 0.645 8.701 27234 Z= 0.359 Chirality : 0.044 0.194 3342 Planarity : 0.005 0.072 3400 Dihedral : 13.558 120.826 6443 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.81 % Allowed : 9.64 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2729 helix: 1.48 (0.14), residues: 1317 sheet: -1.51 (0.31), residues: 263 loop : -1.71 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 91 HIS 0.006 0.001 HIS C 186 PHE 0.018 0.002 PHE E1164 TYR 0.019 0.002 TYR E1254 ARG 0.005 0.001 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 933 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9145 (m-10) cc_final: 0.8635 (m-10) REVERT: A 90 TRP cc_start: 0.9003 (m100) cc_final: 0.6381 (m100) REVERT: A 91 TRP cc_start: 0.9176 (t60) cc_final: 0.8848 (t60) REVERT: A 210 ILE cc_start: 0.8977 (mt) cc_final: 0.8770 (mt) REVERT: A 260 VAL cc_start: 0.8901 (t) cc_final: 0.8423 (p) REVERT: A 299 GLN cc_start: 0.9058 (mt0) cc_final: 0.8837 (tt0) REVERT: A 301 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8154 (mtm-85) REVERT: A 305 LEU cc_start: 0.9111 (mp) cc_final: 0.8907 (mp) REVERT: E 6 CYS cc_start: 0.4872 (m) cc_final: 0.4315 (m) REVERT: E 12 SER cc_start: 0.8966 (m) cc_final: 0.8445 (p) REVERT: E 16 ARG cc_start: 0.8351 (mmt180) cc_final: 0.7918 (mtp85) REVERT: E 71 HIS cc_start: 0.8194 (t70) cc_final: 0.7343 (t70) REVERT: E 126 ASN cc_start: 0.8987 (t0) cc_final: 0.8643 (t0) REVERT: E 135 LEU cc_start: 0.9205 (tp) cc_final: 0.8981 (tp) REVERT: E 193 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8059 (mtt180) REVERT: E 216 ARG cc_start: 0.7286 (mpt90) cc_final: 0.6825 (mmt-90) REVERT: E 260 LEU cc_start: 0.8950 (tp) cc_final: 0.8388 (tp) REVERT: E 263 TYR cc_start: 0.9296 (t80) cc_final: 0.8650 (t80) REVERT: E 377 TYR cc_start: 0.8712 (m-10) cc_final: 0.8487 (m-80) REVERT: E 396 TYR cc_start: 0.8880 (t80) cc_final: 0.8654 (t80) REVERT: E 397 ASN cc_start: 0.8514 (t0) cc_final: 0.8006 (t0) REVERT: E 498 GLN cc_start: 0.7965 (tt0) cc_final: 0.7399 (mt0) REVERT: E 512 TYR cc_start: 0.7445 (m-80) cc_final: 0.7140 (m-80) REVERT: E 577 PHE cc_start: 0.8564 (m-80) cc_final: 0.8357 (m-80) REVERT: E 797 GLN cc_start: 0.8635 (pt0) cc_final: 0.8086 (pm20) REVERT: E 799 TYR cc_start: 0.8813 (t80) cc_final: 0.8414 (t80) REVERT: E 911 GLU cc_start: 0.6558 (pt0) cc_final: 0.4390 (tm-30) REVERT: E 1025 MET cc_start: 0.7427 (mmm) cc_final: 0.7179 (mmp) REVERT: E 1088 TRP cc_start: 0.8023 (t-100) cc_final: 0.7785 (t60) REVERT: E 1149 LEU cc_start: 0.8891 (mp) cc_final: 0.8596 (tp) REVERT: E 1200 LEU cc_start: 0.9236 (tt) cc_final: 0.9036 (tt) REVERT: E 1225 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8262 (tm-30) REVERT: E 1277 SER cc_start: 0.9007 (m) cc_final: 0.8662 (t) REVERT: E 1298 MET cc_start: 0.8705 (ttp) cc_final: 0.8385 (ttp) REVERT: E 1406 ASP cc_start: 0.6570 (m-30) cc_final: 0.6317 (m-30) REVERT: B 60 PHE cc_start: 0.9350 (t80) cc_final: 0.8944 (t80) REVERT: B 83 TRP cc_start: 0.9070 (m-10) cc_final: 0.8680 (m-10) REVERT: B 97 HIS cc_start: 0.8959 (t70) cc_final: 0.8730 (t-90) REVERT: B 123 PHE cc_start: 0.9023 (t80) cc_final: 0.8775 (t80) REVERT: B 129 VAL cc_start: 0.9580 (t) cc_final: 0.9336 (t) REVERT: B 250 PHE cc_start: 0.8976 (t80) cc_final: 0.8724 (t80) REVERT: B 254 PRO cc_start: 0.9512 (Cg_exo) cc_final: 0.9296 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8162 (t70) cc_final: 0.7688 (t-170) REVERT: B 299 GLN cc_start: 0.8796 (mt0) cc_final: 0.8581 (mt0) REVERT: B 313 GLN cc_start: 0.7905 (mt0) cc_final: 0.7445 (tt0) REVERT: B 338 LYS cc_start: 0.8993 (tttm) cc_final: 0.8751 (ttmt) REVERT: C 68 TRP cc_start: 0.8279 (m100) cc_final: 0.7950 (m100) REVERT: C 125 ILE cc_start: 0.9339 (mm) cc_final: 0.8875 (tp) REVERT: C 128 GLN cc_start: 0.8987 (tt0) cc_final: 0.8709 (tt0) REVERT: C 168 PHE cc_start: 0.6905 (t80) cc_final: 0.6582 (t80) REVERT: C 211 ILE cc_start: 0.9546 (mt) cc_final: 0.9296 (mt) REVERT: C 258 TYR cc_start: 0.8580 (p90) cc_final: 0.7939 (p90) REVERT: C 273 SER cc_start: 0.9471 (m) cc_final: 0.9215 (t) REVERT: C 313 GLN cc_start: 0.8704 (mt0) cc_final: 0.8329 (mt0) REVERT: C 318 ILE cc_start: 0.8555 (mm) cc_final: 0.8351 (mm) REVERT: C 333 PHE cc_start: 0.8916 (t80) cc_final: 0.8712 (t80) REVERT: D 37 SER cc_start: 0.8686 (t) cc_final: 0.8434 (p) REVERT: D 97 HIS cc_start: 0.9471 (t-90) cc_final: 0.9192 (t-90) REVERT: D 157 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8097 (tt) REVERT: D 233 LEU cc_start: 0.8581 (mt) cc_final: 0.8180 (mt) REVERT: D 273 SER cc_start: 0.9607 (m) cc_final: 0.9050 (t) REVERT: D 274 ASP cc_start: 0.8527 (t70) cc_final: 0.8001 (t0) REVERT: D 299 GLN cc_start: 0.8822 (mt0) cc_final: 0.8521 (mt0) outliers start: 13 outliers final: 7 residues processed: 938 average time/residue: 0.2997 time to fit residues: 442.7786 Evaluate side-chains 842 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 834 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.0030 chunk 206 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 247 optimal weight: 0.6980 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 216 HIS A 235 GLN E 105 HIS E 131 ASN ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN B 259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19884 Z= 0.165 Angle : 0.521 9.293 27234 Z= 0.272 Chirality : 0.043 0.233 3342 Planarity : 0.005 0.063 3400 Dihedral : 11.793 109.030 3308 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2729 helix: 1.97 (0.14), residues: 1309 sheet: -1.38 (0.33), residues: 244 loop : -1.39 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 739 HIS 0.009 0.001 HIS E 326 PHE 0.037 0.002 PHE C 168 TYR 0.024 0.001 TYR A 258 ARG 0.008 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 917 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9238 (m-10) cc_final: 0.8902 (m-10) REVERT: A 90 TRP cc_start: 0.8894 (m100) cc_final: 0.6487 (m100) REVERT: A 92 LEU cc_start: 0.9392 (tt) cc_final: 0.9165 (tt) REVERT: A 152 GLN cc_start: 0.8838 (tt0) cc_final: 0.8603 (tt0) REVERT: A 201 ARG cc_start: 0.8485 (ttt90) cc_final: 0.7973 (ttt180) REVERT: A 210 ILE cc_start: 0.8987 (mt) cc_final: 0.8759 (mt) REVERT: A 211 ILE cc_start: 0.9408 (mt) cc_final: 0.9065 (mt) REVERT: A 248 SER cc_start: 0.8258 (p) cc_final: 0.8038 (p) REVERT: A 301 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: A 318 ILE cc_start: 0.9347 (mm) cc_final: 0.9128 (mm) REVERT: E 16 ARG cc_start: 0.8321 (mmt180) cc_final: 0.7793 (mtp85) REVERT: E 71 HIS cc_start: 0.7750 (t70) cc_final: 0.7175 (t70) REVERT: E 193 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7958 (mtt180) REVERT: E 262 ASN cc_start: 0.9112 (m110) cc_final: 0.8797 (m110) REVERT: E 263 TYR cc_start: 0.9273 (t80) cc_final: 0.8563 (t80) REVERT: E 396 TYR cc_start: 0.8906 (t80) cc_final: 0.8591 (t80) REVERT: E 397 ASN cc_start: 0.8460 (t0) cc_final: 0.8014 (t0) REVERT: E 498 GLN cc_start: 0.7934 (tt0) cc_final: 0.7368 (mt0) REVERT: E 512 TYR cc_start: 0.7527 (m-80) cc_final: 0.6953 (m-80) REVERT: E 595 SER cc_start: 0.8900 (p) cc_final: 0.8622 (t) REVERT: E 685 PHE cc_start: 0.5952 (m-10) cc_final: 0.5142 (t80) REVERT: E 797 GLN cc_start: 0.8566 (pt0) cc_final: 0.8128 (pm20) REVERT: E 799 TYR cc_start: 0.8843 (t80) cc_final: 0.8536 (t80) REVERT: E 911 GLU cc_start: 0.6933 (pt0) cc_final: 0.4844 (tm-30) REVERT: E 1025 MET cc_start: 0.7400 (mmm) cc_final: 0.7030 (mmp) REVERT: E 1080 LEU cc_start: 0.9223 (tp) cc_final: 0.8922 (tp) REVERT: E 1088 TRP cc_start: 0.8026 (t-100) cc_final: 0.7781 (t60) REVERT: E 1207 THR cc_start: 0.8390 (m) cc_final: 0.8113 (m) REVERT: E 1225 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8258 (tm-30) REVERT: E 1277 SER cc_start: 0.8995 (m) cc_final: 0.8565 (t) REVERT: E 1298 MET cc_start: 0.8686 (ttp) cc_final: 0.8277 (ttp) REVERT: E 1308 GLN cc_start: 0.8700 (mt0) cc_final: 0.8409 (tt0) REVERT: B 60 PHE cc_start: 0.9347 (t80) cc_final: 0.8800 (t80) REVERT: B 64 VAL cc_start: 0.8573 (t) cc_final: 0.8371 (t) REVERT: B 71 THR cc_start: 0.9129 (m) cc_final: 0.8875 (m) REVERT: B 83 TRP cc_start: 0.9273 (m-10) cc_final: 0.8859 (m-10) REVERT: B 97 HIS cc_start: 0.8873 (t70) cc_final: 0.8664 (t-90) REVERT: B 114 ILE cc_start: 0.8833 (mm) cc_final: 0.8404 (tp) REVERT: B 149 LEU cc_start: 0.8438 (tt) cc_final: 0.8157 (tt) REVERT: B 212 SER cc_start: 0.9316 (t) cc_final: 0.9062 (t) REVERT: B 250 PHE cc_start: 0.9064 (t80) cc_final: 0.8777 (t80) REVERT: B 252 VAL cc_start: 0.9316 (t) cc_final: 0.9105 (t) REVERT: B 254 PRO cc_start: 0.9452 (Cg_exo) cc_final: 0.9043 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8141 (t70) cc_final: 0.7658 (t-170) REVERT: B 299 GLN cc_start: 0.8817 (mt0) cc_final: 0.8536 (mt0) REVERT: B 313 GLN cc_start: 0.7901 (mt0) cc_final: 0.7574 (tt0) REVERT: B 338 LYS cc_start: 0.9055 (tttm) cc_final: 0.8837 (ttmt) REVERT: C 68 TRP cc_start: 0.8081 (m100) cc_final: 0.7836 (m100) REVERT: C 117 PHE cc_start: 0.9098 (t80) cc_final: 0.8882 (t80) REVERT: C 128 GLN cc_start: 0.8842 (tt0) cc_final: 0.8450 (tt0) REVERT: C 211 ILE cc_start: 0.9637 (mt) cc_final: 0.9354 (mt) REVERT: C 215 ILE cc_start: 0.9272 (mm) cc_final: 0.8901 (mm) REVERT: C 258 TYR cc_start: 0.8430 (p90) cc_final: 0.7849 (p90) REVERT: D 78 SER cc_start: 0.9527 (p) cc_final: 0.9300 (p) REVERT: D 181 LEU cc_start: 0.9131 (mm) cc_final: 0.8843 (mm) REVERT: D 268 TYR cc_start: 0.8615 (t80) cc_final: 0.8365 (t80) REVERT: D 273 SER cc_start: 0.9610 (m) cc_final: 0.9053 (t) REVERT: D 274 ASP cc_start: 0.8512 (t70) cc_final: 0.7971 (t0) REVERT: D 299 GLN cc_start: 0.8716 (mt0) cc_final: 0.8302 (mt0) outliers start: 0 outliers final: 0 residues processed: 917 average time/residue: 0.2905 time to fit residues: 417.1920 Evaluate side-chains 857 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 857 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 168 optimal weight: 50.0000 chunk 68 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 267 optimal weight: 0.0770 chunk 220 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 198 optimal weight: 8.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 247 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN E1203 HIS B 235 GLN C 46 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19884 Z= 0.216 Angle : 0.521 10.684 27234 Z= 0.272 Chirality : 0.042 0.201 3342 Planarity : 0.004 0.056 3400 Dihedral : 11.327 100.698 3308 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2729 helix: 2.07 (0.14), residues: 1319 sheet: -1.18 (0.33), residues: 244 loop : -1.32 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 65 HIS 0.014 0.001 HIS D 259 PHE 0.030 0.002 PHE E 44 TYR 0.015 0.001 TYR A 258 ARG 0.014 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 903 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9236 (m-10) cc_final: 0.8811 (m-10) REVERT: A 90 TRP cc_start: 0.8914 (m100) cc_final: 0.6514 (m100) REVERT: A 91 TRP cc_start: 0.9111 (t60) cc_final: 0.8312 (t60) REVERT: A 92 LEU cc_start: 0.9317 (tt) cc_final: 0.9020 (tt) REVERT: A 201 ARG cc_start: 0.8482 (ttt90) cc_final: 0.7982 (ttt180) REVERT: A 210 ILE cc_start: 0.9088 (mt) cc_final: 0.8881 (mt) REVERT: A 301 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8187 (mtm-85) REVERT: A 318 ILE cc_start: 0.9256 (mm) cc_final: 0.9041 (mm) REVERT: A 328 VAL cc_start: 0.8414 (t) cc_final: 0.8186 (t) REVERT: E 16 ARG cc_start: 0.8378 (mmt180) cc_final: 0.8008 (mtp85) REVERT: E 71 HIS cc_start: 0.8089 (t70) cc_final: 0.7215 (t70) REVERT: E 104 LEU cc_start: 0.9031 (tp) cc_final: 0.8776 (tp) REVERT: E 145 LEU cc_start: 0.9104 (tp) cc_final: 0.8863 (tp) REVERT: E 150 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8408 (mmmt) REVERT: E 202 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7542 (ttm-80) REVERT: E 262 ASN cc_start: 0.9071 (m110) cc_final: 0.8789 (m110) REVERT: E 263 TYR cc_start: 0.9281 (t80) cc_final: 0.8602 (t80) REVERT: E 396 TYR cc_start: 0.8970 (t80) cc_final: 0.8723 (t80) REVERT: E 397 ASN cc_start: 0.8003 (t0) cc_final: 0.7459 (t0) REVERT: E 398 LYS cc_start: 0.9022 (tptt) cc_final: 0.8766 (tptt) REVERT: E 498 GLN cc_start: 0.7986 (tt0) cc_final: 0.7584 (mt0) REVERT: E 512 TYR cc_start: 0.7372 (m-80) cc_final: 0.6953 (m-80) REVERT: E 685 PHE cc_start: 0.5990 (m-10) cc_final: 0.5141 (t80) REVERT: E 772 TYR cc_start: 0.8721 (t80) cc_final: 0.8390 (t80) REVERT: E 781 ASN cc_start: 0.8195 (p0) cc_final: 0.7822 (p0) REVERT: E 797 GLN cc_start: 0.8621 (pt0) cc_final: 0.8089 (pm20) REVERT: E 799 TYR cc_start: 0.8867 (t80) cc_final: 0.8614 (t80) REVERT: E 911 GLU cc_start: 0.6956 (pt0) cc_final: 0.4977 (tm-30) REVERT: E 1025 MET cc_start: 0.7264 (mmm) cc_final: 0.6954 (mmp) REVERT: E 1080 LEU cc_start: 0.9291 (tp) cc_final: 0.9051 (tp) REVERT: E 1088 TRP cc_start: 0.8047 (t-100) cc_final: 0.7799 (t60) REVERT: E 1138 SER cc_start: 0.8779 (t) cc_final: 0.8382 (t) REVERT: E 1141 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8270 (tm-30) REVERT: E 1215 ARG cc_start: 0.8916 (mtm110) cc_final: 0.7697 (tpm170) REVERT: E 1225 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8268 (tm-30) REVERT: E 1269 SER cc_start: 0.8993 (t) cc_final: 0.8748 (p) REVERT: E 1277 SER cc_start: 0.8591 (m) cc_final: 0.8113 (t) REVERT: E 1419 ARG cc_start: 0.6586 (ttm110) cc_final: 0.5538 (ttm170) REVERT: B 34 ARG cc_start: 0.8504 (mtp180) cc_final: 0.8250 (mtp180) REVERT: B 78 SER cc_start: 0.9105 (p) cc_final: 0.8757 (p) REVERT: B 83 TRP cc_start: 0.9250 (m-10) cc_final: 0.8876 (m-10) REVERT: B 114 ILE cc_start: 0.8834 (mm) cc_final: 0.8396 (tp) REVERT: B 212 SER cc_start: 0.9431 (t) cc_final: 0.9150 (t) REVERT: B 216 HIS cc_start: 0.7010 (m90) cc_final: 0.6724 (m170) REVERT: B 250 PHE cc_start: 0.9128 (t80) cc_final: 0.8773 (t80) REVERT: B 252 VAL cc_start: 0.9305 (t) cc_final: 0.9029 (t) REVERT: B 277 HIS cc_start: 0.8189 (t70) cc_final: 0.7692 (t-170) REVERT: B 299 GLN cc_start: 0.8852 (mt0) cc_final: 0.8405 (mt0) REVERT: B 313 GLN cc_start: 0.7780 (mt0) cc_final: 0.7580 (tt0) REVERT: B 338 LYS cc_start: 0.9096 (tttm) cc_final: 0.8848 (ttmt) REVERT: C 68 TRP cc_start: 0.8077 (m100) cc_final: 0.7802 (m100) REVERT: C 125 ILE cc_start: 0.8812 (tp) cc_final: 0.8523 (tp) REVERT: C 128 GLN cc_start: 0.8831 (tt0) cc_final: 0.8448 (tt0) REVERT: C 146 ILE cc_start: 0.9545 (mt) cc_final: 0.9321 (mt) REVERT: C 147 LEU cc_start: 0.8924 (tp) cc_final: 0.8709 (tp) REVERT: C 211 ILE cc_start: 0.9630 (mt) cc_final: 0.9185 (mt) REVERT: C 215 ILE cc_start: 0.9416 (mm) cc_final: 0.9019 (mm) REVERT: C 248 SER cc_start: 0.8631 (p) cc_final: 0.8401 (p) REVERT: C 258 TYR cc_start: 0.8374 (p90) cc_final: 0.7800 (p90) REVERT: D 112 THR cc_start: 0.9422 (m) cc_final: 0.9151 (m) REVERT: D 201 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7627 (mtt-85) REVERT: D 233 LEU cc_start: 0.8670 (mt) cc_final: 0.8329 (mt) REVERT: D 268 TYR cc_start: 0.8662 (t80) cc_final: 0.8457 (t80) REVERT: D 273 SER cc_start: 0.9605 (m) cc_final: 0.8941 (t) REVERT: D 274 ASP cc_start: 0.8511 (t70) cc_final: 0.7975 (t0) outliers start: 0 outliers final: 0 residues processed: 903 average time/residue: 0.2911 time to fit residues: 412.0145 Evaluate side-chains 847 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 847 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 248 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 235 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 235 GLN ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1296 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 19884 Z= 0.465 Angle : 0.716 9.029 27234 Z= 0.378 Chirality : 0.047 0.195 3342 Planarity : 0.005 0.065 3400 Dihedral : 11.764 104.866 3308 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2729 helix: 1.45 (0.14), residues: 1318 sheet: -1.24 (0.34), residues: 229 loop : -1.41 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 90 HIS 0.024 0.002 HIS D 259 PHE 0.033 0.003 PHE C 168 TYR 0.024 0.003 TYR A 258 ARG 0.025 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 902 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8183 (t) cc_final: 0.7350 (p) REVERT: A 46 HIS cc_start: 0.7902 (m90) cc_final: 0.7406 (m90) REVERT: A 90 TRP cc_start: 0.9017 (m100) cc_final: 0.6277 (m100) REVERT: A 91 TRP cc_start: 0.9209 (t60) cc_final: 0.8830 (t60) REVERT: A 92 LEU cc_start: 0.9476 (tt) cc_final: 0.9211 (tt) REVERT: A 158 MET cc_start: 0.7495 (ttt) cc_final: 0.7247 (ttp) REVERT: A 235 GLN cc_start: 0.8720 (mt0) cc_final: 0.8498 (mt0) REVERT: A 260 VAL cc_start: 0.8973 (t) cc_final: 0.8661 (p) REVERT: A 301 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8257 (mtm-85) REVERT: E 12 SER cc_start: 0.9026 (m) cc_final: 0.8649 (p) REVERT: E 71 HIS cc_start: 0.8404 (t70) cc_final: 0.7337 (t-170) REVERT: E 123 TYR cc_start: 0.9097 (t80) cc_final: 0.8696 (t80) REVERT: E 125 HIS cc_start: 0.8833 (t-90) cc_final: 0.8260 (t-170) REVERT: E 158 TYR cc_start: 0.7941 (t80) cc_final: 0.7681 (t80) REVERT: E 265 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.7858 (mtp180) REVERT: E 377 TYR cc_start: 0.8743 (m-10) cc_final: 0.8539 (m-80) REVERT: E 397 ASN cc_start: 0.8181 (t0) cc_final: 0.7599 (t0) REVERT: E 398 LYS cc_start: 0.9051 (tptt) cc_final: 0.8847 (tptt) REVERT: E 495 ARG cc_start: 0.7638 (tmm160) cc_final: 0.6633 (tmm160) REVERT: E 498 GLN cc_start: 0.8079 (tt0) cc_final: 0.7671 (mt0) REVERT: E 512 TYR cc_start: 0.7667 (m-80) cc_final: 0.7048 (m-80) REVERT: E 524 VAL cc_start: 0.8536 (t) cc_final: 0.7853 (t) REVERT: E 527 ARG cc_start: 0.9003 (ttm110) cc_final: 0.8173 (mtm110) REVERT: E 577 PHE cc_start: 0.9002 (m-80) cc_final: 0.8564 (m-80) REVERT: E 598 ARG cc_start: 0.8809 (tpp80) cc_final: 0.8592 (tpp-160) REVERT: E 689 THR cc_start: 0.7776 (p) cc_final: 0.7260 (t) REVERT: E 772 TYR cc_start: 0.8794 (t80) cc_final: 0.8425 (t80) REVERT: E 781 ASN cc_start: 0.8422 (p0) cc_final: 0.8010 (p0) REVERT: E 788 ILE cc_start: 0.9279 (mm) cc_final: 0.9009 (mm) REVERT: E 797 GLN cc_start: 0.8698 (pt0) cc_final: 0.8112 (pm20) REVERT: E 799 TYR cc_start: 0.8759 (t80) cc_final: 0.8504 (t80) REVERT: E 848 THR cc_start: 0.7969 (p) cc_final: 0.7764 (p) REVERT: E 911 GLU cc_start: 0.7015 (pt0) cc_final: 0.4972 (tm-30) REVERT: E 1025 MET cc_start: 0.7300 (mmm) cc_final: 0.7015 (mmp) REVERT: E 1080 LEU cc_start: 0.9174 (tp) cc_final: 0.8870 (tp) REVERT: E 1088 TRP cc_start: 0.8132 (t-100) cc_final: 0.7796 (t60) REVERT: E 1212 THR cc_start: 0.8908 (p) cc_final: 0.8507 (t) REVERT: E 1215 ARG cc_start: 0.8837 (mtm110) cc_final: 0.7571 (tpm170) REVERT: E 1225 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8534 (tm-30) REVERT: E 1269 SER cc_start: 0.8917 (t) cc_final: 0.8623 (p) REVERT: E 1277 SER cc_start: 0.9160 (m) cc_final: 0.8664 (t) REVERT: B 78 SER cc_start: 0.9097 (p) cc_final: 0.8781 (p) REVERT: B 83 TRP cc_start: 0.9299 (m-10) cc_final: 0.8934 (m-10) REVERT: B 129 VAL cc_start: 0.9561 (t) cc_final: 0.9358 (t) REVERT: B 212 SER cc_start: 0.9693 (t) cc_final: 0.9487 (t) REVERT: B 240 MET cc_start: 0.8420 (tmm) cc_final: 0.8127 (tmm) REVERT: B 254 PRO cc_start: 0.9392 (Cg_exo) cc_final: 0.9015 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8558 (t70) cc_final: 0.8097 (t-170) REVERT: B 313 GLN cc_start: 0.8007 (mt0) cc_final: 0.7488 (tt0) REVERT: B 338 LYS cc_start: 0.9254 (tttm) cc_final: 0.8888 (ttmt) REVERT: C 90 TRP cc_start: 0.8985 (m100) cc_final: 0.8673 (m100) REVERT: C 128 GLN cc_start: 0.9026 (tt0) cc_final: 0.8766 (tt0) REVERT: C 215 ILE cc_start: 0.9404 (mm) cc_final: 0.9139 (mm) REVERT: C 258 TYR cc_start: 0.8546 (p90) cc_final: 0.7912 (p90) REVERT: C 318 ILE cc_start: 0.8694 (mm) cc_final: 0.8416 (mm) REVERT: C 328 VAL cc_start: 0.8749 (t) cc_final: 0.8404 (m) REVERT: C 333 PHE cc_start: 0.8958 (t80) cc_final: 0.8616 (t80) REVERT: D 112 THR cc_start: 0.9291 (m) cc_final: 0.8855 (p) REVERT: D 181 LEU cc_start: 0.9248 (mm) cc_final: 0.8965 (mm) REVERT: D 191 LEU cc_start: 0.8215 (mt) cc_final: 0.7935 (mt) REVERT: D 201 ARG cc_start: 0.8778 (mtt-85) cc_final: 0.8511 (mtt-85) REVERT: D 268 TYR cc_start: 0.8855 (t80) cc_final: 0.8554 (t80) REVERT: D 273 SER cc_start: 0.9604 (m) cc_final: 0.8963 (t) REVERT: D 274 ASP cc_start: 0.8521 (t70) cc_final: 0.7867 (t0) outliers start: 1 outliers final: 1 residues processed: 903 average time/residue: 0.2821 time to fit residues: 403.0174 Evaluate side-chains 840 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 839 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 195 optimal weight: 30.0000 chunk 108 optimal weight: 50.0000 chunk 224 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 134 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 GLN B 46 HIS B 48 ASN B 70 HIS B 218 GLN B 235 GLN B 259 HIS B 299 GLN D 43 ASN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19884 Z= 0.218 Angle : 0.544 10.264 27234 Z= 0.284 Chirality : 0.043 0.179 3342 Planarity : 0.004 0.049 3400 Dihedral : 11.396 100.791 3308 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.19 % Allowed : 2.00 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2729 helix: 2.00 (0.14), residues: 1298 sheet: -1.17 (0.34), residues: 232 loop : -1.22 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 143 HIS 0.010 0.001 HIS E 326 PHE 0.030 0.002 PHE E 44 TYR 0.021 0.002 TYR A 258 ARG 0.011 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 902 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8332 (t) cc_final: 0.7938 (p) REVERT: A 90 TRP cc_start: 0.8930 (m100) cc_final: 0.6467 (m100) REVERT: A 92 LEU cc_start: 0.9383 (tt) cc_final: 0.9081 (tt) REVERT: A 110 CYS cc_start: 0.6299 (m) cc_final: 0.6032 (m) REVERT: A 299 GLN cc_start: 0.9022 (tt0) cc_final: 0.8786 (tt0) REVERT: A 301 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: E 71 HIS cc_start: 0.8261 (t70) cc_final: 0.7264 (t-170) REVERT: E 125 HIS cc_start: 0.8708 (t-90) cc_final: 0.8139 (t-170) REVERT: E 145 LEU cc_start: 0.9319 (tp) cc_final: 0.9094 (tp) REVERT: E 158 TYR cc_start: 0.7853 (t80) cc_final: 0.7635 (t80) REVERT: E 215 VAL cc_start: 0.7223 (p) cc_final: 0.6939 (m) REVERT: E 216 ARG cc_start: 0.8186 (tpp80) cc_final: 0.6319 (tpp80) REVERT: E 260 LEU cc_start: 0.8969 (tp) cc_final: 0.8381 (tp) REVERT: E 262 ASN cc_start: 0.9062 (m110) cc_final: 0.8861 (m110) REVERT: E 263 TYR cc_start: 0.9284 (t80) cc_final: 0.8522 (t80) REVERT: E 397 ASN cc_start: 0.8068 (t0) cc_final: 0.7561 (t0) REVERT: E 398 LYS cc_start: 0.9026 (tptt) cc_final: 0.8726 (tptt) REVERT: E 498 GLN cc_start: 0.8012 (tt0) cc_final: 0.7553 (mt0) REVERT: E 524 VAL cc_start: 0.8499 (t) cc_final: 0.7582 (t) REVERT: E 527 ARG cc_start: 0.8980 (ttm110) cc_final: 0.8067 (mtm110) REVERT: E 577 PHE cc_start: 0.8920 (m-80) cc_final: 0.8494 (m-80) REVERT: E 772 TYR cc_start: 0.8733 (t80) cc_final: 0.8317 (t80) REVERT: E 781 ASN cc_start: 0.8206 (p0) cc_final: 0.7834 (p0) REVERT: E 797 GLN cc_start: 0.8564 (pt0) cc_final: 0.8126 (pm20) REVERT: E 911 GLU cc_start: 0.7146 (pt0) cc_final: 0.5282 (tm-30) REVERT: E 1025 MET cc_start: 0.7163 (mmm) cc_final: 0.6900 (mmp) REVERT: E 1080 LEU cc_start: 0.9268 (tp) cc_final: 0.9035 (tp) REVERT: E 1088 TRP cc_start: 0.8095 (t-100) cc_final: 0.7771 (t60) REVERT: E 1112 PHE cc_start: 0.7567 (t80) cc_final: 0.7287 (t80) REVERT: E 1138 SER cc_start: 0.8796 (t) cc_final: 0.8304 (t) REVERT: E 1215 ARG cc_start: 0.8788 (mtm110) cc_final: 0.7723 (tpm170) REVERT: E 1225 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8578 (tm-30) REVERT: E 1269 SER cc_start: 0.8900 (t) cc_final: 0.8591 (p) REVERT: E 1277 SER cc_start: 0.8702 (m) cc_final: 0.8242 (t) REVERT: E 1419 ARG cc_start: 0.6316 (ttm110) cc_final: 0.5511 (ttm170) REVERT: B 78 SER cc_start: 0.9100 (p) cc_final: 0.8733 (p) REVERT: B 83 TRP cc_start: 0.9195 (m-10) cc_final: 0.8780 (m-10) REVERT: B 129 VAL cc_start: 0.9504 (t) cc_final: 0.9279 (t) REVERT: B 216 HIS cc_start: 0.7448 (m90) cc_final: 0.7233 (m170) REVERT: B 254 PRO cc_start: 0.9517 (Cg_exo) cc_final: 0.9087 (Cg_endo) REVERT: B 259 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7095 (t-90) REVERT: B 277 HIS cc_start: 0.8553 (t70) cc_final: 0.8205 (t-170) REVERT: B 313 GLN cc_start: 0.7987 (mt0) cc_final: 0.7751 (tt0) REVERT: B 338 LYS cc_start: 0.9254 (tttm) cc_final: 0.8935 (ttmt) REVERT: C 90 TRP cc_start: 0.8978 (m100) cc_final: 0.8738 (m100) REVERT: C 128 GLN cc_start: 0.8960 (tt0) cc_final: 0.8604 (tt0) REVERT: C 146 ILE cc_start: 0.9533 (mt) cc_final: 0.9289 (mt) REVERT: C 147 LEU cc_start: 0.8996 (tp) cc_final: 0.8781 (tp) REVERT: C 211 ILE cc_start: 0.9455 (mt) cc_final: 0.9236 (mt) REVERT: C 215 ILE cc_start: 0.9357 (mm) cc_final: 0.9073 (mm) REVERT: C 248 SER cc_start: 0.8702 (p) cc_final: 0.8481 (p) REVERT: C 258 TYR cc_start: 0.8630 (p90) cc_final: 0.7779 (p90) REVERT: D 136 ARG cc_start: 0.8935 (ptp-170) cc_final: 0.8696 (ptp-170) REVERT: D 181 LEU cc_start: 0.9145 (mm) cc_final: 0.8933 (mm) REVERT: D 234 HIS cc_start: 0.8485 (t70) cc_final: 0.7534 (t70) REVERT: D 273 SER cc_start: 0.9505 (m) cc_final: 0.8795 (t) REVERT: D 274 ASP cc_start: 0.8506 (t70) cc_final: 0.7917 (t0) outliers start: 3 outliers final: 1 residues processed: 903 average time/residue: 0.2864 time to fit residues: 407.3015 Evaluate side-chains 836 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 834 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 87 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 277 HIS ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 HIS B 259 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 19884 Z= 0.361 Angle : 0.628 10.537 27234 Z= 0.329 Chirality : 0.045 0.256 3342 Planarity : 0.004 0.049 3400 Dihedral : 11.412 103.851 3308 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.06 % Allowed : 2.07 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2729 helix: 1.88 (0.14), residues: 1299 sheet: -1.29 (0.33), residues: 230 loop : -1.23 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 143 HIS 0.009 0.001 HIS D 259 PHE 0.042 0.002 PHE C 168 TYR 0.021 0.002 TYR A 258 ARG 0.008 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 880 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8377 (t) cc_final: 0.8006 (p) REVERT: A 90 TRP cc_start: 0.8999 (m100) cc_final: 0.6295 (m100) REVERT: A 91 TRP cc_start: 0.9147 (t60) cc_final: 0.8711 (t60) REVERT: A 92 LEU cc_start: 0.9440 (tt) cc_final: 0.9134 (tt) REVERT: A 110 CYS cc_start: 0.6353 (m) cc_final: 0.6098 (m) REVERT: A 277 HIS cc_start: 0.7914 (t70) cc_final: 0.7704 (t-90) REVERT: A 301 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8147 (mtm-85) REVERT: E 71 HIS cc_start: 0.8336 (t70) cc_final: 0.7316 (t-170) REVERT: E 125 HIS cc_start: 0.8806 (t-90) cc_final: 0.8538 (t-170) REVERT: E 131 ASN cc_start: 0.9222 (t0) cc_final: 0.8929 (t0) REVERT: E 148 ILE cc_start: 0.9301 (mm) cc_final: 0.9039 (mm) REVERT: E 158 TYR cc_start: 0.8245 (t80) cc_final: 0.8030 (t80) REVERT: E 164 PHE cc_start: 0.8702 (m-80) cc_final: 0.8384 (m-80) REVERT: E 262 ASN cc_start: 0.9129 (m110) cc_final: 0.8900 (m110) REVERT: E 397 ASN cc_start: 0.8183 (t0) cc_final: 0.7659 (t0) REVERT: E 398 LYS cc_start: 0.9125 (tptt) cc_final: 0.8897 (tptt) REVERT: E 495 ARG cc_start: 0.7539 (tmm160) cc_final: 0.6708 (tmm160) REVERT: E 498 GLN cc_start: 0.8054 (tt0) cc_final: 0.7620 (mt0) REVERT: E 577 PHE cc_start: 0.8856 (m-80) cc_final: 0.8407 (m-80) REVERT: E 598 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8399 (tpp-160) REVERT: E 689 THR cc_start: 0.7725 (p) cc_final: 0.7255 (t) REVERT: E 772 TYR cc_start: 0.8749 (t80) cc_final: 0.8392 (t80) REVERT: E 781 ASN cc_start: 0.8393 (p0) cc_final: 0.8025 (p0) REVERT: E 788 ILE cc_start: 0.9267 (mm) cc_final: 0.9055 (mm) REVERT: E 797 GLN cc_start: 0.8560 (pt0) cc_final: 0.8060 (pm20) REVERT: E 911 GLU cc_start: 0.6689 (pt0) cc_final: 0.4868 (tm-30) REVERT: E 1025 MET cc_start: 0.7268 (mmm) cc_final: 0.6964 (mmp) REVERT: E 1080 LEU cc_start: 0.9268 (tp) cc_final: 0.9005 (tp) REVERT: E 1088 TRP cc_start: 0.8175 (t-100) cc_final: 0.7816 (t60) REVERT: E 1112 PHE cc_start: 0.7344 (t80) cc_final: 0.7055 (t80) REVERT: E 1138 SER cc_start: 0.8975 (t) cc_final: 0.8486 (t) REVERT: E 1149 LEU cc_start: 0.8839 (mp) cc_final: 0.8618 (mp) REVERT: E 1212 THR cc_start: 0.8989 (p) cc_final: 0.8258 (m) REVERT: E 1215 ARG cc_start: 0.8719 (mtm110) cc_final: 0.7551 (tpm170) REVERT: E 1225 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8590 (tm-30) REVERT: E 1269 SER cc_start: 0.8822 (t) cc_final: 0.8390 (p) REVERT: E 1270 ASN cc_start: 0.8361 (m-40) cc_final: 0.8013 (m110) REVERT: E 1277 SER cc_start: 0.9136 (m) cc_final: 0.8688 (t) REVERT: E 1419 ARG cc_start: 0.6819 (ttm110) cc_final: 0.5989 (ttm170) REVERT: B 78 SER cc_start: 0.9120 (p) cc_final: 0.8773 (p) REVERT: B 83 TRP cc_start: 0.9265 (m-10) cc_final: 0.8828 (m-10) REVERT: B 277 HIS cc_start: 0.8602 (t70) cc_final: 0.8222 (t-170) REVERT: B 313 GLN cc_start: 0.8026 (mt0) cc_final: 0.7432 (tt0) REVERT: B 338 LYS cc_start: 0.9279 (tttm) cc_final: 0.8921 (ttmt) REVERT: C 90 TRP cc_start: 0.9003 (m100) cc_final: 0.8748 (m100) REVERT: C 128 GLN cc_start: 0.8975 (tt0) cc_final: 0.8734 (tt0) REVERT: C 215 ILE cc_start: 0.9345 (mm) cc_final: 0.9083 (mm) REVERT: C 248 SER cc_start: 0.8721 (p) cc_final: 0.8506 (p) REVERT: C 258 TYR cc_start: 0.8652 (p90) cc_final: 0.7923 (p90) REVERT: C 333 PHE cc_start: 0.8887 (t80) cc_final: 0.8583 (t80) REVERT: D 112 THR cc_start: 0.9247 (m) cc_final: 0.8756 (p) REVERT: D 136 ARG cc_start: 0.8996 (ptp-170) cc_final: 0.8480 (ptp-170) REVERT: D 181 LEU cc_start: 0.9278 (mm) cc_final: 0.9064 (mm) REVERT: D 234 HIS cc_start: 0.8601 (t70) cc_final: 0.7694 (t70) REVERT: D 273 SER cc_start: 0.9592 (m) cc_final: 0.8951 (t) REVERT: D 274 ASP cc_start: 0.8528 (t70) cc_final: 0.7957 (t0) outliers start: 1 outliers final: 0 residues processed: 880 average time/residue: 0.2875 time to fit residues: 400.9714 Evaluate side-chains 824 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 824 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 262 optimal weight: 0.8980 chunk 164 optimal weight: 30.0000 chunk 159 optimal weight: 40.0000 chunk 121 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 276 HIS A 299 GLN E 24 ASN E 32 ASN ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN D 259 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 19884 Z= 0.306 Angle : 0.601 13.189 27234 Z= 0.314 Chirality : 0.044 0.338 3342 Planarity : 0.004 0.050 3400 Dihedral : 11.331 102.368 3308 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2729 helix: 1.89 (0.14), residues: 1296 sheet: -1.34 (0.32), residues: 244 loop : -1.18 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 778 HIS 0.007 0.001 HIS D 259 PHE 0.037 0.002 PHE D 168 TYR 0.020 0.002 TYR A 258 ARG 0.007 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 888 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8392 (t) cc_final: 0.8143 (p) REVERT: A 90 TRP cc_start: 0.8984 (m100) cc_final: 0.6391 (m100) REVERT: A 91 TRP cc_start: 0.9171 (t60) cc_final: 0.8405 (t60) REVERT: A 92 LEU cc_start: 0.9426 (tt) cc_final: 0.9137 (tt) REVERT: A 110 CYS cc_start: 0.6323 (m) cc_final: 0.6061 (m) REVERT: A 260 VAL cc_start: 0.8977 (t) cc_final: 0.8588 (p) REVERT: A 301 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8143 (mtm-85) REVERT: E 71 HIS cc_start: 0.8301 (t70) cc_final: 0.7701 (t70) REVERT: E 104 LEU cc_start: 0.9026 (tp) cc_final: 0.8825 (tp) REVERT: E 125 HIS cc_start: 0.8763 (t-90) cc_final: 0.8056 (t-170) REVERT: E 131 ASN cc_start: 0.9216 (t0) cc_final: 0.8933 (t0) REVERT: E 164 PHE cc_start: 0.8695 (m-80) cc_final: 0.8343 (m-80) REVERT: E 398 LYS cc_start: 0.9129 (tptt) cc_final: 0.8908 (tptt) REVERT: E 495 ARG cc_start: 0.7523 (tmm160) cc_final: 0.7299 (tmm160) REVERT: E 498 GLN cc_start: 0.8037 (tt0) cc_final: 0.7616 (mt0) REVERT: E 527 ARG cc_start: 0.8953 (ttm110) cc_final: 0.8215 (mtm110) REVERT: E 577 PHE cc_start: 0.8781 (m-80) cc_final: 0.8389 (m-80) REVERT: E 614 LEU cc_start: 0.7829 (tp) cc_final: 0.7382 (tp) REVERT: E 772 TYR cc_start: 0.8791 (t80) cc_final: 0.8366 (t80) REVERT: E 781 ASN cc_start: 0.8401 (p0) cc_final: 0.7982 (p0) REVERT: E 797 GLN cc_start: 0.8538 (pt0) cc_final: 0.7955 (pm20) REVERT: E 911 GLU cc_start: 0.6755 (pt0) cc_final: 0.4856 (tm-30) REVERT: E 1025 MET cc_start: 0.7246 (mmm) cc_final: 0.6946 (mmp) REVERT: E 1080 LEU cc_start: 0.9256 (tp) cc_final: 0.9024 (tp) REVERT: E 1088 TRP cc_start: 0.8168 (t-100) cc_final: 0.7823 (t60) REVERT: E 1112 PHE cc_start: 0.7360 (t80) cc_final: 0.7070 (t80) REVERT: E 1138 SER cc_start: 0.8969 (t) cc_final: 0.8462 (t) REVERT: E 1225 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8633 (tm-30) REVERT: E 1269 SER cc_start: 0.8955 (t) cc_final: 0.8683 (p) REVERT: E 1270 ASN cc_start: 0.8289 (m-40) cc_final: 0.7988 (m110) REVERT: E 1277 SER cc_start: 0.8767 (m) cc_final: 0.8308 (t) REVERT: B 71 THR cc_start: 0.9213 (m) cc_final: 0.9006 (m) REVERT: B 78 SER cc_start: 0.9167 (p) cc_final: 0.8822 (p) REVERT: B 83 TRP cc_start: 0.9243 (m-10) cc_final: 0.8853 (m-10) REVERT: B 254 PRO cc_start: 0.9532 (Cg_exo) cc_final: 0.9107 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8592 (t70) cc_final: 0.8236 (t-170) REVERT: B 313 GLN cc_start: 0.8175 (mt0) cc_final: 0.7571 (tt0) REVERT: B 338 LYS cc_start: 0.9268 (tttm) cc_final: 0.8918 (ttmt) REVERT: C 90 TRP cc_start: 0.8994 (m100) cc_final: 0.8756 (m100) REVERT: C 128 GLN cc_start: 0.8933 (tt0) cc_final: 0.8712 (tt0) REVERT: C 215 ILE cc_start: 0.9350 (mm) cc_final: 0.9016 (mm) REVERT: C 258 TYR cc_start: 0.8681 (p90) cc_final: 0.7929 (p90) REVERT: C 309 ILE cc_start: 0.9448 (mm) cc_final: 0.9205 (mm) REVERT: D 112 THR cc_start: 0.9260 (m) cc_final: 0.8753 (p) REVERT: D 136 ARG cc_start: 0.8914 (ptp-170) cc_final: 0.8429 (ptp-170) REVERT: D 181 LEU cc_start: 0.9187 (mm) cc_final: 0.8959 (mm) REVERT: D 234 HIS cc_start: 0.8590 (t70) cc_final: 0.7723 (t70) REVERT: D 273 SER cc_start: 0.9523 (m) cc_final: 0.8815 (t) REVERT: D 274 ASP cc_start: 0.8517 (t70) cc_final: 0.7940 (t0) outliers start: 1 outliers final: 0 residues processed: 888 average time/residue: 0.2781 time to fit residues: 392.5537 Evaluate side-chains 827 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 827 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 50.0000 chunk 104 optimal weight: 8.9990 chunk 156 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 50.0000 chunk 178 optimal weight: 20.0000 chunk 129 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 276 HIS A 299 GLN E 32 ASN ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 HIS B 46 HIS B 216 HIS B 299 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19884 Z= 0.317 Angle : 0.616 12.435 27234 Z= 0.321 Chirality : 0.044 0.212 3342 Planarity : 0.004 0.049 3400 Dihedral : 11.309 103.735 3308 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.06 % Allowed : 1.44 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2729 helix: 1.84 (0.14), residues: 1298 sheet: -1.39 (0.31), residues: 255 loop : -1.22 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 778 HIS 0.008 0.001 HIS D 259 PHE 0.039 0.002 PHE C 168 TYR 0.019 0.002 TYR A 258 ARG 0.006 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 886 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8413 (t) cc_final: 0.8160 (p) REVERT: A 90 TRP cc_start: 0.9012 (m100) cc_final: 0.6449 (m100) REVERT: A 91 TRP cc_start: 0.9173 (t60) cc_final: 0.8691 (t60) REVERT: A 92 LEU cc_start: 0.9398 (tt) cc_final: 0.9091 (tt) REVERT: A 110 CYS cc_start: 0.6363 (m) cc_final: 0.6133 (m) REVERT: A 183 PHE cc_start: 0.9061 (m-80) cc_final: 0.8647 (m-80) REVERT: A 248 SER cc_start: 0.8411 (p) cc_final: 0.8158 (p) REVERT: A 301 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8206 (mtm-85) REVERT: E 16 ARG cc_start: 0.8259 (mmt180) cc_final: 0.7792 (mtp85) REVERT: E 24 ASN cc_start: 0.8715 (t0) cc_final: 0.8506 (t0) REVERT: E 71 HIS cc_start: 0.8320 (t70) cc_final: 0.7359 (t-170) REVERT: E 104 LEU cc_start: 0.9036 (tp) cc_final: 0.8834 (tp) REVERT: E 123 TYR cc_start: 0.9051 (t80) cc_final: 0.8519 (t80) REVERT: E 125 HIS cc_start: 0.8762 (t-90) cc_final: 0.8039 (t-170) REVERT: E 131 ASN cc_start: 0.9232 (t0) cc_final: 0.8831 (t0) REVERT: E 164 PHE cc_start: 0.8700 (m-80) cc_final: 0.8383 (m-80) REVERT: E 398 LYS cc_start: 0.9198 (tptt) cc_final: 0.8887 (tptt) REVERT: E 495 ARG cc_start: 0.7519 (tmm160) cc_final: 0.7300 (tmm160) REVERT: E 498 GLN cc_start: 0.8012 (tt0) cc_final: 0.7603 (mt0) REVERT: E 577 PHE cc_start: 0.8756 (m-80) cc_final: 0.8372 (m-80) REVERT: E 614 LEU cc_start: 0.7842 (tp) cc_final: 0.7423 (tp) REVERT: E 685 PHE cc_start: 0.6638 (m-10) cc_final: 0.6369 (m-80) REVERT: E 772 TYR cc_start: 0.8781 (t80) cc_final: 0.8347 (t80) REVERT: E 781 ASN cc_start: 0.8536 (p0) cc_final: 0.8204 (p0) REVERT: E 788 ILE cc_start: 0.9254 (mm) cc_final: 0.9037 (mm) REVERT: E 797 GLN cc_start: 0.8532 (pt0) cc_final: 0.7945 (pm20) REVERT: E 848 THR cc_start: 0.8126 (p) cc_final: 0.7912 (p) REVERT: E 911 GLU cc_start: 0.6786 (pt0) cc_final: 0.4665 (tm-30) REVERT: E 1025 MET cc_start: 0.7254 (mmm) cc_final: 0.6954 (mmp) REVERT: E 1080 LEU cc_start: 0.9258 (tp) cc_final: 0.9021 (tp) REVERT: E 1088 TRP cc_start: 0.8174 (t-100) cc_final: 0.7807 (t60) REVERT: E 1112 PHE cc_start: 0.7380 (t80) cc_final: 0.7075 (t80) REVERT: E 1138 SER cc_start: 0.9000 (t) cc_final: 0.8506 (t) REVERT: E 1215 ARG cc_start: 0.8464 (mtm110) cc_final: 0.7269 (tpm170) REVERT: E 1225 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8608 (tm-30) REVERT: E 1269 SER cc_start: 0.8904 (t) cc_final: 0.8599 (p) REVERT: E 1270 ASN cc_start: 0.8272 (m-40) cc_final: 0.7965 (m110) REVERT: E 1277 SER cc_start: 0.8772 (m) cc_final: 0.8310 (t) REVERT: B 78 SER cc_start: 0.9171 (p) cc_final: 0.8818 (p) REVERT: B 83 TRP cc_start: 0.9270 (m-10) cc_final: 0.8806 (m-10) REVERT: B 216 HIS cc_start: 0.8421 (m-70) cc_final: 0.7837 (m-70) REVERT: B 277 HIS cc_start: 0.8625 (t70) cc_final: 0.8261 (t-170) REVERT: B 313 GLN cc_start: 0.8218 (mt0) cc_final: 0.7597 (tt0) REVERT: B 338 LYS cc_start: 0.9277 (tttm) cc_final: 0.8918 (ttmt) REVERT: C 90 TRP cc_start: 0.8984 (m100) cc_final: 0.8735 (m100) REVERT: C 215 ILE cc_start: 0.9359 (mm) cc_final: 0.9001 (mm) REVERT: C 258 TYR cc_start: 0.8766 (p90) cc_final: 0.8047 (p90) REVERT: C 333 PHE cc_start: 0.9005 (t80) cc_final: 0.8552 (t80) REVERT: D 90 TRP cc_start: 0.9008 (m100) cc_final: 0.8411 (m100) REVERT: D 181 LEU cc_start: 0.9260 (mm) cc_final: 0.9049 (mm) REVERT: D 216 HIS cc_start: 0.8531 (m-70) cc_final: 0.8146 (m170) REVERT: D 234 HIS cc_start: 0.8618 (t70) cc_final: 0.7731 (t70) REVERT: D 273 SER cc_start: 0.9526 (m) cc_final: 0.8831 (t) REVERT: D 274 ASP cc_start: 0.8521 (t70) cc_final: 0.7931 (t0) outliers start: 1 outliers final: 0 residues processed: 886 average time/residue: 0.3009 time to fit residues: 420.7349 Evaluate side-chains 826 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 826 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 231 optimal weight: 0.0970 chunk 243 optimal weight: 0.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 299 GLN E 32 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 299 GLN C 128 GLN D 43 ASN D 259 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19884 Z= 0.183 Angle : 0.559 13.130 27234 Z= 0.285 Chirality : 0.043 0.306 3342 Planarity : 0.004 0.050 3400 Dihedral : 11.006 98.474 3308 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.13 % Allowed : 0.75 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2729 helix: 2.11 (0.14), residues: 1294 sheet: -1.29 (0.31), residues: 264 loop : -1.06 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 232 HIS 0.007 0.001 HIS D 259 PHE 0.030 0.002 PHE D 168 TYR 0.018 0.001 TYR A 258 ARG 0.010 0.001 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 879 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8353 (t) cc_final: 0.8006 (p) REVERT: A 90 TRP cc_start: 0.8983 (m100) cc_final: 0.6564 (m100) REVERT: A 92 LEU cc_start: 0.9317 (tt) cc_final: 0.9042 (tt) REVERT: A 110 CYS cc_start: 0.6375 (m) cc_final: 0.6082 (m) REVERT: A 152 GLN cc_start: 0.9243 (tt0) cc_final: 0.8915 (tt0) REVERT: A 248 SER cc_start: 0.8426 (p) cc_final: 0.8168 (p) REVERT: A 301 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8177 (mtm-85) REVERT: A 311 TRP cc_start: 0.8888 (t-100) cc_final: 0.7861 (t60) REVERT: E 24 ASN cc_start: 0.8519 (t0) cc_final: 0.8317 (t0) REVERT: E 71 HIS cc_start: 0.8202 (t70) cc_final: 0.7584 (t70) REVERT: E 123 TYR cc_start: 0.8965 (t80) cc_final: 0.8504 (t80) REVERT: E 145 LEU cc_start: 0.9056 (tp) cc_final: 0.8846 (tp) REVERT: E 164 PHE cc_start: 0.8701 (m-80) cc_final: 0.8342 (m-80) REVERT: E 216 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7662 (tpp80) REVERT: E 398 LYS cc_start: 0.9169 (tptt) cc_final: 0.8885 (tptt) REVERT: E 498 GLN cc_start: 0.7974 (tt0) cc_final: 0.7535 (mt0) REVERT: E 524 VAL cc_start: 0.8366 (t) cc_final: 0.8092 (t) REVERT: E 527 ARG cc_start: 0.8938 (ttm110) cc_final: 0.7864 (mtm110) REVERT: E 577 PHE cc_start: 0.8719 (m-80) cc_final: 0.8453 (m-80) REVERT: E 614 LEU cc_start: 0.7772 (tp) cc_final: 0.7320 (tp) REVERT: E 685 PHE cc_start: 0.6434 (m-10) cc_final: 0.6049 (t80) REVERT: E 772 TYR cc_start: 0.8658 (t80) cc_final: 0.8248 (t80) REVERT: E 781 ASN cc_start: 0.8235 (p0) cc_final: 0.7865 (p0) REVERT: E 797 GLN cc_start: 0.8507 (pt0) cc_final: 0.7980 (pm20) REVERT: E 911 GLU cc_start: 0.7129 (pt0) cc_final: 0.4823 (tm-30) REVERT: E 1025 MET cc_start: 0.7168 (mmm) cc_final: 0.6893 (mmp) REVERT: E 1080 LEU cc_start: 0.9267 (tp) cc_final: 0.9029 (tp) REVERT: E 1088 TRP cc_start: 0.8122 (t-100) cc_final: 0.7774 (t60) REVERT: E 1138 SER cc_start: 0.8915 (t) cc_final: 0.8458 (t) REVERT: E 1225 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8579 (tm-30) REVERT: E 1269 SER cc_start: 0.8876 (t) cc_final: 0.8558 (p) REVERT: E 1277 SER cc_start: 0.8623 (m) cc_final: 0.8201 (t) REVERT: B 78 SER cc_start: 0.9162 (p) cc_final: 0.8825 (p) REVERT: B 83 TRP cc_start: 0.9120 (m-10) cc_final: 0.8722 (m-10) REVERT: B 95 PHE cc_start: 0.9017 (t80) cc_final: 0.8800 (t80) REVERT: B 123 PHE cc_start: 0.8946 (t80) cc_final: 0.8571 (t80) REVERT: B 216 HIS cc_start: 0.8139 (m-70) cc_final: 0.7832 (m-70) REVERT: B 254 PRO cc_start: 0.9647 (Cg_exo) cc_final: 0.9335 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8560 (t70) cc_final: 0.8273 (t-170) REVERT: B 313 GLN cc_start: 0.8160 (mt0) cc_final: 0.7403 (tp40) REVERT: B 338 LYS cc_start: 0.9256 (tttm) cc_final: 0.8889 (ttmt) REVERT: C 90 TRP cc_start: 0.8953 (m100) cc_final: 0.8710 (m100) REVERT: C 146 ILE cc_start: 0.9552 (mt) cc_final: 0.9311 (mt) REVERT: C 215 ILE cc_start: 0.9234 (mm) cc_final: 0.8913 (mm) REVERT: C 242 ASN cc_start: 0.8809 (m110) cc_final: 0.8555 (m110) REVERT: C 258 TYR cc_start: 0.8671 (p90) cc_final: 0.8017 (p90) REVERT: C 309 ILE cc_start: 0.9455 (mm) cc_final: 0.9231 (mm) REVERT: D 77 MET cc_start: 0.8624 (mmm) cc_final: 0.7982 (mtp) REVERT: D 181 LEU cc_start: 0.9268 (mm) cc_final: 0.9057 (mm) REVERT: D 216 HIS cc_start: 0.8445 (m-70) cc_final: 0.8063 (m170) REVERT: D 234 HIS cc_start: 0.8543 (t70) cc_final: 0.7661 (t70) REVERT: D 273 SER cc_start: 0.9505 (m) cc_final: 0.8806 (t) REVERT: D 274 ASP cc_start: 0.8305 (t70) cc_final: 0.7791 (t0) outliers start: 2 outliers final: 1 residues processed: 879 average time/residue: 0.2745 time to fit residues: 383.3364 Evaluate side-chains 839 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 838 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 40.0000 chunk 258 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 166 optimal weight: 50.0000 chunk 132 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 299 GLN E 32 ASN ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS E 262 ASN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN ** E 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 HIS B 46 HIS C 128 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 19884 Z= 0.333 Angle : 0.629 13.156 27234 Z= 0.328 Chirality : 0.045 0.168 3342 Planarity : 0.004 0.048 3400 Dihedral : 11.118 105.327 3308 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2729 helix: 1.91 (0.14), residues: 1296 sheet: -1.38 (0.31), residues: 260 loop : -1.13 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 778 HIS 0.007 0.001 HIS D 259 PHE 0.033 0.002 PHE C 168 TYR 0.019 0.002 TYR A 258 ARG 0.009 0.001 ARG E 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 867 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8413 (t) cc_final: 0.8156 (p) REVERT: A 90 TRP cc_start: 0.9067 (m100) cc_final: 0.6388 (m100) REVERT: A 91 TRP cc_start: 0.9183 (t60) cc_final: 0.8672 (t60) REVERT: A 92 LEU cc_start: 0.9434 (tt) cc_final: 0.9081 (tt) REVERT: A 110 CYS cc_start: 0.6399 (m) cc_final: 0.6083 (m) REVERT: A 130 THR cc_start: 0.9429 (p) cc_final: 0.9228 (p) REVERT: A 183 PHE cc_start: 0.8944 (m-80) cc_final: 0.8607 (m-80) REVERT: A 248 SER cc_start: 0.8400 (p) cc_final: 0.8154 (p) REVERT: A 299 GLN cc_start: 0.9200 (tt0) cc_final: 0.8957 (tt0) REVERT: A 301 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8161 (mtm-85) REVERT: E 24 ASN cc_start: 0.8693 (t0) cc_final: 0.8438 (t0) REVERT: E 71 HIS cc_start: 0.8354 (t70) cc_final: 0.7397 (t-170) REVERT: E 104 LEU cc_start: 0.9048 (tp) cc_final: 0.8807 (tp) REVERT: E 123 TYR cc_start: 0.9001 (t80) cc_final: 0.8742 (t80) REVERT: E 164 PHE cc_start: 0.8703 (m-80) cc_final: 0.8358 (m-80) REVERT: E 216 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7624 (tpp80) REVERT: E 267 CYS cc_start: 0.8571 (t) cc_final: 0.8367 (t) REVERT: E 479 THR cc_start: 0.8131 (m) cc_final: 0.7634 (m) REVERT: E 495 ARG cc_start: 0.7519 (tmm160) cc_final: 0.7310 (tmm160) REVERT: E 498 GLN cc_start: 0.8020 (tt0) cc_final: 0.7603 (mt0) REVERT: E 527 ARG cc_start: 0.8945 (ttm110) cc_final: 0.8257 (mtm110) REVERT: E 577 PHE cc_start: 0.8682 (m-80) cc_final: 0.8283 (m-80) REVERT: E 685 PHE cc_start: 0.6572 (m-10) cc_final: 0.6138 (t80) REVERT: E 772 TYR cc_start: 0.8791 (t80) cc_final: 0.8381 (t80) REVERT: E 781 ASN cc_start: 0.8369 (p0) cc_final: 0.8044 (p0) REVERT: E 797 GLN cc_start: 0.8576 (pt0) cc_final: 0.8020 (pm20) REVERT: E 911 GLU cc_start: 0.7148 (pt0) cc_final: 0.4816 (tm-30) REVERT: E 1025 MET cc_start: 0.7222 (mmm) cc_final: 0.6951 (mmp) REVERT: E 1080 LEU cc_start: 0.9265 (tp) cc_final: 0.9033 (tp) REVERT: E 1088 TRP cc_start: 0.8176 (t-100) cc_final: 0.7819 (t60) REVERT: E 1138 SER cc_start: 0.9029 (t) cc_final: 0.8544 (t) REVERT: E 1207 THR cc_start: 0.8770 (m) cc_final: 0.8347 (m) REVERT: E 1225 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8598 (tm-30) REVERT: E 1269 SER cc_start: 0.8931 (t) cc_final: 0.8512 (p) REVERT: E 1277 SER cc_start: 0.8759 (m) cc_final: 0.8246 (t) REVERT: B 71 THR cc_start: 0.9222 (m) cc_final: 0.8980 (m) REVERT: B 78 SER cc_start: 0.9155 (p) cc_final: 0.8780 (p) REVERT: B 83 TRP cc_start: 0.9245 (m-10) cc_final: 0.8813 (m-10) REVERT: B 158 MET cc_start: 0.9051 (mmp) cc_final: 0.8745 (mmp) REVERT: B 216 HIS cc_start: 0.8169 (m-70) cc_final: 0.7894 (m-70) REVERT: B 277 HIS cc_start: 0.8618 (t70) cc_final: 0.8292 (t-170) REVERT: B 313 GLN cc_start: 0.8116 (mt0) cc_final: 0.7573 (tt0) REVERT: B 338 LYS cc_start: 0.9266 (tttm) cc_final: 0.8915 (ttmt) REVERT: C 34 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7462 (tpp-160) REVERT: C 90 TRP cc_start: 0.8975 (m100) cc_final: 0.8721 (m100) REVERT: C 215 ILE cc_start: 0.9289 (mm) cc_final: 0.8964 (mm) REVERT: C 258 TYR cc_start: 0.8707 (p90) cc_final: 0.7996 (p90) REVERT: C 261 ILE cc_start: 0.9370 (mt) cc_final: 0.9168 (mt) REVERT: C 333 PHE cc_start: 0.8960 (t80) cc_final: 0.8595 (t80) REVERT: D 77 MET cc_start: 0.8615 (mmm) cc_final: 0.7991 (mtp) REVERT: D 157 LEU cc_start: 0.8219 (tt) cc_final: 0.8000 (tt) REVERT: D 216 HIS cc_start: 0.8446 (m-70) cc_final: 0.8047 (m170) REVERT: D 234 HIS cc_start: 0.8525 (t70) cc_final: 0.7762 (t70) REVERT: D 273 SER cc_start: 0.9535 (m) cc_final: 0.8854 (t) REVERT: D 274 ASP cc_start: 0.8387 (t70) cc_final: 0.7872 (t0) outliers start: 1 outliers final: 1 residues processed: 867 average time/residue: 0.2814 time to fit residues: 388.7385 Evaluate side-chains 815 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 814 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 50.0000 chunk 229 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN E 32 ASN ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS E 262 ASN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS C 128 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.167357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.137610 restraints weight = 28808.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.138249 restraints weight = 20022.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139307 restraints weight = 14419.922| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 19884 Z= 0.366 Angle : 0.647 13.996 27234 Z= 0.338 Chirality : 0.046 0.268 3342 Planarity : 0.004 0.049 3400 Dihedral : 11.248 105.157 3308 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.06 % Allowed : 0.63 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2729 helix: 1.76 (0.14), residues: 1295 sheet: -1.42 (0.32), residues: 242 loop : -1.15 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 232 HIS 0.012 0.001 HIS E 326 PHE 0.035 0.002 PHE D 168 TYR 0.019 0.002 TYR A 258 ARG 0.010 0.001 ARG E 168 =============================================================================== Job complete usr+sys time: 6058.01 seconds wall clock time: 108 minutes 53.21 seconds (6533.21 seconds total)