Starting phenix.real_space_refine on Tue Sep 24 12:51:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/09_2024/5yw8_6848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/09_2024/5yw8_6848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/09_2024/5yw8_6848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/09_2024/5yw8_6848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/09_2024/5yw8_6848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/09_2024/5yw8_6848.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 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 24 5.49 5 S 272 5.16 5 C 32848 2.51 5 N 8540 2.21 5 O 8840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50524 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "F" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "G" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "H" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.13, per 1000 atoms: 0.42 Number of scatterers: 50524 At special positions: 0 Unit cell: (210.38, 210.38, 143.38, 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 272 16.00 P 24 15.00 O 8840 8.00 N 8540 7.00 C 32848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.76 Conformation dependent library (CDL) restraints added in 4.8 seconds 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12312 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 40 sheets defined 64.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.631A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.902A pdb=" N LEU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 270 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'B' and resid 25 through 52 Proline residue: B 35 - end of helix removed outlier: 3.941A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 70 through 96 Processing helix chain 'B' and resid 104 through 130 Proline residue: B 109 - end of helix removed outlier: 3.757A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 423 through 457 Proline residue: B 436 - end of helix removed outlier: 3.536A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.595A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 4.017A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 560 removed outlier: 3.654A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.446A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 783 through 790 Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 808 through 815 removed outlier: 3.578A pdb=" N LEU B 815 " --> pdb=" O ASP B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 846 removed outlier: 3.541A pdb=" N GLN B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 893 through 897 removed outlier: 3.651A pdb=" N ALA B 897 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS B1001 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP B1039 " --> pdb=" O ALA B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU B1107 " --> pdb=" O ASN B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1117 through 1127 removed outlier: 3.829A pdb=" N ILE B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1161 Proline residue: B1137 - end of helix Processing helix chain 'B' and resid 1161 through 1210 removed outlier: 4.302A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.525A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1218 Processing helix chain 'B' and resid 1219 through 1271 removed outlier: 3.723A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1278 through 1289 removed outlier: 4.012A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR B1294 " --> pdb=" O MET B1290 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1393 Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1435 through 1441 Processing helix chain 'B' and resid 1447 through 1458 Processing helix chain 'B' and resid 1460 through 1466 Processing helix chain 'B' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS B1499 " --> pdb=" O ALA B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1539 through 1546 removed outlier: 3.675A pdb=" N ILE B1543 " --> pdb=" O ARG B1539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B1546 " --> pdb=" O THR B1542 " (cutoff:3.500A) Processing helix chain 'B' and resid 1562 through 1570 removed outlier: 4.307A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B1570 " --> pdb=" O LEU B1566 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 removed outlier: 3.613A pdb=" N GLY C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.902A pdb=" N LEU C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 270 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'D' and resid 25 through 52 Proline residue: D 35 - end of helix removed outlier: 3.941A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 70 through 96 Processing helix chain 'D' and resid 104 through 130 Proline residue: D 109 - end of helix removed outlier: 3.757A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 355 through 402 removed outlier: 3.631A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 423 through 457 Proline residue: D 436 - end of helix removed outlier: 3.535A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.595A pdb=" N GLU D 501 " --> pdb=" O LYS D 497 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 4.017A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Proline residue: D 551 - end of helix removed outlier: 3.554A pdb=" N VAL D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) Proline residue: D 589 - end of helix removed outlier: 4.446A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 783 through 790 Processing helix chain 'D' and resid 796 through 806 Processing helix chain 'D' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU D 815 " --> pdb=" O ASP D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 846 removed outlier: 3.542A pdb=" N GLN D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 872 Processing helix chain 'D' and resid 893 through 897 removed outlier: 3.651A pdb=" N ALA D 897 " --> pdb=" O LEU D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS D1001 " --> pdb=" O PRO D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1039 removed outlier: 3.531A pdb=" N LEU D1013 " --> pdb=" O GLY D1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D1031 " --> pdb=" O LEU D1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP D1039 " --> pdb=" O ALA D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1116 Processing helix chain 'D' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE D1121 " --> pdb=" O PRO D1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1161 Proline residue: D1137 - end of helix Processing helix chain 'D' and resid 1161 through 1210 removed outlier: 4.301A pdb=" N VAL D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.539A pdb=" N PHE D1177 " --> pdb=" O VAL D1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D1181 " --> pdb=" O PHE D1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP D1188 " --> pdb=" O VAL D1184 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 3.525A pdb=" N GLY D1210 " --> pdb=" O GLU D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1218 Processing helix chain 'D' and resid 1219 through 1271 removed outlier: 3.723A pdb=" N ALA D1237 " --> pdb=" O SER D1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D1269 " --> pdb=" O ALA D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1278 through 1289 removed outlier: 4.012A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR D1294 " --> pdb=" O MET D1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1384 through 1393 Processing helix chain 'D' and resid 1414 through 1420 Processing helix chain 'D' and resid 1435 through 1441 Processing helix chain 'D' and resid 1447 through 1458 Processing helix chain 'D' and resid 1460 through 1466 Processing helix chain 'D' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS D1499 " --> pdb=" O ALA D1495 " (cutoff:3.500A) Processing helix chain 'D' and resid 1513 through 1528 removed outlier: 4.095A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1539 through 1546 removed outlier: 3.676A pdb=" N ILE D1543 " --> pdb=" O ARG D1539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D1546 " --> pdb=" O THR D1542 " (cutoff:3.500A) Processing helix chain 'D' and resid 1562 through 1570 removed outlier: 3.500A pdb=" N LEU D1567 " --> pdb=" O PRO D1563 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER D1568 " --> pdb=" O GLU D1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS D1570 " --> pdb=" O LEU D1566 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 58 through 64 removed outlier: 3.631A pdb=" N LEU E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 98 removed outlier: 3.615A pdb=" N GLY E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.901A pdb=" N LEU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 270 " --> pdb=" O LEU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 356 Processing helix chain 'F' and resid 25 through 52 Proline residue: F 35 - end of helix removed outlier: 3.941A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 70 through 96 Processing helix chain 'F' and resid 104 through 130 Proline residue: F 109 - end of helix removed outlier: 3.758A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.251A pdb=" N PHE F 236 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 423 through 457 Proline residue: F 436 - end of helix removed outlier: 3.536A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.595A pdb=" N GLU F 501 " --> pdb=" O LYS F 497 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 512 removed outlier: 4.017A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 548 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.554A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA F 576 " --> pdb=" O SER F 572 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 4.446A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 783 through 790 Processing helix chain 'F' and resid 796 through 806 Processing helix chain 'F' and resid 808 through 815 removed outlier: 3.578A pdb=" N LEU F 815 " --> pdb=" O ASP F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 846 removed outlier: 3.542A pdb=" N GLN F 846 " --> pdb=" O ARG F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 872 Processing helix chain 'F' and resid 893 through 897 removed outlier: 3.652A pdb=" N ALA F 897 " --> pdb=" O LEU F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 919 Processing helix chain 'F' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS F1001 " --> pdb=" O PRO F 997 " (cutoff:3.500A) Processing helix chain 'F' and resid 1009 through 1039 removed outlier: 3.531A pdb=" N LEU F1013 " --> pdb=" O GLY F1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER F1019 " --> pdb=" O LEU F1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP F1039 " --> pdb=" O ALA F1035 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU F1107 " --> pdb=" O ASN F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1116 Processing helix chain 'F' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE F1121 " --> pdb=" O PRO F1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1161 Proline residue: F1137 - end of helix Processing helix chain 'F' and resid 1161 through 1210 removed outlier: 4.301A pdb=" N VAL F1166 " --> pdb=" O PRO F1162 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.539A pdb=" N PHE F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F1181 " --> pdb=" O PHE F1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP F1188 " --> pdb=" O VAL F1184 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.526A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1210 through 1218 Processing helix chain 'F' and resid 1219 through 1271 removed outlier: 3.724A pdb=" N ALA F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR F1242 " --> pdb=" O SER F1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F1260 " --> pdb=" O GLY F1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER F1269 " --> pdb=" O ALA F1265 " (cutoff:3.500A) Processing helix chain 'F' and resid 1278 through 1289 removed outlier: 4.011A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR F1294 " --> pdb=" O MET F1290 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'F' and resid 1384 through 1393 Processing helix chain 'F' and resid 1414 through 1420 Processing helix chain 'F' and resid 1435 through 1441 Processing helix chain 'F' and resid 1447 through 1458 Processing helix chain 'F' and resid 1460 through 1466 Processing helix chain 'F' and resid 1483 through 1499 removed outlier: 3.857A pdb=" N LYS F1499 " --> pdb=" O ALA F1495 " (cutoff:3.500A) Processing helix chain 'F' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1539 through 1546 removed outlier: 3.675A pdb=" N ILE F1543 " --> pdb=" O ARG F1539 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F1546 " --> pdb=" O THR F1542 " (cutoff:3.500A) Processing helix chain 'F' and resid 1562 through 1570 removed outlier: 3.500A pdb=" N LEU F1567 " --> pdb=" O PRO F1563 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F1568 " --> pdb=" O GLU F1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS F1570 " --> pdb=" O LEU F1566 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 Processing helix chain 'G' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL G 129 " --> pdb=" O ILE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE G 146 " --> pdb=" O CYS G 142 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 181 removed outlier: 3.901A pdb=" N LEU G 181 " --> pdb=" O ARG G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 270 " --> pdb=" O LEU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 356 Processing helix chain 'H' and resid 25 through 52 Proline residue: H 35 - end of helix removed outlier: 3.941A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 70 through 96 Processing helix chain 'H' and resid 104 through 130 Proline residue: H 109 - end of helix removed outlier: 3.757A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE H 137 " --> pdb=" O PRO H 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG H 193 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 212 Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN H 262 " --> pdb=" O ARG H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 329 removed outlier: 6.308A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU H 402 " --> pdb=" O LYS H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 423 Processing helix chain 'H' and resid 423 through 457 Proline residue: H 436 - end of helix removed outlier: 3.536A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.595A pdb=" N GLU H 501 " --> pdb=" O LYS H 497 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 560 removed outlier: 3.654A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.553A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA H 576 " --> pdb=" O SER H 572 " (cutoff:3.500A) Proline residue: H 589 - end of helix removed outlier: 4.446A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 727 Processing helix chain 'H' and resid 783 through 790 Processing helix chain 'H' and resid 796 through 806 Processing helix chain 'H' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU H 815 " --> pdb=" O ASP H 811 " (cutoff:3.500A) Processing helix chain 'H' and resid 831 through 846 removed outlier: 3.542A pdb=" N GLN H 846 " --> pdb=" O ARG H 842 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 872 Processing helix chain 'H' and resid 893 through 897 removed outlier: 3.651A pdb=" N ALA H 897 " --> pdb=" O LEU H 894 " (cutoff:3.500A) Processing helix chain 'H' and resid 914 through 919 Processing helix chain 'H' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS H1001 " --> pdb=" O PRO H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU H1013 " --> pdb=" O GLY H1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER H1019 " --> pdb=" O LEU H1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP H1039 " --> pdb=" O ALA H1035 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU H1107 " --> pdb=" O ASN H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1116 Processing helix chain 'H' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE H1121 " --> pdb=" O PRO H1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1127 through 1161 Proline residue: H1137 - end of helix Processing helix chain 'H' and resid 1161 through 1210 removed outlier: 4.301A pdb=" N VAL H1166 " --> pdb=" O PRO H1162 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.539A pdb=" N PHE H1177 " --> pdb=" O VAL H1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H1181 " --> pdb=" O PHE H1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP H1188 " --> pdb=" O VAL H1184 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.525A pdb=" N GLY H1210 " --> pdb=" O GLU H1206 " (cutoff:3.500A) Processing helix chain 'H' and resid 1210 through 1218 Processing helix chain 'H' and resid 1219 through 1271 removed outlier: 3.723A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL H1260 " --> pdb=" O GLY H1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H1269 " --> pdb=" O ALA H1265 " (cutoff:3.500A) Processing helix chain 'H' and resid 1278 through 1289 removed outlier: 4.012A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) Processing helix chain 'H' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR H1294 " --> pdb=" O MET H1290 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE H1315 " --> pdb=" O ALA H1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H1316 " --> pdb=" O VAL H1312 " (cutoff:3.500A) Processing helix chain 'H' and resid 1384 through 1393 Processing helix chain 'H' and resid 1414 through 1420 Processing helix chain 'H' and resid 1435 through 1441 Processing helix chain 'H' and resid 1447 through 1458 Processing helix chain 'H' and resid 1460 through 1466 Processing helix chain 'H' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS H1499 " --> pdb=" O ALA H1495 " (cutoff:3.500A) Processing helix chain 'H' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1539 through 1546 removed outlier: 3.675A pdb=" N ILE H1543 " --> pdb=" O ARG H1539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA H1546 " --> pdb=" O THR H1542 " (cutoff:3.500A) Processing helix chain 'H' and resid 1562 through 1570 removed outlier: 4.307A pdb=" N SER H1568 " --> pdb=" O GLU H1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS H1570 " --> pdb=" O LEU H1566 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.727A pdb=" N VAL C 328 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS A 259 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 200 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.012A pdb=" N TYR A 326 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS G 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL A 328 " --> pdb=" O LYS G 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AA8, first strand: chain 'B' and resid 685 through 686 Processing sheet with id=AA9, first strand: chain 'B' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL B 851 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 887 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 853 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA B1367 " --> pdb=" O GLN B1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN B1348 " --> pdb=" O ALA B1367 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE B1369 " --> pdb=" O GLN B1346 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN B1346 " --> pdb=" O ILE B1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE B1347 " --> pdb=" O ILE B1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B1404 " --> pdb=" O ILE B1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN B1349 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG B1402 " --> pdb=" O ASN B1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.727A pdb=" N VAL E 328 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.782A pdb=" N HIS C 259 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 200 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 213 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU C 288 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 215 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 286 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET C 217 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 284 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL C 219 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU C 282 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AB7, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB8, first strand: chain 'D' and resid 701 through 703 Processing sheet with id=AB9, first strand: chain 'D' and resid 685 through 686 Processing sheet with id=AC1, first strand: chain 'D' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 851 " --> pdb=" O VAL D 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL D 887 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU D 853 " --> pdb=" O VAL D 887 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE D 900 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU D 911 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA D 902 " --> pdb=" O GLN D 909 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA D1367 " --> pdb=" O GLN D1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN D1348 " --> pdb=" O ALA D1367 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE D1369 " --> pdb=" O GLN D1346 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN D1346 " --> pdb=" O ILE D1369 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE D1347 " --> pdb=" O ILE D1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE D1404 " --> pdb=" O ILE D1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN D1349 " --> pdb=" O ARG D1402 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG D1402 " --> pdb=" O ASN D1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D1398 " --> pdb=" O ARG D1353 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER D1423 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP D1506 " --> pdb=" O SER D1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D1425 " --> pdb=" O ASP D1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D1503 " --> pdb=" O VAL D1534 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE D1536 " --> pdb=" O PHE D1503 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET D1505 " --> pdb=" O ILE D1536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D1550 " --> pdb=" O GLY D1376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.727A pdb=" N VAL G 328 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS E 259 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 200 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET E 217 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 213 " --> pdb=" O GLU E 288 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU E 288 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE E 215 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE E 286 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET E 217 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE E 284 " --> pdb=" O MET E 217 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL E 219 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU E 282 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 223 through 224 Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC9, first strand: chain 'F' and resid 701 through 703 Processing sheet with id=AD1, first strand: chain 'F' and resid 685 through 686 Processing sheet with id=AD2, first strand: chain 'F' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL F 851 " --> pdb=" O VAL F 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL F 887 " --> pdb=" O VAL F 851 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU F 853 " --> pdb=" O VAL F 887 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA F1367 " --> pdb=" O GLN F1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN F1348 " --> pdb=" O ALA F1367 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE F1369 " --> pdb=" O GLN F1346 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN F1346 " --> pdb=" O ILE F1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE F1347 " --> pdb=" O ILE F1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE F1404 " --> pdb=" O ILE F1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN F1349 " --> pdb=" O ARG F1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG F1402 " --> pdb=" O ASN F1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F1398 " --> pdb=" O ARG F1353 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER F1423 " --> pdb=" O ILE F1504 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP F1506 " --> pdb=" O SER F1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE F1425 " --> pdb=" O ASP F1506 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE F1503 " --> pdb=" O VAL F1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE F1536 " --> pdb=" O PHE F1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET F1505 " --> pdb=" O ILE F1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET F1550 " --> pdb=" O GLY F1376 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS G 259 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 200 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET G 217 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA G 213 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU G 288 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE G 215 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE G 286 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N MET G 217 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE G 284 " --> pdb=" O MET G 217 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL G 219 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU G 282 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 223 through 224 Processing sheet with id=AD8, first strand: chain 'G' and resid 313 through 315 Processing sheet with id=AD9, first strand: chain 'H' and resid 701 through 703 Processing sheet with id=AE1, first strand: chain 'H' and resid 685 through 686 Processing sheet with id=AE2, first strand: chain 'H' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL H 851 " --> pdb=" O VAL H 885 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL H 887 " --> pdb=" O VAL H 851 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU H 853 " --> pdb=" O VAL H 887 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 1365 through 1369 removed outlier: 7.091A pdb=" N ALA H1367 " --> pdb=" O GLN H1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN H1348 " --> pdb=" O ALA H1367 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE H1369 " --> pdb=" O GLN H1346 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN H1346 " --> pdb=" O ILE H1369 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE H1347 " --> pdb=" O ILE H1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE H1404 " --> pdb=" O ILE H1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN H1349 " --> pdb=" O ARG H1402 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG H1402 " --> pdb=" O ASN H1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET H1398 " --> pdb=" O ARG H1353 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER H1423 " --> pdb=" O ILE H1504 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP H1506 " --> pdb=" O SER H1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE H1425 " --> pdb=" O ASP H1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE H1503 " --> pdb=" O VAL H1534 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET H1550 " --> pdb=" O GLY H1376 " (cutoff:3.500A) 3132 hydrogen bonds defined for protein. 9195 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: 17.67 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 20094 1.39 - 1.58: 31022 1.58 - 1.76: 32 1.76 - 1.94: 420 1.94 - 2.12: 8 Bond restraints: 51576 Sorted by residual: bond pdb=" PG AGS A 401 " pdb=" S1G AGS A 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS G 401 " pdb=" S1G AGS G 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS E 401 " pdb=" S1G AGS E 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS C 401 " pdb=" S1G AGS C 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C4 AGS F2501 " pdb=" C5 AGS F2501 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.26e+01 ... (remaining 51571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 68512 2.31 - 4.62: 1365 4.62 - 6.92: 215 6.92 - 9.23: 52 9.23 - 11.54: 28 Bond angle restraints: 70172 Sorted by residual: angle pdb=" C5 AGS F2501 " pdb=" C4 AGS F2501 " pdb=" N3 AGS F2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS D2501 " pdb=" C4 AGS D2501 " pdb=" N3 AGS D2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS B2501 " pdb=" C4 AGS B2501 " pdb=" N3 AGS B2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS H2501 " pdb=" C4 AGS H2501 " pdb=" N3 AGS H2501 " ideal model delta sigma weight residual 126.80 118.61 8.19 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS G 401 " pdb=" C4 AGS G 401 " pdb=" N3 AGS G 401 " ideal model delta sigma weight residual 126.80 119.10 7.70 7.41e-01 1.82e+00 1.08e+02 ... (remaining 70167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 29654 31.24 - 62.49: 918 62.49 - 93.73: 12 93.73 - 124.97: 8 124.97 - 156.22: 4 Dihedral angle restraints: 30596 sinusoidal: 11668 harmonic: 18928 Sorted by residual: dihedral pdb=" CA ASP B 212 " pdb=" C ASP B 212 " pdb=" N LEU B 213 " pdb=" CA LEU B 213 " ideal model delta harmonic sigma weight residual -180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ASP H 212 " pdb=" C ASP H 212 " pdb=" N LEU H 213 " pdb=" CA LEU H 213 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP D 212 " pdb=" C ASP D 212 " pdb=" N LEU D 213 " pdb=" CA LEU D 213 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 30593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 8424 0.158 - 0.316: 72 0.316 - 0.474: 16 0.474 - 0.632: 0 0.632 - 0.790: 4 Chirality restraints: 8516 Sorted by residual: chirality pdb=" PB AGS A 401 " pdb=" O2B AGS A 401 " pdb=" O3A AGS A 401 " pdb=" O3B AGS A 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PB AGS C 401 " pdb=" O2B AGS C 401 " pdb=" O3A AGS C 401 " pdb=" O3B AGS C 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PB AGS G 401 " pdb=" O2B AGS G 401 " pdb=" O3A AGS G 401 " pdb=" O3B AGS G 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 8513 not shown) Planarity restraints: 8588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F1273 " 0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C HIS F1273 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS F1273 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG F1274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D1273 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C HIS D1273 " -0.070 2.00e-02 2.50e+03 pdb=" O HIS D1273 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG D1274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H1273 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C HIS H1273 " 0.070 2.00e-02 2.50e+03 pdb=" O HIS H1273 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG H1274 " -0.023 2.00e-02 2.50e+03 ... (remaining 8585 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 468 2.60 - 3.18: 45550 3.18 - 3.75: 79780 3.75 - 4.33: 102235 4.33 - 4.90: 167732 Nonbonded interactions: 395765 Sorted by model distance: nonbonded pdb=" O ILE B 196 " pdb=" O PHE B 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE D 196 " pdb=" O PHE D 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE F 196 " pdb=" O PHE F 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE H 196 " pdb=" O PHE H 197 " model vdw 2.030 3.040 nonbonded pdb=" CD1 LEU C 200 " pdb=" N ARG C 201 " model vdw 2.049 3.540 ... (remaining 395760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 0.550 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: 0.030 Extract box with map and model: 1.370 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 85.500 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.173 51576 Z= 0.350 Angle : 0.804 11.538 70172 Z= 0.504 Chirality : 0.052 0.790 8516 Planarity : 0.005 0.074 8588 Dihedral : 13.785 156.217 18272 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.43 % Favored : 95.13 % Rotamer: Outliers : 8.11 % Allowed : 9.38 % Favored : 82.51 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.09), residues: 6408 helix: -1.03 (0.07), residues: 3948 sheet: -1.58 (0.20), residues: 536 loop : -2.64 (0.12), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D1339 HIS 0.012 0.001 HIS C 175 PHE 0.035 0.002 PHE G 168 TYR 0.015 0.002 TYR B 378 ARG 0.003 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1576 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1140 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 77 MET cc_start: 0.8703 (mmt) cc_final: 0.8378 (tpt) REVERT: A 78 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 81 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (p) REVERT: A 88 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8642 (tmm) REVERT: A 92 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9405 (tt) REVERT: A 95 PHE cc_start: 0.8860 (t80) cc_final: 0.8646 (t80) REVERT: A 163 MET cc_start: 0.7818 (ttp) cc_final: 0.7241 (ttt) REVERT: A 182 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7684 (pt) REVERT: A 204 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 238 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.6990 (tt) REVERT: A 286 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.3925 (tt) REVERT: A 293 THR cc_start: 0.5405 (OUTLIER) cc_final: 0.5182 (t) REVERT: A 332 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7529 (mtmm) REVERT: B 89 ILE cc_start: 0.9164 (mt) cc_final: 0.8844 (mm) REVERT: B 91 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8175 (tm-30) REVERT: B 135 LEU cc_start: 0.8255 (mt) cc_final: 0.7834 (mt) REVERT: B 175 LEU cc_start: 0.9072 (mt) cc_final: 0.8698 (tt) REVERT: B 233 MET cc_start: 0.9398 (mmm) cc_final: 0.8902 (mmm) REVERT: B 253 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 319 CYS cc_start: 0.9056 (m) cc_final: 0.8748 (p) REVERT: B 327 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8403 (tt) REVERT: B 432 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9116 (t80) REVERT: B 710 MET cc_start: 0.6727 (mmt) cc_final: 0.6047 (tpp) REVERT: B 727 LEU cc_start: 0.7894 (tp) cc_final: 0.7488 (mt) REVERT: B 1020 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8370 (mp10) REVERT: B 1031 ASP cc_start: 0.8228 (m-30) cc_final: 0.7388 (t0) REVERT: B 1246 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8401 (mmp80) REVERT: B 1251 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8492 (mmt180) REVERT: B 1252 MET cc_start: 0.8900 (ttm) cc_final: 0.8476 (tpp) REVERT: B 1432 PHE cc_start: 0.2989 (OUTLIER) cc_final: 0.2234 (p90) REVERT: B 1536 ILE cc_start: 0.0379 (OUTLIER) cc_final: -0.0020 (pt) REVERT: B 1561 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6337 (t0) REVERT: B 1566 LEU cc_start: 0.1664 (OUTLIER) cc_final: 0.1152 (pt) REVERT: C 74 ILE cc_start: 0.9432 (tt) cc_final: 0.9227 (tt) REVERT: C 77 MET cc_start: 0.8697 (mmt) cc_final: 0.8377 (tpt) REVERT: C 78 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 81 CYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7678 (p) REVERT: C 88 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8647 (tmm) REVERT: C 92 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9409 (tt) REVERT: C 95 PHE cc_start: 0.8870 (t80) cc_final: 0.8659 (t80) REVERT: C 122 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (tt) REVERT: C 163 MET cc_start: 0.7894 (ttp) cc_final: 0.7240 (ttt) REVERT: C 182 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7690 (pt) REVERT: C 204 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7733 (t0) REVERT: C 238 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.6978 (tt) REVERT: C 286 ILE cc_start: 0.4390 (OUTLIER) cc_final: 0.3740 (tt) REVERT: C 293 THR cc_start: 0.5385 (OUTLIER) cc_final: 0.5156 (t) REVERT: C 332 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7599 (mtmm) REVERT: D 89 ILE cc_start: 0.9121 (mt) cc_final: 0.8785 (mm) REVERT: D 91 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8189 (tm-30) REVERT: D 126 ASN cc_start: 0.8361 (m-40) cc_final: 0.7919 (t0) REVERT: D 135 LEU cc_start: 0.8266 (mt) cc_final: 0.7785 (mt) REVERT: D 175 LEU cc_start: 0.9070 (mt) cc_final: 0.8700 (tt) REVERT: D 233 MET cc_start: 0.9401 (mmm) cc_final: 0.8909 (mmm) REVERT: D 253 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8871 (mt) REVERT: D 319 CYS cc_start: 0.9067 (m) cc_final: 0.8750 (p) REVERT: D 327 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 432 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.9105 (t80) REVERT: D 710 MET cc_start: 0.6732 (mmt) cc_final: 0.6053 (tpp) REVERT: D 727 LEU cc_start: 0.7903 (tp) cc_final: 0.7495 (mt) REVERT: D 1020 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8366 (mp10) REVERT: D 1031 ASP cc_start: 0.8146 (m-30) cc_final: 0.7259 (t0) REVERT: D 1165 LEU cc_start: 0.8538 (tt) cc_final: 0.8297 (tt) REVERT: D 1246 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8464 (mmp80) REVERT: D 1251 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8488 (mmt180) REVERT: D 1252 MET cc_start: 0.8909 (ttm) cc_final: 0.8342 (tpp) REVERT: D 1432 PHE cc_start: 0.2940 (OUTLIER) cc_final: 0.2146 (p90) REVERT: D 1536 ILE cc_start: 0.0407 (OUTLIER) cc_final: -0.0008 (pt) REVERT: D 1561 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6353 (t0) REVERT: D 1566 LEU cc_start: 0.1848 (OUTLIER) cc_final: 0.1189 (pt) REVERT: E 74 ILE cc_start: 0.9437 (tt) cc_final: 0.9236 (tt) REVERT: E 77 MET cc_start: 0.8706 (mmt) cc_final: 0.8376 (tpt) REVERT: E 78 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8777 (p) REVERT: E 81 CYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7664 (p) REVERT: E 88 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8658 (tmm) REVERT: E 92 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9411 (tt) REVERT: E 95 PHE cc_start: 0.8867 (t80) cc_final: 0.8658 (t80) REVERT: E 122 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9034 (tt) REVERT: E 163 MET cc_start: 0.7874 (ttp) cc_final: 0.7375 (ttt) REVERT: E 182 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7732 (pt) REVERT: E 204 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7727 (t0) REVERT: E 238 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.6974 (tt) REVERT: E 286 ILE cc_start: 0.4402 (OUTLIER) cc_final: 0.3732 (tt) REVERT: E 293 THR cc_start: 0.5372 (OUTLIER) cc_final: 0.5162 (t) REVERT: E 332 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7877 (mtmm) REVERT: F 89 ILE cc_start: 0.9103 (mt) cc_final: 0.8756 (mm) REVERT: F 91 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8174 (tm-30) REVERT: F 135 LEU cc_start: 0.8271 (mt) cc_final: 0.7838 (mt) REVERT: F 175 LEU cc_start: 0.9077 (mt) cc_final: 0.8695 (tt) REVERT: F 233 MET cc_start: 0.9424 (mmm) cc_final: 0.8967 (mmm) REVERT: F 253 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8888 (mt) REVERT: F 319 CYS cc_start: 0.9065 (m) cc_final: 0.8742 (p) REVERT: F 327 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8414 (tt) REVERT: F 432 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (t80) REVERT: F 710 MET cc_start: 0.6729 (mmt) cc_final: 0.6046 (tpp) REVERT: F 727 LEU cc_start: 0.7888 (tp) cc_final: 0.7480 (mt) REVERT: F 1020 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8330 (mp10) REVERT: F 1031 ASP cc_start: 0.8206 (m-30) cc_final: 0.7377 (t0) REVERT: F 1165 LEU cc_start: 0.8539 (tt) cc_final: 0.8294 (tt) REVERT: F 1246 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8455 (mmp80) REVERT: F 1251 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8498 (mmt180) REVERT: F 1252 MET cc_start: 0.8901 (ttm) cc_final: 0.8410 (tpp) REVERT: F 1432 PHE cc_start: 0.2928 (OUTLIER) cc_final: 0.2137 (p90) REVERT: F 1536 ILE cc_start: 0.0414 (OUTLIER) cc_final: -0.0004 (pt) REVERT: F 1561 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6353 (t0) REVERT: F 1566 LEU cc_start: 0.2135 (OUTLIER) cc_final: 0.1464 (pt) REVERT: G 74 ILE cc_start: 0.9434 (tt) cc_final: 0.9233 (tt) REVERT: G 77 MET cc_start: 0.8714 (mmt) cc_final: 0.8373 (tpt) REVERT: G 78 SER cc_start: 0.9346 (OUTLIER) cc_final: 0.8770 (p) REVERT: G 81 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7653 (p) REVERT: G 88 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8635 (tmm) REVERT: G 92 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9406 (tt) REVERT: G 95 PHE cc_start: 0.8861 (t80) cc_final: 0.8643 (t80) REVERT: G 122 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9033 (tt) REVERT: G 163 MET cc_start: 0.7807 (ttp) cc_final: 0.7356 (ttt) REVERT: G 182 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7726 (pt) REVERT: G 204 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7741 (t0) REVERT: G 238 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.6964 (tt) REVERT: G 286 ILE cc_start: 0.4597 (OUTLIER) cc_final: 0.3908 (tt) REVERT: G 293 THR cc_start: 0.5367 (OUTLIER) cc_final: 0.5159 (t) REVERT: G 332 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7823 (mtmm) REVERT: H 89 ILE cc_start: 0.9171 (mt) cc_final: 0.8956 (mm) REVERT: H 91 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8159 (tm-30) REVERT: H 135 LEU cc_start: 0.8264 (mt) cc_final: 0.7825 (mt) REVERT: H 175 LEU cc_start: 0.9081 (mt) cc_final: 0.8698 (tt) REVERT: H 233 MET cc_start: 0.9402 (mmm) cc_final: 0.8907 (mmm) REVERT: H 253 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8889 (mt) REVERT: H 319 CYS cc_start: 0.9056 (m) cc_final: 0.8742 (p) REVERT: H 327 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8407 (tt) REVERT: H 710 MET cc_start: 0.6721 (mmt) cc_final: 0.6041 (tpp) REVERT: H 727 LEU cc_start: 0.7899 (tp) cc_final: 0.7488 (mt) REVERT: H 1020 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8341 (mp10) REVERT: H 1031 ASP cc_start: 0.8223 (m-30) cc_final: 0.7388 (t0) REVERT: H 1103 ASN cc_start: 0.8002 (m-40) cc_final: 0.7675 (m-40) REVERT: H 1165 LEU cc_start: 0.8539 (tt) cc_final: 0.8291 (tt) REVERT: H 1246 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8387 (mmp80) REVERT: H 1251 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8497 (mmt180) REVERT: H 1252 MET cc_start: 0.8892 (ttm) cc_final: 0.8409 (tpp) REVERT: H 1432 PHE cc_start: 0.2922 (OUTLIER) cc_final: 0.2133 (p90) REVERT: H 1536 ILE cc_start: 0.0558 (OUTLIER) cc_final: 0.0166 (pt) REVERT: H 1561 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6334 (t0) REVERT: H 1566 LEU cc_start: 0.2070 (OUTLIER) cc_final: 0.1411 (pt) outliers start: 436 outliers final: 58 residues processed: 1493 average time/residue: 0.4911 time to fit residues: 1228.4146 Evaluate side-chains 702 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 570 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 10.0000 chunk 491 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 331 optimal weight: 9.9990 chunk 262 optimal weight: 40.0000 chunk 507 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 588 optimal weight: 0.4980 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 48 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN A 348 GLN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN B 809 GLN B1135 HIS C 46 HIS C 48 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN C 348 GLN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN D 809 GLN D1135 HIS D1416 HIS E 46 HIS E 48 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN E 348 GLN F 485 GLN F 809 GLN F1135 HIS G 46 HIS G 48 ASN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN G 348 GLN H 485 GLN H 809 GLN H1135 HIS H1296 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 51576 Z= 0.338 Angle : 0.788 10.572 70172 Z= 0.412 Chirality : 0.047 0.275 8516 Planarity : 0.005 0.051 8588 Dihedral : 8.771 159.298 7064 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 0.24 % Allowed : 4.30 % Favored : 95.46 % 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: -0.89 (0.10), residues: 6408 helix: 0.29 (0.08), residues: 3948 sheet: -1.25 (0.20), residues: 552 loop : -2.11 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 514 HIS 0.012 0.002 HIS D 863 PHE 0.025 0.002 PHE F1182 TYR 0.028 0.002 TYR D 123 ARG 0.013 0.001 ARG F1394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 726 time to evaluate : 4.345 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 48 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.6927 (t0) REVERT: A 81 CYS cc_start: 0.8667 (t) cc_final: 0.7426 (t) REVERT: A 88 MET cc_start: 0.9003 (tpt) cc_final: 0.8722 (tmm) REVERT: A 95 PHE cc_start: 0.9026 (t80) cc_final: 0.8654 (t80) REVERT: A 199 MET cc_start: 0.7655 (mmp) cc_final: 0.6453 (mmm) REVERT: A 329 ASP cc_start: 0.7126 (p0) cc_final: 0.6915 (p0) REVERT: B 88 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8670 (tm-30) REVERT: B 89 ILE cc_start: 0.9234 (mt) cc_final: 0.8894 (mp) REVERT: B 91 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7965 (tt0) REVERT: B 233 MET cc_start: 0.9511 (mmm) cc_final: 0.9023 (mmm) REVERT: B 257 MET cc_start: 0.8896 (pmm) cc_final: 0.8457 (ptm) REVERT: B 319 CYS cc_start: 0.9233 (m) cc_final: 0.8995 (m) REVERT: B 423 ILE cc_start: 0.9412 (pt) cc_final: 0.9212 (tt) REVERT: B 710 MET cc_start: 0.6554 (mmt) cc_final: 0.5815 (tpt) REVERT: B 903 MET cc_start: 0.6966 (mmp) cc_final: 0.6074 (mmm) REVERT: B 1031 ASP cc_start: 0.8612 (m-30) cc_final: 0.7756 (t0) REVERT: B 1142 CYS cc_start: 0.9320 (t) cc_final: 0.8712 (m) REVERT: B 1252 MET cc_start: 0.8907 (ttm) cc_final: 0.8431 (tpp) REVERT: B 1514 MET cc_start: 0.7367 (mpp) cc_final: 0.7137 (mtp) REVERT: C 48 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.6741 (t0) REVERT: C 81 CYS cc_start: 0.8544 (t) cc_final: 0.7299 (t) REVERT: C 83 TRP cc_start: 0.8483 (m-10) cc_final: 0.8269 (m-10) REVERT: C 88 MET cc_start: 0.9003 (tpt) cc_final: 0.8719 (tmm) REVERT: C 95 PHE cc_start: 0.9032 (t80) cc_final: 0.8654 (t80) REVERT: C 199 MET cc_start: 0.7628 (mmp) cc_final: 0.6471 (mmm) REVERT: C 329 ASP cc_start: 0.7287 (p0) cc_final: 0.6425 (p0) REVERT: C 332 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7787 (mtmm) REVERT: D 88 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8662 (tm-30) REVERT: D 89 ILE cc_start: 0.9233 (mt) cc_final: 0.8902 (mp) REVERT: D 91 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7972 (tt0) REVERT: D 126 ASN cc_start: 0.8580 (m-40) cc_final: 0.7846 (t0) REVERT: D 233 MET cc_start: 0.9527 (mmm) cc_final: 0.9084 (mmm) REVERT: D 257 MET cc_start: 0.8885 (pmm) cc_final: 0.8460 (ptm) REVERT: D 319 CYS cc_start: 0.9238 (m) cc_final: 0.8999 (m) REVERT: D 423 ILE cc_start: 0.9416 (pt) cc_final: 0.9215 (tt) REVERT: D 710 MET cc_start: 0.6566 (mmt) cc_final: 0.5819 (tpt) REVERT: D 903 MET cc_start: 0.6897 (mmp) cc_final: 0.6045 (mmm) REVERT: D 1031 ASP cc_start: 0.8607 (m-30) cc_final: 0.7750 (t0) REVERT: D 1142 CYS cc_start: 0.9293 (t) cc_final: 0.8686 (m) REVERT: D 1252 MET cc_start: 0.8884 (ttm) cc_final: 0.8350 (tpp) REVERT: D 1514 MET cc_start: 0.7371 (mpp) cc_final: 0.7136 (mtp) REVERT: E 48 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.6946 (t0) REVERT: E 81 CYS cc_start: 0.8527 (t) cc_final: 0.7268 (t) REVERT: E 83 TRP cc_start: 0.8474 (m-10) cc_final: 0.8245 (m-10) REVERT: E 88 MET cc_start: 0.9007 (tpt) cc_final: 0.8716 (tmm) REVERT: E 95 PHE cc_start: 0.9095 (t80) cc_final: 0.8729 (t80) REVERT: E 199 MET cc_start: 0.7649 (mmp) cc_final: 0.6647 (mmm) REVERT: E 332 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7930 (mtpp) REVERT: F 88 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8659 (tm-30) REVERT: F 89 ILE cc_start: 0.9237 (mt) cc_final: 0.8896 (mp) REVERT: F 91 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7966 (tt0) REVERT: F 233 MET cc_start: 0.9529 (mmm) cc_final: 0.9091 (mmm) REVERT: F 257 MET cc_start: 0.8882 (pmm) cc_final: 0.8458 (ptm) REVERT: F 319 CYS cc_start: 0.9238 (m) cc_final: 0.8997 (m) REVERT: F 423 ILE cc_start: 0.9419 (pt) cc_final: 0.9217 (tt) REVERT: F 710 MET cc_start: 0.6577 (mmt) cc_final: 0.5812 (tpt) REVERT: F 903 MET cc_start: 0.6904 (mmp) cc_final: 0.6053 (mmm) REVERT: F 1031 ASP cc_start: 0.8604 (m-30) cc_final: 0.7753 (t0) REVERT: F 1142 CYS cc_start: 0.9294 (t) cc_final: 0.8684 (m) REVERT: F 1252 MET cc_start: 0.8898 (ttm) cc_final: 0.8381 (tpp) REVERT: F 1514 MET cc_start: 0.7366 (mpp) cc_final: 0.7100 (mtp) REVERT: G 48 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.6667 (t0) REVERT: G 81 CYS cc_start: 0.8524 (t) cc_final: 0.7264 (t) REVERT: G 83 TRP cc_start: 0.8516 (m-10) cc_final: 0.8245 (m-10) REVERT: G 88 MET cc_start: 0.9005 (tpt) cc_final: 0.8727 (tmm) REVERT: G 95 PHE cc_start: 0.9073 (t80) cc_final: 0.8708 (t80) REVERT: G 150 ILE cc_start: 0.9319 (tp) cc_final: 0.9118 (tp) REVERT: G 163 MET cc_start: 0.8133 (ttt) cc_final: 0.7507 (ttt) REVERT: G 199 MET cc_start: 0.7801 (mmp) cc_final: 0.6764 (mmm) REVERT: G 332 LYS cc_start: 0.8415 (mtmt) cc_final: 0.7902 (mtpp) REVERT: H 88 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8668 (tm-30) REVERT: H 89 ILE cc_start: 0.9233 (mt) cc_final: 0.8888 (mp) REVERT: H 91 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7961 (tt0) REVERT: H 233 MET cc_start: 0.9516 (mmm) cc_final: 0.9049 (mmm) REVERT: H 257 MET cc_start: 0.8888 (pmm) cc_final: 0.8463 (ptm) REVERT: H 319 CYS cc_start: 0.9227 (m) cc_final: 0.8986 (m) REVERT: H 423 ILE cc_start: 0.9408 (pt) cc_final: 0.9197 (tt) REVERT: H 710 MET cc_start: 0.6571 (mmt) cc_final: 0.5815 (tpt) REVERT: H 844 LEU cc_start: 0.8901 (tp) cc_final: 0.8691 (mm) REVERT: H 903 MET cc_start: 0.6973 (mmp) cc_final: 0.6079 (mmm) REVERT: H 1031 ASP cc_start: 0.8622 (m-30) cc_final: 0.7725 (t0) REVERT: H 1103 ASN cc_start: 0.7869 (m-40) cc_final: 0.7556 (m-40) REVERT: H 1142 CYS cc_start: 0.9277 (t) cc_final: 0.8674 (m) REVERT: H 1252 MET cc_start: 0.8898 (ttm) cc_final: 0.8373 (tpp) REVERT: H 1514 MET cc_start: 0.7367 (mpp) cc_final: 0.7102 (mtp) outliers start: 13 outliers final: 0 residues processed: 739 average time/residue: 0.4440 time to fit residues: 582.8638 Evaluate side-chains 487 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 483 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 489 optimal weight: 5.9990 chunk 400 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 589 optimal weight: 30.0000 chunk 636 optimal weight: 8.9990 chunk 525 optimal weight: 7.9990 chunk 584 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 472 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 152 GLN A 173 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 152 GLN C 173 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** D1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN E 152 GLN E 173 GLN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F 822 GLN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN G 152 GLN G 173 GLN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 822 GLN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 51576 Z= 0.338 Angle : 0.748 11.449 70172 Z= 0.389 Chirality : 0.047 0.295 8516 Planarity : 0.005 0.048 8588 Dihedral : 8.476 137.823 7064 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 0.02 % Allowed : 5.58 % Favored : 94.40 % 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: -0.23 (0.10), residues: 6408 helix: 0.76 (0.08), residues: 3960 sheet: -1.12 (0.20), residues: 548 loop : -1.70 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B1452 HIS 0.010 0.001 HIS H1024 PHE 0.037 0.003 PHE B 295 TYR 0.015 0.002 TYR G 268 ARG 0.015 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 639 time to evaluate : 4.426 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: A 81 CYS cc_start: 0.8255 (t) cc_final: 0.7753 (t) REVERT: A 95 PHE cc_start: 0.9192 (t80) cc_final: 0.8850 (t80) REVERT: A 163 MET cc_start: 0.8057 (ttt) cc_final: 0.7620 (ttt) REVERT: A 329 ASP cc_start: 0.7283 (p0) cc_final: 0.6950 (p0) REVERT: A 332 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8191 (mtpp) REVERT: B 89 ILE cc_start: 0.9261 (mt) cc_final: 0.8884 (mp) REVERT: B 91 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8225 (tt0) REVERT: B 233 MET cc_start: 0.9541 (mmm) cc_final: 0.9032 (mmm) REVERT: B 257 MET cc_start: 0.8821 (pmm) cc_final: 0.8471 (ptm) REVERT: B 319 CYS cc_start: 0.9136 (m) cc_final: 0.8872 (m) REVERT: B 423 ILE cc_start: 0.9410 (pt) cc_final: 0.9188 (tt) REVERT: B 433 PHE cc_start: 0.8786 (m-10) cc_final: 0.8539 (m-10) REVERT: B 710 MET cc_start: 0.6493 (mmt) cc_final: 0.5770 (tpt) REVERT: B 1025 MET cc_start: 0.7983 (mmm) cc_final: 0.7748 (mmm) REVERT: B 1031 ASP cc_start: 0.8562 (m-30) cc_final: 0.7570 (t0) REVERT: B 1118 LEU cc_start: 0.8436 (tp) cc_final: 0.8214 (mp) REVERT: B 1142 CYS cc_start: 0.9295 (t) cc_final: 0.8809 (m) REVERT: B 1283 LEU cc_start: 0.9219 (mp) cc_final: 0.8881 (mp) REVERT: B 1395 MET cc_start: 0.8356 (mmp) cc_final: 0.8063 (mmm) REVERT: B 1514 MET cc_start: 0.7372 (mpp) cc_final: 0.7048 (mtp) REVERT: C 81 CYS cc_start: 0.8225 (t) cc_final: 0.7595 (t) REVERT: C 83 TRP cc_start: 0.8505 (m-10) cc_final: 0.8259 (m-10) REVERT: C 95 PHE cc_start: 0.9187 (t80) cc_final: 0.8868 (t80) REVERT: C 329 ASP cc_start: 0.7539 (p0) cc_final: 0.6763 (p0) REVERT: C 332 LYS cc_start: 0.8504 (mtmt) cc_final: 0.7751 (mtmm) REVERT: D 89 ILE cc_start: 0.9254 (mt) cc_final: 0.8883 (mp) REVERT: D 91 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8317 (tt0) REVERT: D 126 ASN cc_start: 0.8861 (m-40) cc_final: 0.8102 (t0) REVERT: D 233 MET cc_start: 0.9540 (mmm) cc_final: 0.9027 (mmm) REVERT: D 257 MET cc_start: 0.8813 (pmm) cc_final: 0.8458 (ptm) REVERT: D 319 CYS cc_start: 0.9167 (m) cc_final: 0.8923 (m) REVERT: D 423 ILE cc_start: 0.9412 (pt) cc_final: 0.9195 (tt) REVERT: D 433 PHE cc_start: 0.8784 (m-10) cc_final: 0.8428 (m-10) REVERT: D 710 MET cc_start: 0.6505 (mmt) cc_final: 0.5771 (tpt) REVERT: D 801 MET cc_start: 0.8888 (ptt) cc_final: 0.8562 (tpt) REVERT: D 1025 MET cc_start: 0.7856 (mmm) cc_final: 0.7595 (mmm) REVERT: D 1031 ASP cc_start: 0.8612 (m-30) cc_final: 0.7623 (t0) REVERT: D 1118 LEU cc_start: 0.8436 (tp) cc_final: 0.8211 (mp) REVERT: D 1142 CYS cc_start: 0.9295 (t) cc_final: 0.8811 (m) REVERT: D 1283 LEU cc_start: 0.9220 (mp) cc_final: 0.8901 (mp) REVERT: D 1395 MET cc_start: 0.8397 (mmp) cc_final: 0.8147 (mmm) REVERT: D 1514 MET cc_start: 0.7352 (mpp) cc_final: 0.7057 (mtp) REVERT: E 81 CYS cc_start: 0.8182 (t) cc_final: 0.7560 (t) REVERT: E 83 TRP cc_start: 0.8493 (m-10) cc_final: 0.8247 (m-10) REVERT: E 95 PHE cc_start: 0.9185 (t80) cc_final: 0.8865 (t80) REVERT: E 163 MET cc_start: 0.8111 (ttt) cc_final: 0.7555 (ttt) REVERT: E 329 ASP cc_start: 0.7316 (p0) cc_final: 0.6136 (p0) REVERT: E 332 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7773 (mtmm) REVERT: F 89 ILE cc_start: 0.9262 (mt) cc_final: 0.8880 (mp) REVERT: F 91 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8321 (tt0) REVERT: F 233 MET cc_start: 0.9539 (mmm) cc_final: 0.9045 (mmm) REVERT: F 257 MET cc_start: 0.8807 (pmm) cc_final: 0.8449 (ptm) REVERT: F 319 CYS cc_start: 0.9164 (m) cc_final: 0.8922 (m) REVERT: F 423 ILE cc_start: 0.9415 (pt) cc_final: 0.9193 (tt) REVERT: F 433 PHE cc_start: 0.8771 (m-10) cc_final: 0.8426 (m-10) REVERT: F 710 MET cc_start: 0.6523 (mmt) cc_final: 0.5769 (tpt) REVERT: F 801 MET cc_start: 0.8893 (ptt) cc_final: 0.8556 (tpt) REVERT: F 1025 MET cc_start: 0.7920 (mmm) cc_final: 0.7672 (mmm) REVERT: F 1031 ASP cc_start: 0.8611 (m-30) cc_final: 0.7624 (t0) REVERT: F 1118 LEU cc_start: 0.8436 (tp) cc_final: 0.8203 (mp) REVERT: F 1142 CYS cc_start: 0.9290 (t) cc_final: 0.8810 (m) REVERT: F 1283 LEU cc_start: 0.9217 (mp) cc_final: 0.8901 (mp) REVERT: F 1395 MET cc_start: 0.8382 (mmp) cc_final: 0.8099 (mmm) REVERT: F 1514 MET cc_start: 0.7306 (mpp) cc_final: 0.7023 (mtp) REVERT: G 81 CYS cc_start: 0.8217 (t) cc_final: 0.7557 (t) REVERT: G 95 PHE cc_start: 0.9194 (t80) cc_final: 0.8860 (t80) REVERT: G 122 LEU cc_start: 0.9535 (tt) cc_final: 0.9314 (tt) REVERT: G 329 ASP cc_start: 0.7398 (p0) cc_final: 0.6412 (p0) REVERT: G 332 LYS cc_start: 0.8572 (mtmt) cc_final: 0.7908 (mtmm) REVERT: H 89 ILE cc_start: 0.9260 (mt) cc_final: 0.8875 (mp) REVERT: H 91 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8238 (tt0) REVERT: H 233 MET cc_start: 0.9541 (mmm) cc_final: 0.9038 (mmm) REVERT: H 257 MET cc_start: 0.8825 (pmm) cc_final: 0.8475 (ptm) REVERT: H 319 CYS cc_start: 0.9135 (m) cc_final: 0.8871 (m) REVERT: H 423 ILE cc_start: 0.9389 (pt) cc_final: 0.9151 (tt) REVERT: H 433 PHE cc_start: 0.8721 (m-10) cc_final: 0.8446 (m-80) REVERT: H 710 MET cc_start: 0.6513 (mmt) cc_final: 0.5775 (tpt) REVERT: H 1025 MET cc_start: 0.7993 (mmm) cc_final: 0.7755 (mmm) REVERT: H 1031 ASP cc_start: 0.8635 (m-30) cc_final: 0.7579 (t0) REVERT: H 1103 ASN cc_start: 0.7722 (m-40) cc_final: 0.7437 (m-40) REVERT: H 1118 LEU cc_start: 0.8444 (tp) cc_final: 0.8222 (pt) REVERT: H 1142 CYS cc_start: 0.9287 (t) cc_final: 0.8800 (m) REVERT: H 1283 LEU cc_start: 0.9219 (mp) cc_final: 0.8882 (mp) REVERT: H 1395 MET cc_start: 0.8364 (mmp) cc_final: 0.8077 (mmm) REVERT: H 1514 MET cc_start: 0.7351 (mpp) cc_final: 0.7074 (mtp) outliers start: 1 outliers final: 1 residues processed: 640 average time/residue: 0.5134 time to fit residues: 590.0009 Evaluate side-chains 464 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 1.9990 chunk 443 optimal weight: 0.9980 chunk 305 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 281 optimal weight: 0.0070 chunk 395 optimal weight: 7.9990 chunk 591 optimal weight: 20.0000 chunk 626 optimal weight: 7.9990 chunk 309 optimal weight: 0.9980 chunk 560 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 48 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 GLN C 41 ASN C 48 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 GLN E 41 ASN E 48 ASN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F1020 GLN G 41 ASN G 48 ASN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H1020 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 51576 Z= 0.189 Angle : 0.650 9.036 70172 Z= 0.329 Chirality : 0.043 0.252 8516 Planarity : 0.004 0.076 8588 Dihedral : 8.350 136.623 7064 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 0.20 (0.10), residues: 6408 helix: 1.11 (0.08), residues: 3980 sheet: -1.00 (0.20), residues: 548 loop : -1.56 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1452 HIS 0.006 0.001 HIS C 259 PHE 0.035 0.002 PHE D 295 TYR 0.046 0.002 TYR F1254 ARG 0.004 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 CYS cc_start: 0.8582 (t) cc_final: 0.7384 (t) REVERT: A 88 MET cc_start: 0.8874 (tmm) cc_final: 0.8588 (tmm) REVERT: A 95 PHE cc_start: 0.9004 (t80) cc_final: 0.8612 (t80) REVERT: A 329 ASP cc_start: 0.7007 (p0) cc_final: 0.6414 (p0) REVERT: A 332 LYS cc_start: 0.8503 (mtpt) cc_final: 0.7974 (mtpp) REVERT: B 233 MET cc_start: 0.9498 (mmm) cc_final: 0.8947 (mmm) REVERT: B 257 MET cc_start: 0.8698 (pmm) cc_final: 0.8433 (ptm) REVERT: B 319 CYS cc_start: 0.9127 (m) cc_final: 0.8899 (m) REVERT: B 423 ILE cc_start: 0.9431 (pt) cc_final: 0.9210 (tt) REVERT: B 433 PHE cc_start: 0.8600 (m-10) cc_final: 0.8304 (m-80) REVERT: B 592 LEU cc_start: 0.8616 (mp) cc_final: 0.8413 (mp) REVERT: B 710 MET cc_start: 0.6441 (mmt) cc_final: 0.5777 (tpt) REVERT: B 903 MET cc_start: 0.6810 (mmp) cc_final: 0.6149 (mmm) REVERT: B 1025 MET cc_start: 0.7898 (mmm) cc_final: 0.7568 (mmm) REVERT: B 1031 ASP cc_start: 0.8595 (m-30) cc_final: 0.7562 (t0) REVERT: B 1142 CYS cc_start: 0.9255 (t) cc_final: 0.8808 (m) REVERT: B 1252 MET cc_start: 0.8927 (tpp) cc_final: 0.8693 (tpp) REVERT: B 1283 LEU cc_start: 0.9153 (mp) cc_final: 0.8734 (mp) REVERT: B 1395 MET cc_start: 0.8246 (mmp) cc_final: 0.7970 (mmm) REVERT: B 1514 MET cc_start: 0.7296 (mpp) cc_final: 0.7011 (mtp) REVERT: C 81 CYS cc_start: 0.8664 (t) cc_final: 0.7403 (t) REVERT: C 83 TRP cc_start: 0.8458 (m-10) cc_final: 0.8202 (m-10) REVERT: C 88 MET cc_start: 0.8888 (tmm) cc_final: 0.8620 (tmm) REVERT: C 95 PHE cc_start: 0.9009 (t80) cc_final: 0.8649 (t80) REVERT: C 199 MET cc_start: 0.7231 (mmp) cc_final: 0.6811 (mmm) REVERT: C 329 ASP cc_start: 0.7337 (p0) cc_final: 0.6624 (p0) REVERT: C 332 LYS cc_start: 0.8464 (mtmt) cc_final: 0.7720 (mtmm) REVERT: D 126 ASN cc_start: 0.8847 (m-40) cc_final: 0.8083 (t0) REVERT: D 233 MET cc_start: 0.9501 (mmm) cc_final: 0.8950 (mmm) REVERT: D 257 MET cc_start: 0.8699 (pmm) cc_final: 0.8428 (ptm) REVERT: D 319 CYS cc_start: 0.9132 (m) cc_final: 0.8903 (m) REVERT: D 385 ILE cc_start: 0.9454 (mt) cc_final: 0.9094 (tp) REVERT: D 423 ILE cc_start: 0.9430 (pt) cc_final: 0.9215 (tt) REVERT: D 433 PHE cc_start: 0.8665 (m-10) cc_final: 0.8373 (m-80) REVERT: D 710 MET cc_start: 0.6449 (mmt) cc_final: 0.5772 (tpt) REVERT: D 801 MET cc_start: 0.8850 (ptt) cc_final: 0.8484 (tpt) REVERT: D 903 MET cc_start: 0.6798 (mmp) cc_final: 0.6137 (mmm) REVERT: D 1025 MET cc_start: 0.7902 (mmm) cc_final: 0.7574 (mmm) REVERT: D 1031 ASP cc_start: 0.8590 (m-30) cc_final: 0.7533 (t0) REVERT: D 1142 CYS cc_start: 0.9243 (t) cc_final: 0.8769 (m) REVERT: D 1252 MET cc_start: 0.8987 (tpp) cc_final: 0.8757 (tpp) REVERT: D 1283 LEU cc_start: 0.9196 (mp) cc_final: 0.8807 (mp) REVERT: D 1395 MET cc_start: 0.8190 (mmp) cc_final: 0.7960 (mmm) REVERT: D 1514 MET cc_start: 0.7297 (mpp) cc_final: 0.7012 (mtp) REVERT: E 81 CYS cc_start: 0.8612 (t) cc_final: 0.7320 (t) REVERT: E 83 TRP cc_start: 0.8465 (m-10) cc_final: 0.8178 (m-10) REVERT: E 88 MET cc_start: 0.8874 (tmm) cc_final: 0.8610 (tmm) REVERT: E 95 PHE cc_start: 0.9054 (t80) cc_final: 0.8708 (t80) REVERT: E 329 ASP cc_start: 0.7127 (p0) cc_final: 0.6067 (p0) REVERT: E 332 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7546 (mtmm) REVERT: F 233 MET cc_start: 0.9501 (mmm) cc_final: 0.8952 (mmm) REVERT: F 257 MET cc_start: 0.8692 (pmm) cc_final: 0.8427 (ptm) REVERT: F 319 CYS cc_start: 0.9131 (m) cc_final: 0.8902 (m) REVERT: F 423 ILE cc_start: 0.9426 (pt) cc_final: 0.9203 (tt) REVERT: F 433 PHE cc_start: 0.8671 (m-10) cc_final: 0.8367 (m-80) REVERT: F 710 MET cc_start: 0.6466 (mmt) cc_final: 0.5770 (tpt) REVERT: F 801 MET cc_start: 0.8852 (ptt) cc_final: 0.8490 (tpt) REVERT: F 903 MET cc_start: 0.6799 (mmp) cc_final: 0.6140 (mmm) REVERT: F 1025 MET cc_start: 0.7916 (mmm) cc_final: 0.7583 (mmm) REVERT: F 1031 ASP cc_start: 0.8580 (m-30) cc_final: 0.7532 (t0) REVERT: F 1142 CYS cc_start: 0.9243 (t) cc_final: 0.8762 (m) REVERT: F 1252 MET cc_start: 0.8968 (tpp) cc_final: 0.8696 (tpp) REVERT: F 1283 LEU cc_start: 0.9197 (mp) cc_final: 0.8811 (mp) REVERT: F 1395 MET cc_start: 0.8250 (mmp) cc_final: 0.7990 (mmm) REVERT: F 1514 MET cc_start: 0.7292 (mpp) cc_final: 0.7008 (mtp) REVERT: G 81 CYS cc_start: 0.8571 (t) cc_final: 0.7291 (t) REVERT: G 83 TRP cc_start: 0.8511 (m-10) cc_final: 0.8118 (m-10) REVERT: G 95 PHE cc_start: 0.9000 (t80) cc_final: 0.8605 (t80) REVERT: G 329 ASP cc_start: 0.7135 (p0) cc_final: 0.6081 (p0) REVERT: G 332 LYS cc_start: 0.8511 (mtmt) cc_final: 0.7706 (mtmm) REVERT: H 233 MET cc_start: 0.9505 (mmm) cc_final: 0.8961 (mmm) REVERT: H 257 MET cc_start: 0.8645 (pmm) cc_final: 0.8325 (ptm) REVERT: H 319 CYS cc_start: 0.9123 (m) cc_final: 0.8893 (m) REVERT: H 423 ILE cc_start: 0.9436 (pt) cc_final: 0.9216 (tt) REVERT: H 433 PHE cc_start: 0.8548 (m-10) cc_final: 0.8340 (m-80) REVERT: H 592 LEU cc_start: 0.8617 (mp) cc_final: 0.8416 (mp) REVERT: H 710 MET cc_start: 0.6454 (mmt) cc_final: 0.5784 (tpt) REVERT: H 903 MET cc_start: 0.6808 (mmp) cc_final: 0.6155 (mmm) REVERT: H 1025 MET cc_start: 0.7909 (mmm) cc_final: 0.7577 (mmm) REVERT: H 1031 ASP cc_start: 0.8593 (m-30) cc_final: 0.7566 (t0) REVERT: H 1103 ASN cc_start: 0.7819 (m-40) cc_final: 0.7536 (m-40) REVERT: H 1142 CYS cc_start: 0.9239 (t) cc_final: 0.8749 (m) REVERT: H 1252 MET cc_start: 0.8896 (tpp) cc_final: 0.8629 (tpp) REVERT: H 1283 LEU cc_start: 0.9198 (mp) cc_final: 0.8810 (mp) REVERT: H 1395 MET cc_start: 0.8235 (mmp) cc_final: 0.7964 (mmm) REVERT: H 1514 MET cc_start: 0.7296 (mpp) cc_final: 0.7012 (mtp) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.4304 time to fit residues: 505.6925 Evaluate side-chains 449 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 9.9990 chunk 355 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 466 optimal weight: 9.9990 chunk 258 optimal weight: 0.3980 chunk 534 optimal weight: 9.9990 chunk 432 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 319 optimal weight: 50.0000 chunk 562 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 48 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS B 822 GLN B1245 ASN C 41 ASN C 48 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 HIS D1245 ASN E 41 ASN E 48 ASN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 HIS F1245 ASN G 41 ASN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 HIS H 822 GLN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 51576 Z= 0.303 Angle : 0.719 11.551 70172 Z= 0.369 Chirality : 0.045 0.275 8516 Planarity : 0.004 0.064 8588 Dihedral : 8.282 124.415 7064 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.10), residues: 6408 helix: 1.07 (0.08), residues: 4012 sheet: -1.23 (0.20), residues: 548 loop : -1.26 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 83 HIS 0.009 0.001 HIS E 259 PHE 0.039 0.002 PHE G 75 TYR 0.022 0.002 TYR F 124 ARG 0.015 0.001 ARG D1419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 CYS cc_start: 0.8323 (t) cc_final: 0.7850 (t) REVERT: A 88 MET cc_start: 0.9011 (tmm) cc_final: 0.8655 (tmm) REVERT: A 95 PHE cc_start: 0.9175 (t80) cc_final: 0.8826 (t80) REVERT: A 256 ILE cc_start: 0.8744 (mp) cc_final: 0.8347 (tt) REVERT: A 329 ASP cc_start: 0.7430 (p0) cc_final: 0.7198 (p0) REVERT: A 332 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8070 (mtpp) REVERT: B 91 GLU cc_start: 0.9068 (tt0) cc_final: 0.8426 (tt0) REVERT: B 233 MET cc_start: 0.9604 (mmm) cc_final: 0.9009 (mmm) REVERT: B 257 MET cc_start: 0.8747 (pmm) cc_final: 0.8545 (ptm) REVERT: B 271 ASP cc_start: 0.9100 (t70) cc_final: 0.8746 (t0) REVERT: B 319 CYS cc_start: 0.9045 (m) cc_final: 0.8789 (m) REVERT: B 423 ILE cc_start: 0.9417 (pt) cc_final: 0.9167 (tt) REVERT: B 433 PHE cc_start: 0.8582 (m-10) cc_final: 0.8334 (m-80) REVERT: B 710 MET cc_start: 0.6535 (mmt) cc_final: 0.5970 (tpt) REVERT: B 730 MET cc_start: -0.0049 (ppp) cc_final: -0.0277 (ttt) REVERT: B 903 MET cc_start: 0.6803 (mmp) cc_final: 0.5968 (mmm) REVERT: B 1025 MET cc_start: 0.7806 (mmm) cc_final: 0.7569 (mmm) REVERT: B 1031 ASP cc_start: 0.8659 (m-30) cc_final: 0.7599 (t0) REVERT: B 1142 CYS cc_start: 0.9250 (t) cc_final: 0.8843 (m) REVERT: B 1283 LEU cc_start: 0.9149 (mp) cc_final: 0.8617 (mp) REVERT: B 1305 MET cc_start: 0.8835 (mmm) cc_final: 0.8478 (mmm) REVERT: B 1514 MET cc_start: 0.7387 (mpp) cc_final: 0.7066 (ttt) REVERT: C 77 MET cc_start: 0.8845 (tpt) cc_final: 0.8509 (tpp) REVERT: C 81 CYS cc_start: 0.8311 (t) cc_final: 0.6688 (t) REVERT: C 88 MET cc_start: 0.8996 (tmm) cc_final: 0.8660 (tmm) REVERT: C 95 PHE cc_start: 0.9217 (t80) cc_final: 0.8904 (t80) REVERT: C 199 MET cc_start: 0.7281 (mmp) cc_final: 0.6823 (mmp) REVERT: C 329 ASP cc_start: 0.7809 (p0) cc_final: 0.7078 (p0) REVERT: C 332 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7776 (mtmm) REVERT: D 91 GLU cc_start: 0.9070 (tt0) cc_final: 0.8428 (tt0) REVERT: D 233 MET cc_start: 0.9613 (mmm) cc_final: 0.9008 (mmm) REVERT: D 271 ASP cc_start: 0.9117 (t70) cc_final: 0.8777 (t0) REVERT: D 319 CYS cc_start: 0.9053 (m) cc_final: 0.8794 (m) REVERT: D 423 ILE cc_start: 0.9411 (pt) cc_final: 0.9151 (tt) REVERT: D 433 PHE cc_start: 0.8654 (m-10) cc_final: 0.8376 (m-80) REVERT: D 710 MET cc_start: 0.6544 (mmt) cc_final: 0.5958 (tpt) REVERT: D 730 MET cc_start: 0.0152 (ppp) cc_final: -0.0112 (ttt) REVERT: D 903 MET cc_start: 0.6736 (mmp) cc_final: 0.5943 (mmm) REVERT: D 1025 MET cc_start: 0.7813 (mmm) cc_final: 0.7573 (mmm) REVERT: D 1031 ASP cc_start: 0.8657 (m-30) cc_final: 0.7603 (t0) REVERT: D 1142 CYS cc_start: 0.9240 (t) cc_final: 0.8801 (m) REVERT: D 1252 MET cc_start: 0.9038 (tpp) cc_final: 0.8787 (tpp) REVERT: D 1283 LEU cc_start: 0.9150 (mp) cc_final: 0.8618 (mp) REVERT: D 1395 MET cc_start: 0.8377 (mmp) cc_final: 0.8121 (mmm) REVERT: D 1514 MET cc_start: 0.7390 (mpp) cc_final: 0.7062 (ttt) REVERT: E 77 MET cc_start: 0.8842 (tpt) cc_final: 0.8533 (tpp) REVERT: E 81 CYS cc_start: 0.8289 (t) cc_final: 0.7645 (t) REVERT: E 88 MET cc_start: 0.8983 (tmm) cc_final: 0.8665 (tmm) REVERT: E 95 PHE cc_start: 0.9216 (t80) cc_final: 0.8898 (t80) REVERT: E 329 ASP cc_start: 0.7617 (p0) cc_final: 0.6770 (p0) REVERT: E 332 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8031 (mtmm) REVERT: F 91 GLU cc_start: 0.9105 (tt0) cc_final: 0.8505 (tt0) REVERT: F 233 MET cc_start: 0.9609 (mmm) cc_final: 0.9014 (mmm) REVERT: F 271 ASP cc_start: 0.9119 (t70) cc_final: 0.8772 (t0) REVERT: F 319 CYS cc_start: 0.9051 (m) cc_final: 0.8790 (m) REVERT: F 423 ILE cc_start: 0.9412 (pt) cc_final: 0.9149 (tt) REVERT: F 433 PHE cc_start: 0.8669 (m-10) cc_final: 0.8383 (m-80) REVERT: F 710 MET cc_start: 0.6748 (mmt) cc_final: 0.5979 (tpt) REVERT: F 903 MET cc_start: 0.6860 (mmp) cc_final: 0.6112 (mmm) REVERT: F 1025 MET cc_start: 0.7825 (mmm) cc_final: 0.7582 (mmm) REVERT: F 1031 ASP cc_start: 0.8651 (m-30) cc_final: 0.7605 (t0) REVERT: F 1142 CYS cc_start: 0.9237 (t) cc_final: 0.8794 (m) REVERT: F 1283 LEU cc_start: 0.9151 (mp) cc_final: 0.8622 (mp) REVERT: F 1514 MET cc_start: 0.7384 (mpp) cc_final: 0.7062 (ttt) REVERT: G 73 LEU cc_start: 0.9223 (tt) cc_final: 0.8948 (pp) REVERT: G 81 CYS cc_start: 0.8627 (t) cc_final: 0.7306 (t) REVERT: G 95 PHE cc_start: 0.9174 (t80) cc_final: 0.8852 (t80) REVERT: G 199 MET cc_start: 0.7441 (mmp) cc_final: 0.7239 (mmp) REVERT: G 329 ASP cc_start: 0.7606 (p0) cc_final: 0.6798 (p0) REVERT: G 332 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8037 (mtmm) REVERT: H 91 GLU cc_start: 0.9081 (tt0) cc_final: 0.8429 (tt0) REVERT: H 233 MET cc_start: 0.9609 (mmm) cc_final: 0.9019 (mmm) REVERT: H 257 MET cc_start: 0.8748 (pmm) cc_final: 0.8477 (ptm) REVERT: H 271 ASP cc_start: 0.9117 (t70) cc_final: 0.8768 (t0) REVERT: H 319 CYS cc_start: 0.9043 (m) cc_final: 0.8784 (m) REVERT: H 423 ILE cc_start: 0.9401 (pt) cc_final: 0.9169 (tt) REVERT: H 433 PHE cc_start: 0.8531 (m-10) cc_final: 0.8315 (m-80) REVERT: H 710 MET cc_start: 0.6550 (mmt) cc_final: 0.5968 (tpt) REVERT: H 730 MET cc_start: -0.0400 (ppp) cc_final: -0.0602 (ttt) REVERT: H 903 MET cc_start: 0.6875 (mmp) cc_final: 0.6129 (mmm) REVERT: H 1025 MET cc_start: 0.7819 (mmm) cc_final: 0.7577 (mmm) REVERT: H 1031 ASP cc_start: 0.8654 (m-30) cc_final: 0.7610 (t0) REVERT: H 1103 ASN cc_start: 0.7763 (m-40) cc_final: 0.7480 (m-40) REVERT: H 1142 CYS cc_start: 0.9237 (t) cc_final: 0.8781 (m) REVERT: H 1283 LEU cc_start: 0.9150 (mp) cc_final: 0.8617 (mp) REVERT: H 1395 MET cc_start: 0.8389 (mmp) cc_final: 0.8137 (mmm) REVERT: H 1514 MET cc_start: 0.7389 (mpp) cc_final: 0.7068 (ttt) outliers start: 0 outliers final: 0 residues processed: 570 average time/residue: 0.4390 time to fit residues: 445.5294 Evaluate side-chains 433 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 30.0000 chunk 564 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 367 optimal weight: 5.9990 chunk 154 optimal weight: 50.0000 chunk 626 optimal weight: 30.0000 chunk 520 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 329 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 48 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 48 ASN C 259 HIS D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN ** D1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 GLN ** F1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 369 GLN ** H1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 51576 Z= 0.197 Angle : 0.647 10.077 70172 Z= 0.326 Chirality : 0.043 0.251 8516 Planarity : 0.004 0.092 8588 Dihedral : 8.172 123.245 7064 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 6408 helix: 1.30 (0.08), residues: 4020 sheet: -1.03 (0.21), residues: 516 loop : -1.20 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 83 HIS 0.008 0.001 HIS B 584 PHE 0.035 0.002 PHE C 75 TYR 0.015 0.001 TYR H 107 ARG 0.006 0.000 ARG D1419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8859 (tpt) cc_final: 0.8526 (tpp) REVERT: A 81 CYS cc_start: 0.8339 (t) cc_final: 0.7086 (t) REVERT: A 88 MET cc_start: 0.8989 (tmm) cc_final: 0.8726 (tmm) REVERT: A 95 PHE cc_start: 0.9078 (t80) cc_final: 0.8693 (t80) REVERT: A 256 ILE cc_start: 0.8947 (mp) cc_final: 0.8640 (tt) REVERT: A 329 ASP cc_start: 0.7296 (p0) cc_final: 0.6843 (p0) REVERT: A 332 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8158 (mtpp) REVERT: B 91 GLU cc_start: 0.9213 (tt0) cc_final: 0.8617 (tt0) REVERT: B 233 MET cc_start: 0.9559 (mmm) cc_final: 0.8950 (mmm) REVERT: B 271 ASP cc_start: 0.9053 (t70) cc_final: 0.8565 (t0) REVERT: B 275 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7612 (ttp-110) REVERT: B 319 CYS cc_start: 0.9002 (m) cc_final: 0.8747 (m) REVERT: B 423 ILE cc_start: 0.9454 (pt) cc_final: 0.9191 (tt) REVERT: B 710 MET cc_start: 0.6471 (mmt) cc_final: 0.5950 (tpt) REVERT: B 903 MET cc_start: 0.6990 (mmp) cc_final: 0.6750 (mmp) REVERT: B 1025 MET cc_start: 0.7851 (mmm) cc_final: 0.7643 (mmm) REVERT: B 1031 ASP cc_start: 0.8638 (m-30) cc_final: 0.7550 (t0) REVERT: B 1066 MET cc_start: 0.7778 (mtm) cc_final: 0.6952 (mmm) REVERT: B 1142 CYS cc_start: 0.9187 (t) cc_final: 0.8874 (m) REVERT: B 1149 LEU cc_start: 0.9005 (mt) cc_final: 0.8776 (mt) REVERT: B 1252 MET cc_start: 0.8937 (tpp) cc_final: 0.8729 (tpp) REVERT: B 1283 LEU cc_start: 0.9188 (mp) cc_final: 0.8614 (mp) REVERT: B 1395 MET cc_start: 0.8297 (mmp) cc_final: 0.8089 (mmm) REVERT: B 1514 MET cc_start: 0.7460 (mpp) cc_final: 0.7145 (ttt) REVERT: C 77 MET cc_start: 0.8817 (tpt) cc_final: 0.8451 (tpp) REVERT: C 81 CYS cc_start: 0.8558 (t) cc_final: 0.7263 (t) REVERT: C 88 MET cc_start: 0.8959 (tmm) cc_final: 0.8632 (tmm) REVERT: C 95 PHE cc_start: 0.9103 (t80) cc_final: 0.8765 (t80) REVERT: C 150 ILE cc_start: 0.9334 (tp) cc_final: 0.9104 (tp) REVERT: C 166 CYS cc_start: 0.8865 (p) cc_final: 0.8633 (p) REVERT: C 199 MET cc_start: 0.7106 (mmp) cc_final: 0.6490 (mmp) REVERT: C 329 ASP cc_start: 0.7739 (p0) cc_final: 0.6687 (p0) REVERT: C 332 LYS cc_start: 0.8475 (mtmt) cc_final: 0.7878 (mtmm) REVERT: D 91 GLU cc_start: 0.9202 (tt0) cc_final: 0.8606 (tt0) REVERT: D 139 LEU cc_start: 0.9006 (tp) cc_final: 0.8771 (tp) REVERT: D 233 MET cc_start: 0.9568 (mmm) cc_final: 0.8964 (mmm) REVERT: D 257 MET cc_start: 0.8529 (ptm) cc_final: 0.7894 (ppp) REVERT: D 271 ASP cc_start: 0.9056 (t70) cc_final: 0.8563 (t0) REVERT: D 275 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7608 (ttp-110) REVERT: D 319 CYS cc_start: 0.9005 (m) cc_final: 0.8758 (m) REVERT: D 423 ILE cc_start: 0.9439 (pt) cc_final: 0.9171 (tt) REVERT: D 433 PHE cc_start: 0.8528 (m-10) cc_final: 0.8282 (m-80) REVERT: D 710 MET cc_start: 0.6477 (mmt) cc_final: 0.5942 (tpt) REVERT: D 801 MET cc_start: 0.9042 (ptp) cc_final: 0.8769 (tpt) REVERT: D 903 MET cc_start: 0.7033 (mmp) cc_final: 0.6763 (mmp) REVERT: D 1025 MET cc_start: 0.7796 (mmm) cc_final: 0.7574 (mmm) REVERT: D 1031 ASP cc_start: 0.8638 (m-30) cc_final: 0.7548 (t0) REVERT: D 1066 MET cc_start: 0.7772 (mtm) cc_final: 0.6946 (mmm) REVERT: D 1142 CYS cc_start: 0.9198 (t) cc_final: 0.8827 (m) REVERT: D 1149 LEU cc_start: 0.9013 (mt) cc_final: 0.8786 (mt) REVERT: D 1252 MET cc_start: 0.9019 (tpp) cc_final: 0.8698 (tpp) REVERT: D 1283 LEU cc_start: 0.9186 (mp) cc_final: 0.8620 (mp) REVERT: D 1395 MET cc_start: 0.8413 (mmp) cc_final: 0.8146 (mmm) REVERT: D 1514 MET cc_start: 0.7461 (mpp) cc_final: 0.7143 (ttt) REVERT: E 77 MET cc_start: 0.8790 (tpt) cc_final: 0.8446 (tpp) REVERT: E 81 CYS cc_start: 0.8613 (t) cc_final: 0.7372 (t) REVERT: E 83 TRP cc_start: 0.8669 (m-10) cc_final: 0.7530 (m-10) REVERT: E 88 MET cc_start: 0.9000 (tmm) cc_final: 0.8720 (tmm) REVERT: E 95 PHE cc_start: 0.9099 (t80) cc_final: 0.8752 (t80) REVERT: E 199 MET cc_start: 0.7515 (mmp) cc_final: 0.7271 (mmm) REVERT: E 329 ASP cc_start: 0.7503 (p0) cc_final: 0.6845 (p0) REVERT: E 332 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7899 (mtmm) REVERT: F 91 GLU cc_start: 0.9219 (tt0) cc_final: 0.8622 (tt0) REVERT: F 233 MET cc_start: 0.9568 (mmm) cc_final: 0.8967 (mmm) REVERT: F 257 MET cc_start: 0.8532 (ptm) cc_final: 0.7893 (ppp) REVERT: F 271 ASP cc_start: 0.9052 (t70) cc_final: 0.8560 (t0) REVERT: F 275 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7599 (ttp-110) REVERT: F 319 CYS cc_start: 0.9004 (m) cc_final: 0.8753 (m) REVERT: F 423 ILE cc_start: 0.9442 (pt) cc_final: 0.9169 (tt) REVERT: F 433 PHE cc_start: 0.8537 (m-10) cc_final: 0.8309 (m-80) REVERT: F 710 MET cc_start: 0.6491 (mmt) cc_final: 0.5940 (tpt) REVERT: F 730 MET cc_start: 0.0867 (ttt) cc_final: -0.0543 (ppp) REVERT: F 801 MET cc_start: 0.9043 (ptp) cc_final: 0.8758 (tpt) REVERT: F 903 MET cc_start: 0.7035 (mmp) cc_final: 0.6765 (mmp) REVERT: F 1025 MET cc_start: 0.7808 (mmm) cc_final: 0.7586 (mmm) REVERT: F 1031 ASP cc_start: 0.8631 (m-30) cc_final: 0.7551 (t0) REVERT: F 1142 CYS cc_start: 0.9192 (t) cc_final: 0.8818 (m) REVERT: F 1149 LEU cc_start: 0.9007 (mt) cc_final: 0.8780 (mt) REVERT: F 1252 MET cc_start: 0.8975 (tpp) cc_final: 0.8725 (tpp) REVERT: F 1283 LEU cc_start: 0.9187 (mp) cc_final: 0.8626 (mp) REVERT: F 1395 MET cc_start: 0.8363 (mmp) cc_final: 0.8120 (mmm) REVERT: F 1514 MET cc_start: 0.7457 (mpp) cc_final: 0.7140 (ttt) REVERT: G 73 LEU cc_start: 0.9140 (tt) cc_final: 0.8889 (pp) REVERT: G 77 MET cc_start: 0.8813 (tpt) cc_final: 0.8443 (tpp) REVERT: G 81 CYS cc_start: 0.8708 (t) cc_final: 0.7681 (t) REVERT: G 95 PHE cc_start: 0.9088 (t80) cc_final: 0.8722 (t80) REVERT: G 159 ILE cc_start: 0.9172 (tp) cc_final: 0.8875 (pt) REVERT: G 329 ASP cc_start: 0.7489 (p0) cc_final: 0.6835 (p0) REVERT: G 332 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7883 (mtmm) REVERT: H 91 GLU cc_start: 0.9223 (tt0) cc_final: 0.8618 (tt0) REVERT: H 233 MET cc_start: 0.9566 (mmm) cc_final: 0.8960 (mmm) REVERT: H 271 ASP cc_start: 0.9053 (t70) cc_final: 0.8559 (t0) REVERT: H 275 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.7610 (ttp-110) REVERT: H 319 CYS cc_start: 0.8997 (m) cc_final: 0.8741 (m) REVERT: H 423 ILE cc_start: 0.9447 (pt) cc_final: 0.9211 (tt) REVERT: H 710 MET cc_start: 0.6488 (mmt) cc_final: 0.5950 (tpt) REVERT: H 903 MET cc_start: 0.7054 (mmp) cc_final: 0.6785 (mmp) REVERT: H 1025 MET cc_start: 0.7799 (mmm) cc_final: 0.7580 (mmm) REVERT: H 1031 ASP cc_start: 0.8638 (m-30) cc_final: 0.7556 (t0) REVERT: H 1066 MET cc_start: 0.7779 (mtm) cc_final: 0.6952 (mmm) REVERT: H 1103 ASN cc_start: 0.7813 (m-40) cc_final: 0.7538 (m-40) REVERT: H 1142 CYS cc_start: 0.9144 (t) cc_final: 0.8761 (m) REVERT: H 1149 LEU cc_start: 0.9015 (mt) cc_final: 0.8789 (mt) REVERT: H 1283 LEU cc_start: 0.9189 (mp) cc_final: 0.8609 (mp) REVERT: H 1395 MET cc_start: 0.8438 (mmp) cc_final: 0.8195 (mmm) REVERT: H 1514 MET cc_start: 0.7460 (mpp) cc_final: 0.7143 (ttt) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.4419 time to fit residues: 468.5667 Evaluate side-chains 447 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 457 optimal weight: 20.0000 chunk 354 optimal weight: 7.9990 chunk 527 optimal weight: 0.9990 chunk 350 optimal weight: 20.0000 chunk 624 optimal weight: 3.9990 chunk 390 optimal weight: 2.9990 chunk 380 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 48 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 GLN C 41 ASN C 48 ASN D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 51576 Z= 0.215 Angle : 0.653 10.897 70172 Z= 0.330 Chirality : 0.043 0.274 8516 Planarity : 0.004 0.068 8588 Dihedral : 8.091 123.010 7064 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 0.55 (0.11), residues: 6408 helix: 1.34 (0.08), residues: 4020 sheet: -1.16 (0.20), residues: 544 loop : -1.26 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP H1452 HIS 0.006 0.001 HIS E 259 PHE 0.042 0.002 PHE H 433 TYR 0.021 0.001 TYR B 124 ARG 0.006 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 4.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8819 (tpt) cc_final: 0.8463 (tpp) REVERT: A 81 CYS cc_start: 0.8521 (t) cc_final: 0.7412 (t) REVERT: A 88 MET cc_start: 0.8997 (tmm) cc_final: 0.8696 (tmm) REVERT: A 166 CYS cc_start: 0.9019 (p) cc_final: 0.8755 (p) REVERT: A 329 ASP cc_start: 0.7394 (p0) cc_final: 0.7035 (p0) REVERT: A 332 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8131 (mtpp) REVERT: B 91 GLU cc_start: 0.9195 (tt0) cc_final: 0.8557 (tt0) REVERT: B 233 MET cc_start: 0.9570 (mmm) cc_final: 0.8989 (mmm) REVERT: B 271 ASP cc_start: 0.9087 (t70) cc_final: 0.8614 (t0) REVERT: B 275 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7657 (ttp-110) REVERT: B 319 CYS cc_start: 0.8929 (m) cc_final: 0.8636 (m) REVERT: B 423 ILE cc_start: 0.9421 (pt) cc_final: 0.9156 (tt) REVERT: B 468 ILE cc_start: 0.8998 (tp) cc_final: 0.8789 (pt) REVERT: B 710 MET cc_start: 0.6486 (mmt) cc_final: 0.5942 (tpt) REVERT: B 903 MET cc_start: 0.7114 (mmp) cc_final: 0.6864 (mmp) REVERT: B 1025 MET cc_start: 0.7851 (mmm) cc_final: 0.7541 (mmm) REVERT: B 1031 ASP cc_start: 0.8712 (m-30) cc_final: 0.7606 (t0) REVERT: B 1066 MET cc_start: 0.7769 (mtm) cc_final: 0.6990 (mmm) REVERT: B 1142 CYS cc_start: 0.9181 (t) cc_final: 0.8812 (m) REVERT: B 1149 LEU cc_start: 0.9003 (mt) cc_final: 0.8788 (mt) REVERT: B 1252 MET cc_start: 0.8964 (tpp) cc_final: 0.8702 (tpp) REVERT: B 1283 LEU cc_start: 0.9180 (mp) cc_final: 0.8593 (mp) REVERT: B 1395 MET cc_start: 0.8454 (mmp) cc_final: 0.8219 (mmm) REVERT: B 1514 MET cc_start: 0.7464 (mpp) cc_final: 0.7150 (ttt) REVERT: C 77 MET cc_start: 0.8846 (tpt) cc_final: 0.8474 (tpp) REVERT: C 81 CYS cc_start: 0.8628 (t) cc_final: 0.7451 (t) REVERT: C 88 MET cc_start: 0.8986 (tmm) cc_final: 0.8702 (tmm) REVERT: C 164 LEU cc_start: 0.9281 (tt) cc_final: 0.8860 (tt) REVERT: C 166 CYS cc_start: 0.8946 (p) cc_final: 0.8725 (p) REVERT: C 199 MET cc_start: 0.7066 (mmp) cc_final: 0.6505 (mmp) REVERT: C 256 ILE cc_start: 0.8920 (mp) cc_final: 0.8630 (tt) REVERT: C 329 ASP cc_start: 0.7818 (p0) cc_final: 0.6828 (p0) REVERT: C 332 LYS cc_start: 0.8427 (mtmt) cc_final: 0.7874 (mtmm) REVERT: D 91 GLU cc_start: 0.9194 (tt0) cc_final: 0.8579 (tt0) REVERT: D 233 MET cc_start: 0.9587 (mmm) cc_final: 0.8999 (mmm) REVERT: D 271 ASP cc_start: 0.9087 (t70) cc_final: 0.8602 (t0) REVERT: D 275 ARG cc_start: 0.8312 (ttp-110) cc_final: 0.7769 (ttp-110) REVERT: D 319 CYS cc_start: 0.8980 (m) cc_final: 0.8698 (m) REVERT: D 423 ILE cc_start: 0.9428 (pt) cc_final: 0.9155 (tt) REVERT: D 710 MET cc_start: 0.6498 (mmt) cc_final: 0.5934 (tpt) REVERT: D 801 MET cc_start: 0.9010 (ptp) cc_final: 0.8776 (tpt) REVERT: D 903 MET cc_start: 0.7154 (mmp) cc_final: 0.6904 (mmp) REVERT: D 1025 MET cc_start: 0.7860 (mmm) cc_final: 0.7544 (mmm) REVERT: D 1031 ASP cc_start: 0.8707 (m-30) cc_final: 0.7610 (t0) REVERT: D 1066 MET cc_start: 0.7767 (mtm) cc_final: 0.6989 (mmm) REVERT: D 1142 CYS cc_start: 0.9182 (t) cc_final: 0.8817 (m) REVERT: D 1252 MET cc_start: 0.8957 (tpp) cc_final: 0.8648 (tpp) REVERT: D 1283 LEU cc_start: 0.9184 (mp) cc_final: 0.8610 (mp) REVERT: D 1514 MET cc_start: 0.7463 (mpp) cc_final: 0.7148 (ttt) REVERT: E 77 MET cc_start: 0.8847 (tpt) cc_final: 0.8513 (tpp) REVERT: E 81 CYS cc_start: 0.8597 (t) cc_final: 0.7450 (t) REVERT: E 88 MET cc_start: 0.8984 (tmm) cc_final: 0.8706 (tmm) REVERT: E 164 LEU cc_start: 0.9354 (tt) cc_final: 0.9044 (tt) REVERT: E 166 CYS cc_start: 0.8890 (p) cc_final: 0.8681 (p) REVERT: E 329 ASP cc_start: 0.7625 (p0) cc_final: 0.7003 (p0) REVERT: E 332 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7769 (mtmm) REVERT: F 91 GLU cc_start: 0.9197 (tt0) cc_final: 0.8572 (tt0) REVERT: F 233 MET cc_start: 0.9584 (mmm) cc_final: 0.9005 (mmm) REVERT: F 271 ASP cc_start: 0.9088 (t70) cc_final: 0.8601 (t0) REVERT: F 275 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.7766 (ttp-110) REVERT: F 319 CYS cc_start: 0.8940 (m) cc_final: 0.8647 (m) REVERT: F 423 ILE cc_start: 0.9431 (pt) cc_final: 0.9155 (tt) REVERT: F 710 MET cc_start: 0.6503 (mmt) cc_final: 0.5933 (tpt) REVERT: F 730 MET cc_start: 0.0656 (ttt) cc_final: 0.0445 (ppp) REVERT: F 801 MET cc_start: 0.9001 (ptp) cc_final: 0.8686 (tpt) REVERT: F 903 MET cc_start: 0.7098 (mmp) cc_final: 0.6859 (mmp) REVERT: F 1025 MET cc_start: 0.7873 (mmm) cc_final: 0.7554 (mmm) REVERT: F 1031 ASP cc_start: 0.8701 (m-30) cc_final: 0.7609 (t0) REVERT: F 1066 MET cc_start: 0.7765 (mtm) cc_final: 0.6987 (mmm) REVERT: F 1142 CYS cc_start: 0.9156 (t) cc_final: 0.8754 (m) REVERT: F 1252 MET cc_start: 0.8944 (tpp) cc_final: 0.8648 (tpp) REVERT: F 1283 LEU cc_start: 0.9180 (mp) cc_final: 0.8604 (mp) REVERT: F 1395 MET cc_start: 0.8295 (mmp) cc_final: 0.8094 (mmm) REVERT: F 1514 MET cc_start: 0.7460 (mpp) cc_final: 0.7145 (ttt) REVERT: G 73 LEU cc_start: 0.9120 (tt) cc_final: 0.8878 (pp) REVERT: G 77 MET cc_start: 0.8853 (tpt) cc_final: 0.8522 (tpp) REVERT: G 81 CYS cc_start: 0.8679 (t) cc_final: 0.7761 (t) REVERT: G 329 ASP cc_start: 0.7610 (p0) cc_final: 0.7006 (p0) REVERT: G 332 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7753 (mtmm) REVERT: H 91 GLU cc_start: 0.9201 (tt0) cc_final: 0.8564 (tt0) REVERT: H 115 MET cc_start: 0.9210 (mmm) cc_final: 0.8902 (mpp) REVERT: H 233 MET cc_start: 0.9574 (mmm) cc_final: 0.8995 (mmm) REVERT: H 257 MET cc_start: 0.8616 (ptm) cc_final: 0.8132 (ppp) REVERT: H 271 ASP cc_start: 0.9085 (t70) cc_final: 0.8608 (t0) REVERT: H 275 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.7791 (ttp-110) REVERT: H 319 CYS cc_start: 0.8921 (m) cc_final: 0.8630 (m) REVERT: H 423 ILE cc_start: 0.9419 (pt) cc_final: 0.9160 (tt) REVERT: H 468 ILE cc_start: 0.8981 (tp) cc_final: 0.8779 (pt) REVERT: H 710 MET cc_start: 0.6500 (mmt) cc_final: 0.5941 (tpt) REVERT: H 903 MET cc_start: 0.7109 (mmp) cc_final: 0.6844 (mmp) REVERT: H 1025 MET cc_start: 0.7862 (mmm) cc_final: 0.7546 (mmm) REVERT: H 1031 ASP cc_start: 0.8707 (m-30) cc_final: 0.7619 (t0) REVERT: H 1066 MET cc_start: 0.7747 (mtm) cc_final: 0.6947 (mmm) REVERT: H 1103 ASN cc_start: 0.7683 (m-40) cc_final: 0.7401 (m-40) REVERT: H 1142 CYS cc_start: 0.9154 (t) cc_final: 0.8740 (m) REVERT: H 1149 LEU cc_start: 0.9016 (mt) cc_final: 0.8800 (mt) REVERT: H 1252 MET cc_start: 0.8884 (tpp) cc_final: 0.8661 (tpp) REVERT: H 1283 LEU cc_start: 0.9177 (mp) cc_final: 0.8603 (mp) REVERT: H 1514 MET cc_start: 0.7461 (mpp) cc_final: 0.7146 (ttt) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.4316 time to fit residues: 424.7711 Evaluate side-chains 429 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 10.0000 chunk 249 optimal weight: 0.0030 chunk 373 optimal weight: 9.9990 chunk 188 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 397 optimal weight: 20.0000 chunk 425 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 490 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51576 Z= 0.185 Angle : 0.650 14.112 70172 Z= 0.323 Chirality : 0.043 0.275 8516 Planarity : 0.004 0.100 8588 Dihedral : 8.011 122.989 7064 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.64 (0.11), residues: 6408 helix: 1.42 (0.08), residues: 4004 sheet: -1.04 (0.21), residues: 516 loop : -1.26 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H1452 HIS 0.005 0.001 HIS G 259 PHE 0.053 0.002 PHE F 433 TYR 0.025 0.001 TYR H 124 ARG 0.006 0.000 ARG D1419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8840 (tpt) cc_final: 0.8524 (tpp) REVERT: A 81 CYS cc_start: 0.8370 (t) cc_final: 0.8000 (t) REVERT: A 88 MET cc_start: 0.8979 (tmm) cc_final: 0.8699 (tmm) REVERT: A 164 LEU cc_start: 0.9286 (tt) cc_final: 0.8883 (tt) REVERT: A 166 CYS cc_start: 0.8953 (p) cc_final: 0.8725 (p) REVERT: A 199 MET cc_start: 0.7274 (mmp) cc_final: 0.6572 (mmp) REVERT: A 329 ASP cc_start: 0.7346 (p0) cc_final: 0.6973 (p0) REVERT: A 332 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8075 (mtpp) REVERT: B 91 GLU cc_start: 0.9184 (tt0) cc_final: 0.8535 (tt0) REVERT: B 233 MET cc_start: 0.9550 (mmm) cc_final: 0.8977 (mmm) REVERT: B 257 MET cc_start: 0.8846 (pmm) cc_final: 0.8620 (ptm) REVERT: B 271 ASP cc_start: 0.9079 (t70) cc_final: 0.8628 (t0) REVERT: B 275 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7737 (ttp-110) REVERT: B 319 CYS cc_start: 0.8889 (m) cc_final: 0.8602 (m) REVERT: B 423 ILE cc_start: 0.9402 (pt) cc_final: 0.9127 (tt) REVERT: B 710 MET cc_start: 0.6482 (mmt) cc_final: 0.5946 (tpt) REVERT: B 1025 MET cc_start: 0.7846 (mmm) cc_final: 0.7509 (mmm) REVERT: B 1031 ASP cc_start: 0.8704 (m-30) cc_final: 0.7601 (t0) REVERT: B 1066 MET cc_start: 0.7735 (mtm) cc_final: 0.6990 (mmm) REVERT: B 1142 CYS cc_start: 0.9170 (t) cc_final: 0.8834 (m) REVERT: B 1283 LEU cc_start: 0.9173 (mp) cc_final: 0.8562 (mp) REVERT: B 1395 MET cc_start: 0.8433 (mmp) cc_final: 0.8202 (mmm) REVERT: B 1514 MET cc_start: 0.7364 (mpp) cc_final: 0.7040 (ttt) REVERT: C 77 MET cc_start: 0.8857 (tpt) cc_final: 0.8499 (tpp) REVERT: C 81 CYS cc_start: 0.8588 (t) cc_final: 0.7663 (t) REVERT: C 88 MET cc_start: 0.8972 (tmm) cc_final: 0.8699 (tmm) REVERT: C 137 MET cc_start: 0.8306 (mmm) cc_final: 0.8072 (mmm) REVERT: C 159 ILE cc_start: 0.9166 (tp) cc_final: 0.8847 (pt) REVERT: C 166 CYS cc_start: 0.9021 (p) cc_final: 0.8735 (p) REVERT: C 199 MET cc_start: 0.7000 (mmp) cc_final: 0.6573 (mmp) REVERT: C 256 ILE cc_start: 0.8935 (mp) cc_final: 0.8620 (tt) REVERT: C 329 ASP cc_start: 0.7668 (p0) cc_final: 0.6628 (p0) REVERT: C 332 LYS cc_start: 0.8446 (mtmt) cc_final: 0.7731 (mtmm) REVERT: D 91 GLU cc_start: 0.9179 (tt0) cc_final: 0.8538 (tt0) REVERT: D 233 MET cc_start: 0.9569 (mmm) cc_final: 0.8985 (mmm) REVERT: D 271 ASP cc_start: 0.9079 (t70) cc_final: 0.8626 (t0) REVERT: D 275 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7726 (ttp-110) REVERT: D 319 CYS cc_start: 0.8895 (m) cc_final: 0.8606 (m) REVERT: D 423 ILE cc_start: 0.9416 (pt) cc_final: 0.9153 (tt) REVERT: D 710 MET cc_start: 0.6500 (mmt) cc_final: 0.5942 (tpt) REVERT: D 801 MET cc_start: 0.9013 (ptp) cc_final: 0.8775 (tpt) REVERT: D 1025 MET cc_start: 0.7856 (mmm) cc_final: 0.7515 (mmm) REVERT: D 1031 ASP cc_start: 0.8699 (m-30) cc_final: 0.7599 (t0) REVERT: D 1066 MET cc_start: 0.7726 (mtm) cc_final: 0.6984 (mmm) REVERT: D 1142 CYS cc_start: 0.9170 (t) cc_final: 0.8795 (m) REVERT: D 1252 MET cc_start: 0.8949 (tpp) cc_final: 0.8738 (tpp) REVERT: D 1283 LEU cc_start: 0.9171 (mp) cc_final: 0.8560 (mp) REVERT: D 1395 MET cc_start: 0.8606 (mmp) cc_final: 0.8324 (mmm) REVERT: D 1514 MET cc_start: 0.7363 (mpp) cc_final: 0.7040 (ttt) REVERT: E 77 MET cc_start: 0.8931 (tpt) cc_final: 0.8603 (tpp) REVERT: E 81 CYS cc_start: 0.8512 (t) cc_final: 0.7490 (t) REVERT: E 88 MET cc_start: 0.8961 (tmm) cc_final: 0.8685 (tmm) REVERT: E 164 LEU cc_start: 0.9333 (tt) cc_final: 0.9043 (tt) REVERT: E 329 ASP cc_start: 0.7544 (p0) cc_final: 0.6927 (p0) REVERT: E 332 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7769 (mtmm) REVERT: F 91 GLU cc_start: 0.9189 (tt0) cc_final: 0.8546 (tt0) REVERT: F 233 MET cc_start: 0.9519 (mmm) cc_final: 0.8988 (mmm) REVERT: F 271 ASP cc_start: 0.9073 (t70) cc_final: 0.8614 (t0) REVERT: F 275 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.7797 (ttp-110) REVERT: F 319 CYS cc_start: 0.8888 (m) cc_final: 0.8603 (m) REVERT: F 423 ILE cc_start: 0.9420 (pt) cc_final: 0.9150 (tt) REVERT: F 710 MET cc_start: 0.6509 (mmt) cc_final: 0.5939 (tpt) REVERT: F 730 MET cc_start: 0.1499 (ttt) cc_final: 0.0743 (ppp) REVERT: F 801 MET cc_start: 0.9009 (ptp) cc_final: 0.8773 (tpt) REVERT: F 1025 MET cc_start: 0.7870 (mmm) cc_final: 0.7524 (mmm) REVERT: F 1031 ASP cc_start: 0.8691 (m-30) cc_final: 0.7602 (t0) REVERT: F 1066 MET cc_start: 0.7724 (mtm) cc_final: 0.6984 (mmm) REVERT: F 1142 CYS cc_start: 0.9131 (t) cc_final: 0.8690 (m) REVERT: F 1283 LEU cc_start: 0.9167 (mp) cc_final: 0.8700 (mp) REVERT: F 1395 MET cc_start: 0.8396 (mmp) cc_final: 0.8168 (mmm) REVERT: F 1514 MET cc_start: 0.7362 (mpp) cc_final: 0.7034 (ttt) REVERT: G 73 LEU cc_start: 0.9069 (tt) cc_final: 0.8865 (pp) REVERT: G 81 CYS cc_start: 0.8572 (t) cc_final: 0.7443 (t) REVERT: G 88 MET cc_start: 0.9129 (tmm) cc_final: 0.8726 (tmm) REVERT: G 199 MET cc_start: 0.7199 (mmp) cc_final: 0.6611 (mmp) REVERT: G 329 ASP cc_start: 0.7544 (p0) cc_final: 0.6948 (p0) REVERT: G 332 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7711 (mtmm) REVERT: H 91 GLU cc_start: 0.9195 (tt0) cc_final: 0.8538 (tt0) REVERT: H 115 MET cc_start: 0.9198 (mmm) cc_final: 0.8884 (mpp) REVERT: H 233 MET cc_start: 0.9500 (mmm) cc_final: 0.8980 (mmm) REVERT: H 271 ASP cc_start: 0.9060 (t70) cc_final: 0.8590 (t0) REVERT: H 275 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7761 (ttp-110) REVERT: H 319 CYS cc_start: 0.8883 (m) cc_final: 0.8601 (m) REVERT: H 423 ILE cc_start: 0.9416 (pt) cc_final: 0.9142 (tt) REVERT: H 710 MET cc_start: 0.6499 (mmt) cc_final: 0.5947 (tpt) REVERT: H 1025 MET cc_start: 0.7859 (mmm) cc_final: 0.7518 (mmm) REVERT: H 1031 ASP cc_start: 0.8703 (m-30) cc_final: 0.7611 (t0) REVERT: H 1066 MET cc_start: 0.7735 (mtm) cc_final: 0.6992 (mmm) REVERT: H 1103 ASN cc_start: 0.7700 (m-40) cc_final: 0.7429 (m-40) REVERT: H 1142 CYS cc_start: 0.9134 (t) cc_final: 0.8670 (m) REVERT: H 1149 LEU cc_start: 0.9040 (mt) cc_final: 0.8817 (mt) REVERT: H 1252 MET cc_start: 0.8982 (tpp) cc_final: 0.8716 (tpp) REVERT: H 1283 LEU cc_start: 0.9174 (mp) cc_final: 0.8593 (mp) REVERT: H 1395 MET cc_start: 0.8433 (mmp) cc_final: 0.8205 (mmm) REVERT: H 1514 MET cc_start: 0.7363 (mpp) cc_final: 0.7043 (ttt) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.4365 time to fit residues: 432.8943 Evaluate side-chains 435 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 10.0000 chunk 598 optimal weight: 30.0000 chunk 545 optimal weight: 3.9990 chunk 582 optimal weight: 8.9990 chunk 350 optimal weight: 20.0000 chunk 253 optimal weight: 30.0000 chunk 457 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 525 optimal weight: 0.9990 chunk 550 optimal weight: 10.0000 chunk 579 optimal weight: 20.0000 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 41 ASN A 216 HIS ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN B 863 HIS ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 909 GLN ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 863 HIS F 909 GLN ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 863 HIS H 909 GLN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 51576 Z= 0.301 Angle : 0.726 15.659 70172 Z= 0.369 Chirality : 0.045 0.295 8516 Planarity : 0.005 0.083 8588 Dihedral : 8.192 124.681 7064 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.11), residues: 6408 helix: 1.23 (0.08), residues: 4016 sheet: -1.18 (0.20), residues: 524 loop : -1.13 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP E 83 HIS 0.009 0.001 HIS F 67 PHE 0.042 0.002 PHE A 75 TYR 0.027 0.002 TYR B 124 ARG 0.011 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8897 (tpt) cc_final: 0.8515 (tpp) REVERT: A 81 CYS cc_start: 0.8776 (t) cc_final: 0.8550 (t) REVERT: A 88 MET cc_start: 0.9015 (tmm) cc_final: 0.8625 (tmm) REVERT: A 164 LEU cc_start: 0.9383 (tt) cc_final: 0.9032 (tt) REVERT: A 256 ILE cc_start: 0.8954 (mp) cc_final: 0.8538 (tt) REVERT: A 332 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8266 (mtpp) REVERT: B 91 GLU cc_start: 0.9102 (tt0) cc_final: 0.8720 (tt0) REVERT: B 233 MET cc_start: 0.9630 (mmm) cc_final: 0.9006 (mmm) REVERT: B 271 ASP cc_start: 0.9004 (t70) cc_final: 0.8502 (t0) REVERT: B 275 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7795 (ttp-110) REVERT: B 319 CYS cc_start: 0.8817 (m) cc_final: 0.8511 (m) REVERT: B 423 ILE cc_start: 0.9428 (pt) cc_final: 0.9154 (tt) REVERT: B 710 MET cc_start: 0.6658 (mmt) cc_final: 0.5998 (tpt) REVERT: B 730 MET cc_start: 0.0115 (ppp) cc_final: -0.0163 (ttt) REVERT: B 1025 MET cc_start: 0.7833 (mmm) cc_final: 0.7492 (mmm) REVERT: B 1031 ASP cc_start: 0.8736 (m-30) cc_final: 0.7739 (t0) REVERT: B 1066 MET cc_start: 0.7799 (mtm) cc_final: 0.7011 (mmm) REVERT: B 1142 CYS cc_start: 0.9182 (t) cc_final: 0.8800 (m) REVERT: B 1252 MET cc_start: 0.9058 (tpp) cc_final: 0.8852 (tpp) REVERT: B 1283 LEU cc_start: 0.9055 (mp) cc_final: 0.8410 (mp) REVERT: B 1395 MET cc_start: 0.8448 (mmp) cc_final: 0.8224 (mmm) REVERT: B 1514 MET cc_start: 0.7393 (mpp) cc_final: 0.7106 (ttt) REVERT: C 77 MET cc_start: 0.8877 (tpt) cc_final: 0.8490 (tpp) REVERT: C 81 CYS cc_start: 0.8550 (t) cc_final: 0.7409 (t) REVERT: C 88 MET cc_start: 0.9024 (tmm) cc_final: 0.8627 (tmm) REVERT: C 137 MET cc_start: 0.8362 (mmm) cc_final: 0.8075 (mmm) REVERT: C 164 LEU cc_start: 0.9346 (tt) cc_final: 0.8909 (tt) REVERT: C 166 CYS cc_start: 0.9026 (p) cc_final: 0.8769 (p) REVERT: C 256 ILE cc_start: 0.8881 (mp) cc_final: 0.8452 (tt) REVERT: C 329 ASP cc_start: 0.7925 (p0) cc_final: 0.6989 (p0) REVERT: C 332 LYS cc_start: 0.8480 (mtmt) cc_final: 0.7919 (mtmm) REVERT: D 91 GLU cc_start: 0.9110 (tt0) cc_final: 0.8711 (tt0) REVERT: D 233 MET cc_start: 0.9550 (mmm) cc_final: 0.9011 (mmm) REVERT: D 271 ASP cc_start: 0.9001 (t70) cc_final: 0.8503 (t0) REVERT: D 275 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7787 (ttp-110) REVERT: D 319 CYS cc_start: 0.8827 (m) cc_final: 0.8520 (m) REVERT: D 423 ILE cc_start: 0.9424 (pt) cc_final: 0.9156 (tt) REVERT: D 468 ILE cc_start: 0.9087 (tp) cc_final: 0.8840 (pt) REVERT: D 710 MET cc_start: 0.6674 (mmt) cc_final: 0.5986 (tpt) REVERT: D 730 MET cc_start: 0.0085 (ppp) cc_final: -0.0151 (ttt) REVERT: D 1025 MET cc_start: 0.7840 (mmm) cc_final: 0.7497 (mmm) REVERT: D 1031 ASP cc_start: 0.8732 (m-30) cc_final: 0.7740 (t0) REVERT: D 1066 MET cc_start: 0.7721 (mtm) cc_final: 0.6941 (mmm) REVERT: D 1142 CYS cc_start: 0.9172 (t) cc_final: 0.8809 (m) REVERT: D 1252 MET cc_start: 0.8888 (tpp) cc_final: 0.8653 (tpp) REVERT: D 1283 LEU cc_start: 0.9052 (mp) cc_final: 0.8405 (mp) REVERT: D 1395 MET cc_start: 0.8509 (mmp) cc_final: 0.8308 (mmm) REVERT: D 1514 MET cc_start: 0.7530 (mpp) cc_final: 0.7238 (ttt) REVERT: E 77 MET cc_start: 0.8894 (tpt) cc_final: 0.8532 (tpp) REVERT: E 81 CYS cc_start: 0.8592 (t) cc_final: 0.7596 (t) REVERT: E 88 MET cc_start: 0.9044 (tmm) cc_final: 0.8653 (tmm) REVERT: E 332 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7730 (mtmm) REVERT: F 91 GLU cc_start: 0.9101 (tt0) cc_final: 0.8720 (tt0) REVERT: F 233 MET cc_start: 0.9631 (mmm) cc_final: 0.9015 (mmm) REVERT: F 271 ASP cc_start: 0.9003 (t70) cc_final: 0.8500 (t0) REVERT: F 275 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7784 (ttp-110) REVERT: F 319 CYS cc_start: 0.8820 (m) cc_final: 0.8512 (m) REVERT: F 423 ILE cc_start: 0.9424 (pt) cc_final: 0.9155 (tt) REVERT: F 710 MET cc_start: 0.6683 (mmt) cc_final: 0.5986 (tpt) REVERT: F 730 MET cc_start: 0.1851 (ttt) cc_final: 0.1506 (ttt) REVERT: F 1025 MET cc_start: 0.7848 (mmm) cc_final: 0.7505 (mmm) REVERT: F 1031 ASP cc_start: 0.8732 (m-30) cc_final: 0.7714 (t0) REVERT: F 1066 MET cc_start: 0.7720 (mtm) cc_final: 0.6943 (mmm) REVERT: F 1142 CYS cc_start: 0.9166 (t) cc_final: 0.8754 (m) REVERT: F 1283 LEU cc_start: 0.9054 (mp) cc_final: 0.8411 (mp) REVERT: F 1514 MET cc_start: 0.7528 (mpp) cc_final: 0.7239 (ttt) REVERT: G 77 MET cc_start: 0.8809 (tpt) cc_final: 0.8507 (tpp) REVERT: G 81 CYS cc_start: 0.8683 (t) cc_final: 0.7740 (t) REVERT: G 164 LEU cc_start: 0.9441 (tt) cc_final: 0.9160 (tt) REVERT: G 199 MET cc_start: 0.7169 (mmp) cc_final: 0.6945 (mmp) REVERT: G 332 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7806 (mtmm) REVERT: H 91 GLU cc_start: 0.9094 (tt0) cc_final: 0.8729 (tt0) REVERT: H 115 MET cc_start: 0.9271 (mmm) cc_final: 0.8987 (mpp) REVERT: H 233 MET cc_start: 0.9636 (mmm) cc_final: 0.9022 (mmm) REVERT: H 271 ASP cc_start: 0.9007 (t70) cc_final: 0.8501 (t0) REVERT: H 275 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7792 (ttp-110) REVERT: H 319 CYS cc_start: 0.8813 (m) cc_final: 0.8504 (m) REVERT: H 423 ILE cc_start: 0.9437 (pt) cc_final: 0.9160 (tt) REVERT: H 468 ILE cc_start: 0.9089 (tp) cc_final: 0.8848 (pt) REVERT: H 710 MET cc_start: 0.6674 (mmt) cc_final: 0.5994 (tpt) REVERT: H 730 MET cc_start: 0.0049 (ppp) cc_final: -0.0186 (ttt) REVERT: H 1025 MET cc_start: 0.7840 (mmm) cc_final: 0.7496 (mmm) REVERT: H 1031 ASP cc_start: 0.8737 (m-30) cc_final: 0.7720 (t0) REVERT: H 1066 MET cc_start: 0.7803 (mtm) cc_final: 0.7012 (mmm) REVERT: H 1103 ASN cc_start: 0.7652 (m-40) cc_final: 0.7369 (m110) REVERT: H 1142 CYS cc_start: 0.9144 (t) cc_final: 0.8683 (m) REVERT: H 1283 LEU cc_start: 0.9053 (mp) cc_final: 0.8404 (mp) REVERT: H 1290 MET cc_start: 0.8899 (ttm) cc_final: 0.8243 (tpp) REVERT: H 1395 MET cc_start: 0.8439 (mmp) cc_final: 0.8216 (mmm) REVERT: H 1514 MET cc_start: 0.7531 (mpp) cc_final: 0.7243 (ttt) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.4402 time to fit residues: 405.1737 Evaluate side-chains 396 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 4.9990 chunk 615 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 291 optimal weight: 0.9990 chunk 427 optimal weight: 7.9990 chunk 645 optimal weight: 3.9990 chunk 594 optimal weight: 0.0060 chunk 514 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 397 optimal weight: 10.0000 chunk 315 optimal weight: 8.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 51576 Z= 0.197 Angle : 0.664 12.053 70172 Z= 0.330 Chirality : 0.043 0.272 8516 Planarity : 0.004 0.063 8588 Dihedral : 8.023 124.100 7064 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.11), residues: 6408 helix: 1.43 (0.08), residues: 4000 sheet: -1.04 (0.20), residues: 532 loop : -1.19 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 83 HIS 0.006 0.001 HIS E 259 PHE 0.038 0.002 PHE A 168 TYR 0.033 0.001 TYR F 124 ARG 0.008 0.000 ARG G 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 4.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8846 (tpt) cc_final: 0.8561 (tpp) REVERT: A 81 CYS cc_start: 0.8463 (t) cc_final: 0.7608 (t) REVERT: A 88 MET cc_start: 0.9045 (tmm) cc_final: 0.8733 (tmm) REVERT: A 332 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8124 (mtpp) REVERT: B 44 PHE cc_start: 0.8889 (m-80) cc_final: 0.8669 (m-80) REVERT: B 66 LEU cc_start: 0.8891 (mm) cc_final: 0.8555 (mp) REVERT: B 91 GLU cc_start: 0.9030 (tt0) cc_final: 0.8741 (tt0) REVERT: B 233 MET cc_start: 0.9611 (mmm) cc_final: 0.8978 (mmm) REVERT: B 271 ASP cc_start: 0.9009 (t70) cc_final: 0.8561 (t0) REVERT: B 275 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7808 (ttp-110) REVERT: B 319 CYS cc_start: 0.8850 (m) cc_final: 0.8559 (m) REVERT: B 423 ILE cc_start: 0.9409 (pt) cc_final: 0.9138 (tt) REVERT: B 710 MET cc_start: 0.6641 (mmt) cc_final: 0.5991 (tpt) REVERT: B 903 MET cc_start: 0.7569 (mmp) cc_final: 0.7081 (mmp) REVERT: B 1025 MET cc_start: 0.7856 (mmm) cc_final: 0.7537 (mmm) REVERT: B 1031 ASP cc_start: 0.8705 (m-30) cc_final: 0.7629 (t0) REVERT: B 1066 MET cc_start: 0.7850 (mtm) cc_final: 0.7111 (mmm) REVERT: B 1142 CYS cc_start: 0.9084 (t) cc_final: 0.8666 (m) REVERT: B 1252 MET cc_start: 0.9035 (tpp) cc_final: 0.8678 (tpp) REVERT: B 1283 LEU cc_start: 0.9099 (mp) cc_final: 0.8489 (mp) REVERT: B 1395 MET cc_start: 0.8493 (mmp) cc_final: 0.8230 (mmm) REVERT: B 1514 MET cc_start: 0.7327 (mpp) cc_final: 0.7025 (ttt) REVERT: B 1550 MET cc_start: 0.5613 (ptm) cc_final: 0.5331 (ppp) REVERT: C 77 MET cc_start: 0.8840 (tpt) cc_final: 0.8463 (tpp) REVERT: C 81 CYS cc_start: 0.8485 (t) cc_final: 0.7376 (t) REVERT: C 88 MET cc_start: 0.9011 (tmm) cc_final: 0.8730 (tmm) REVERT: C 137 MET cc_start: 0.8140 (mmm) cc_final: 0.7878 (mmm) REVERT: C 164 LEU cc_start: 0.9294 (tt) cc_final: 0.8965 (tt) REVERT: C 166 CYS cc_start: 0.8896 (p) cc_final: 0.8665 (p) REVERT: C 256 ILE cc_start: 0.8842 (mp) cc_final: 0.8490 (tt) REVERT: C 329 ASP cc_start: 0.7770 (p0) cc_final: 0.6814 (p0) REVERT: C 332 LYS cc_start: 0.8515 (mtmt) cc_final: 0.7869 (mtmm) REVERT: D 66 LEU cc_start: 0.8849 (mm) cc_final: 0.8520 (mp) REVERT: D 91 GLU cc_start: 0.9030 (tt0) cc_final: 0.8754 (tt0) REVERT: D 233 MET cc_start: 0.9632 (mmm) cc_final: 0.9006 (mmm) REVERT: D 271 ASP cc_start: 0.9006 (t70) cc_final: 0.8556 (t0) REVERT: D 275 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7800 (ttp-110) REVERT: D 319 CYS cc_start: 0.8856 (m) cc_final: 0.8529 (m) REVERT: D 423 ILE cc_start: 0.9408 (pt) cc_final: 0.9137 (tt) REVERT: D 710 MET cc_start: 0.6651 (mmt) cc_final: 0.5982 (tpt) REVERT: D 801 MET cc_start: 0.9007 (ptp) cc_final: 0.8790 (tpt) REVERT: D 903 MET cc_start: 0.7518 (mmp) cc_final: 0.7021 (mmp) REVERT: D 1025 MET cc_start: 0.7863 (mmm) cc_final: 0.7549 (mmm) REVERT: D 1031 ASP cc_start: 0.8699 (m-30) cc_final: 0.7645 (t0) REVERT: D 1066 MET cc_start: 0.7823 (mtm) cc_final: 0.7071 (mmm) REVERT: D 1142 CYS cc_start: 0.9091 (t) cc_final: 0.8672 (m) REVERT: D 1252 MET cc_start: 0.8896 (tpp) cc_final: 0.8544 (tpp) REVERT: D 1283 LEU cc_start: 0.9098 (mp) cc_final: 0.8518 (mp) REVERT: D 1305 MET cc_start: 0.8555 (mmm) cc_final: 0.8330 (mmm) REVERT: D 1395 MET cc_start: 0.8339 (mmp) cc_final: 0.8020 (mmm) REVERT: D 1514 MET cc_start: 0.7322 (mpp) cc_final: 0.7020 (ttt) REVERT: D 1550 MET cc_start: 0.5629 (ptm) cc_final: 0.5355 (ppp) REVERT: E 77 MET cc_start: 0.8844 (tpt) cc_final: 0.8525 (tpp) REVERT: E 81 CYS cc_start: 0.8540 (t) cc_final: 0.7530 (t) REVERT: E 88 MET cc_start: 0.9022 (tmm) cc_final: 0.8737 (tmm) REVERT: E 164 LEU cc_start: 0.9402 (tt) cc_final: 0.9089 (tt) REVERT: E 166 CYS cc_start: 0.8952 (p) cc_final: 0.8751 (p) REVERT: E 329 ASP cc_start: 0.7698 (p0) cc_final: 0.7133 (p0) REVERT: E 332 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7860 (mtmm) REVERT: F 66 LEU cc_start: 0.8904 (mm) cc_final: 0.8557 (mp) REVERT: F 91 GLU cc_start: 0.9045 (tt0) cc_final: 0.8758 (tt0) REVERT: F 233 MET cc_start: 0.9618 (mmm) cc_final: 0.8986 (mmm) REVERT: F 271 ASP cc_start: 0.9000 (t70) cc_final: 0.8541 (t0) REVERT: F 275 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7862 (ttp-110) REVERT: F 319 CYS cc_start: 0.8854 (m) cc_final: 0.8559 (m) REVERT: F 423 ILE cc_start: 0.9408 (pt) cc_final: 0.9138 (tt) REVERT: F 710 MET cc_start: 0.6661 (mmt) cc_final: 0.5983 (tpt) REVERT: F 801 MET cc_start: 0.9006 (ptp) cc_final: 0.8787 (tpt) REVERT: F 903 MET cc_start: 0.7530 (mmp) cc_final: 0.7029 (mmp) REVERT: F 1025 MET cc_start: 0.7872 (mmm) cc_final: 0.7551 (mmm) REVERT: F 1031 ASP cc_start: 0.8701 (m-30) cc_final: 0.7650 (t0) REVERT: F 1066 MET cc_start: 0.7778 (mtm) cc_final: 0.7049 (mmm) REVERT: F 1142 CYS cc_start: 0.9080 (t) cc_final: 0.8602 (m) REVERT: F 1283 LEU cc_start: 0.9104 (mp) cc_final: 0.8505 (mp) REVERT: F 1514 MET cc_start: 0.7465 (mpp) cc_final: 0.7161 (ttt) REVERT: F 1550 MET cc_start: 0.5417 (ptm) cc_final: 0.5079 (ppp) REVERT: G 73 LEU cc_start: 0.9083 (tt) cc_final: 0.8860 (pp) REVERT: G 81 CYS cc_start: 0.8464 (t) cc_final: 0.7389 (t) REVERT: G 166 CYS cc_start: 0.9080 (p) cc_final: 0.8836 (p) REVERT: G 168 PHE cc_start: 0.8453 (t80) cc_final: 0.8050 (t80) REVERT: G 329 ASP cc_start: 0.7679 (p0) cc_final: 0.7083 (p0) REVERT: G 332 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7923 (mtmm) REVERT: H 66 LEU cc_start: 0.8854 (mm) cc_final: 0.8503 (mp) REVERT: H 91 GLU cc_start: 0.9059 (tt0) cc_final: 0.8772 (tt0) REVERT: H 233 MET cc_start: 0.9616 (mmm) cc_final: 0.8996 (mmm) REVERT: H 271 ASP cc_start: 0.9003 (t70) cc_final: 0.8546 (t0) REVERT: H 275 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7847 (ttp-110) REVERT: H 319 CYS cc_start: 0.8839 (m) cc_final: 0.8519 (m) REVERT: H 423 ILE cc_start: 0.9419 (pt) cc_final: 0.9155 (tt) REVERT: H 468 ILE cc_start: 0.9071 (tp) cc_final: 0.8841 (pt) REVERT: H 502 MET cc_start: 0.7947 (mmm) cc_final: 0.7255 (mmm) REVERT: H 710 MET cc_start: 0.6659 (mmt) cc_final: 0.5994 (tpt) REVERT: H 903 MET cc_start: 0.7547 (mmp) cc_final: 0.7047 (mmp) REVERT: H 1025 MET cc_start: 0.7861 (mmm) cc_final: 0.7542 (mmm) REVERT: H 1031 ASP cc_start: 0.8706 (m-30) cc_final: 0.7655 (t0) REVERT: H 1066 MET cc_start: 0.7856 (mtm) cc_final: 0.7113 (mmm) REVERT: H 1103 ASN cc_start: 0.7579 (m-40) cc_final: 0.7298 (m-40) REVERT: H 1142 CYS cc_start: 0.9070 (t) cc_final: 0.8584 (m) REVERT: H 1283 LEU cc_start: 0.9099 (mp) cc_final: 0.8504 (mp) REVERT: H 1290 MET cc_start: 0.8835 (ttm) cc_final: 0.8256 (tpp) REVERT: H 1514 MET cc_start: 0.7325 (mpp) cc_final: 0.7024 (ttt) REVERT: H 1550 MET cc_start: 0.5633 (ptm) cc_final: 0.5347 (ppp) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.4377 time to fit residues: 431.2614 Evaluate side-chains 438 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 20.0000 chunk 547 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 474 optimal weight: 30.0000 chunk 75 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 514 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 528 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 ASN C 216 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1293 ASN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.083481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065766 restraints weight = 304131.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064386 restraints weight = 198172.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064518 restraints weight = 171211.850| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 51576 Z= 0.295 Angle : 0.715 13.040 70172 Z= 0.362 Chirality : 0.044 0.264 8516 Planarity : 0.004 0.075 8588 Dihedral : 8.176 125.372 7064 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.56 (0.11), residues: 6408 helix: 1.32 (0.08), residues: 3996 sheet: -1.17 (0.20), residues: 532 loop : -1.16 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 83 HIS 0.007 0.001 HIS A 259 PHE 0.046 0.002 PHE B 433 TYR 0.028 0.002 TYR F 124 ARG 0.019 0.001 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9542.09 seconds wall clock time: 167 minutes 8.18 seconds (10028.18 seconds total)