Starting phenix.real_space_refine on Mon Nov 20 16:13:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/11_2023/5yke_6831_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/11_2023/5yke_6831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/11_2023/5yke_6831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/11_2023/5yke_6831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/11_2023/5yke_6831_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/11_2023/5yke_6831_updated.pdb" } resolution = 4.11 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= 0.001 sd= 0.005 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 S 188 5.16 5 Cl 4 4.86 5 C 20196 2.51 5 N 5116 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 999": "NH1" <-> "NH2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "B ARG 1111": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "B ARG 1218": "NH1" <-> "NH2" Residue "B ARG 1274": "NH1" <-> "NH2" Residue "B ARG 1300": "NH1" <-> "NH2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 999": "NH1" <-> "NH2" Residue "D ARG 1099": "NH1" <-> "NH2" Residue "D ARG 1104": "NH1" <-> "NH2" Residue "D ARG 1111": "NH1" <-> "NH2" Residue "D ARG 1145": "NH1" <-> "NH2" Residue "D TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1183": "NH1" <-> "NH2" Residue "D ARG 1218": "NH1" <-> "NH2" Residue "D ARG 1274": "NH1" <-> "NH2" Residue "D ARG 1300": "NH1" <-> "NH2" Residue "F ARG 248": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "F ARG 486": "NH1" <-> "NH2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 527": "NH1" <-> "NH2" Residue "F ARG 534": "NH1" <-> "NH2" Residue "F ARG 598": "NH1" <-> "NH2" Residue "F ARG 999": "NH1" <-> "NH2" Residue "F ARG 1099": "NH1" <-> "NH2" Residue "F ARG 1104": "NH1" <-> "NH2" Residue "F ARG 1111": "NH1" <-> "NH2" Residue "F ARG 1145": "NH1" <-> "NH2" Residue "F TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1183": "NH1" <-> "NH2" Residue "F ARG 1218": "NH1" <-> "NH2" Residue "F ARG 1274": "NH1" <-> "NH2" Residue "F ARG 1300": "NH1" <-> "NH2" Residue "H ARG 248": "NH1" <-> "NH2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "H ARG 486": "NH1" <-> "NH2" Residue "H ARG 504": "NH1" <-> "NH2" Residue "H ARG 521": "NH1" <-> "NH2" Residue "H ARG 527": "NH1" <-> "NH2" Residue "H ARG 534": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 999": "NH1" <-> "NH2" Residue "H ARG 1099": "NH1" <-> "NH2" Residue "H ARG 1104": "NH1" <-> "NH2" Residue "H ARG 1111": "NH1" <-> "NH2" Residue "H ARG 1145": "NH1" <-> "NH2" Residue "H TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1183": "NH1" <-> "NH2" Residue "H ARG 1218": "NH1" <-> "NH2" Residue "H ARG 1274": "NH1" <-> "NH2" Residue "H ARG 1300": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 30636 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 128} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6598 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 819} Chain breaks: 8 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 128} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6598 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 819} Chain breaks: 8 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "E" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 128} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6598 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 819} Chain breaks: 8 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 128} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6598 Classifications: {'peptide': 845} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 819} Chain breaks: 8 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.92, per 1000 atoms: 0.52 Number of scatterers: 30636 At special positions: 0 Unit cell: (174.075, 174.075, 110.775, 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) Cl 4 17.00 S 188 16.00 O 5132 8.00 N 5116 7.00 C 20196 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.03 Conformation dependent library (CDL) restraints added in 5.9 seconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.077A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 51 Proline residue: B 35 - end of helix removed outlier: 3.942A 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 71 through 95 Processing helix chain 'B' and resid 104 through 129 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 134 through 159 removed outlier: 3.855A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 192 Processing helix chain 'B' and resid 208 through 211 No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 226 through 229 No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 328 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 356 through 401 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 424 through 500 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 removed outlier: 8.211A pdb=" N VAL B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.652A 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 Processing helix chain 'B' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.612A 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 573 through 614 Proline residue: B 589 - end of helix removed outlier: 4.447A 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: 3.846A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1008 removed outlier: 3.804A pdb=" N ALA B1008 " --> pdb=" O TYR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.637A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1106 Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1160 Proline residue: B1137 - end of helix Processing helix chain 'B' and resid 1162 through 1216 removed outlier: 3.820A 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: 3.561A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.914A 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) removed outlier: 5.695A pdb=" N THR B1212 " --> pdb=" O VAL B1208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1270 removed outlier: 3.725A 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 1288 removed outlier: 4.013A 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 1291 through 1319 removed outlier: 4.141A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 97 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 removed outlier: 4.077A 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 'D' and resid 25 through 51 Proline residue: D 35 - end of helix removed outlier: 3.942A 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 71 through 95 Processing helix chain 'D' and resid 104 through 129 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 134 through 159 removed outlier: 3.855A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 192 Processing helix chain 'D' and resid 208 through 211 No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 226 through 229 No H-bonds generated for 'chain 'D' and resid 226 through 229' Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA D 235 " --> pdb=" O TRP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.080A 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 356 through 401 removed outlier: 3.630A 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) Processing helix chain 'D' and resid 412 through 422 Processing helix chain 'D' and resid 424 through 500 Proline residue: D 436 - end of helix removed outlier: 3.536A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix removed outlier: 8.211A pdb=" N VAL D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.667A 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 Processing helix chain 'D' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.612A 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 573 through 614 Proline residue: D 589 - end of helix removed outlier: 4.447A 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 998 through 1008 removed outlier: 3.804A pdb=" N ALA D1008 " --> pdb=" O TYR D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.637A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1106 Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1128 through 1160 Proline residue: D1137 - end of helix Processing helix chain 'D' and resid 1162 through 1216 removed outlier: 3.820A 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: 3.561A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.914A 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) removed outlier: 5.695A pdb=" N THR D1212 " --> pdb=" O VAL D1208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR D1213 " --> pdb=" O GLU D1209 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1270 removed outlier: 3.725A 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 1288 removed outlier: 4.013A 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 1291 through 1319 removed outlier: 4.141A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 57 No H-bonds generated for 'chain 'E' and resid 54 through 57' Processing helix chain 'E' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 97 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 143 through 171 removed outlier: 4.077A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 51 Proline residue: F 35 - end of helix removed outlier: 3.942A 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 71 through 95 Processing helix chain 'F' and resid 104 through 129 Proline residue: F 109 - end of helix removed outlier: 3.757A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 removed outlier: 3.855A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 192 Processing helix chain 'F' and resid 208 through 211 No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA F 235 " --> pdb=" O TRP F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 328 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 356 through 401 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) Processing helix chain 'F' and resid 412 through 422 Processing helix chain 'F' and resid 424 through 500 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 removed outlier: 8.211A pdb=" N VAL F 458 " --> pdb=" O TYR F 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.667A 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 Processing helix chain 'F' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.612A 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 573 through 614 Proline residue: F 589 - end of helix removed outlier: 4.447A 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 998 through 1008 removed outlier: 3.804A pdb=" N ALA F1008 " --> pdb=" O TYR F1004 " (cutoff:3.500A) Processing helix chain 'F' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.637A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1106 Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1128 through 1160 Proline residue: F1137 - end of helix Processing helix chain 'F' and resid 1162 through 1216 removed outlier: 3.820A 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: 3.561A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.914A 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: 3.525A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR F1212 " --> pdb=" O VAL F1208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR F1213 " --> pdb=" O GLU F1209 " (cutoff:3.500A) Processing helix chain 'F' and resid 1220 through 1270 removed outlier: 3.725A 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 1288 removed outlier: 4.013A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1291 through 1319 removed outlier: 4.141A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 57 No H-bonds generated for 'chain 'G' and resid 54 through 57' Processing helix chain 'G' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 97 Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 143 through 171 removed outlier: 4.077A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 51 Proline residue: H 35 - end of helix removed outlier: 3.942A 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 71 through 95 Processing helix chain 'H' and resid 104 through 129 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 134 through 159 removed outlier: 3.855A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 192 Processing helix chain 'H' and resid 208 through 211 No H-bonds generated for 'chain 'H' and resid 208 through 211' Processing helix chain 'H' and resid 226 through 229 No H-bonds generated for 'chain 'H' and resid 226 through 229' Processing helix chain 'H' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA H 235 " --> pdb=" O TRP H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.382A 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 356 through 401 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) Processing helix chain 'H' and resid 412 through 422 Processing helix chain 'H' and resid 424 through 500 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 removed outlier: 8.211A pdb=" N VAL H 458 " --> pdb=" O TYR H 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER H 459 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix Processing helix chain 'H' and resid 506 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 515 through 559 removed outlier: 3.655A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.554A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 614 Proline residue: H 589 - end of helix removed outlier: 4.447A 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 998 through 1008 removed outlier: 3.804A pdb=" N ALA H1008 " --> pdb=" O TYR H1004 " (cutoff:3.500A) Processing helix chain 'H' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.637A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1106 Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1126 removed outlier: 4.265A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1128 through 1160 Proline residue: H1137 - end of helix Processing helix chain 'H' and resid 1162 through 1216 removed outlier: 3.820A 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: 3.561A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.914A 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) removed outlier: 5.695A pdb=" N THR H1212 " --> pdb=" O VAL H1208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR H1213 " --> pdb=" O GLU H1209 " (cutoff:3.500A) Processing helix chain 'H' and resid 1220 through 1270 removed outlier: 3.725A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.722A 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 1288 removed outlier: 4.013A 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 1291 through 1319 removed outlier: 4.141A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.369A 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) 2336 hydrogen bonds defined for protein. 6912 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: 9.36 Time building geometry restraints manager: 13.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8600 1.34 - 1.46: 6252 1.46 - 1.58: 16160 1.58 - 1.70: 8 1.70 - 1.82: 292 Bond restraints: 31312 Sorted by residual: bond pdb=" C18 GBM B2001 " pdb=" S2 GBM B2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM D2001 " pdb=" S2 GBM D2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM F2001 " pdb=" S2 GBM F2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C18 GBM H2001 " pdb=" S2 GBM H2001 " ideal model delta sigma weight residual 1.765 1.603 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C27 GBM F2001 " pdb=" C28 GBM F2001 " ideal model delta sigma weight residual 1.401 1.490 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 31307 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.85: 548 105.85 - 112.91: 17812 112.91 - 119.98: 10736 119.98 - 127.04: 13112 127.04 - 134.11: 380 Bond angle restraints: 42588 Sorted by residual: angle pdb=" N THR B 200 " pdb=" CA THR B 200 " pdb=" C THR B 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR D 200 " pdb=" CA THR D 200 " pdb=" C THR D 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR H 200 " pdb=" CA THR H 200 " pdb=" C THR H 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" N THR F 200 " pdb=" CA THR F 200 " pdb=" C THR F 200 " ideal model delta sigma weight residual 109.83 120.85 -11.02 1.27e+00 6.20e-01 7.53e+01 angle pdb=" C SER D 532 " pdb=" N LEU D 533 " pdb=" CA LEU D 533 " ideal model delta sigma weight residual 120.28 130.85 -10.57 1.44e+00 4.82e-01 5.38e+01 ... (remaining 42583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 16812 16.31 - 32.62: 1092 32.62 - 48.93: 348 48.93 - 65.24: 124 65.24 - 81.55: 8 Dihedral angle restraints: 18384 sinusoidal: 6928 harmonic: 11456 Sorted by residual: dihedral pdb=" CA PHE D 295 " pdb=" C PHE D 295 " pdb=" N GLY D 296 " pdb=" CA GLY D 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE F 295 " pdb=" C PHE F 295 " pdb=" N GLY F 296 " pdb=" CA GLY F 296 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 18381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4420 0.058 - 0.117: 692 0.117 - 0.175: 44 0.175 - 0.233: 16 0.233 - 0.292: 24 Chirality restraints: 5196 Sorted by residual: chirality pdb=" CA ASP B1133 " pdb=" N ASP B1133 " pdb=" C ASP B1133 " pdb=" CB ASP B1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP F1133 " pdb=" N ASP F1133 " pdb=" C ASP F1133 " pdb=" CB ASP F1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP D1133 " pdb=" N ASP D1133 " pdb=" C ASP D1133 " pdb=" CB ASP D1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 5193 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM F2001 " 0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM F2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM F2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM F2001 " -0.478 2.00e-02 2.50e+03 pdb=" O6 GBM F2001 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM H2001 " -0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM H2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM H2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM H2001 " 0.478 2.00e-02 2.50e+03 pdb=" O6 GBM H2001 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM D2001 " 0.321 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C26 GBM D2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM D2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM D2001 " -0.478 2.00e-02 2.50e+03 pdb=" O6 GBM D2001 " 0.063 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6512 2.78 - 3.31: 32700 3.31 - 3.84: 51184 3.84 - 4.37: 55958 4.37 - 4.90: 94296 Nonbonded interactions: 240650 Sorted by model distance: nonbonded pdb=" OD2 ASP B1031 " pdb=" OH TYR B1287 " model vdw 2.246 2.440 nonbonded pdb=" OD2 ASP D1031 " pdb=" OH TYR D1287 " model vdw 2.246 2.440 nonbonded pdb=" OD2 ASP F1031 " pdb=" OH TYR F1287 " model vdw 2.246 2.440 nonbonded pdb=" OD2 ASP H1031 " pdb=" OH TYR H1287 " model vdw 2.246 2.440 nonbonded pdb=" O SER F1126 " pdb=" ND2 ASN F1130 " model vdw 2.276 2.520 ... (remaining 240645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.110 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 80.310 Find NCS groups from input model: 1.910 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 0.162 31312 Z= 0.329 Angle : 0.809 12.002 42588 Z= 0.463 Chirality : 0.046 0.292 5196 Planarity : 0.010 0.272 5116 Dihedral : 13.283 81.548 10900 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.65 % Favored : 95.93 % Rotamer: Outliers : 7.60 % Allowed : 10.29 % Favored : 82.11 % 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: -1.76 (0.12), residues: 3832 helix: -0.74 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 664 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 930 time to evaluate : 3.767 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 48 residues processed: 1114 average time/residue: 0.3981 time to fit residues: 712.8367 Evaluate side-chains 473 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 425 time to evaluate : 3.621 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3876 time to fit residues: 34.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 4.9990 chunk 294 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 304 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 352 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 397 ASN B 485 GLN B1020 GLN B1296 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 326 HIS D 397 ASN D 485 GLN D1020 GLN D1296 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN F 397 ASN F 485 GLN F1020 GLN F1296 ASN H 262 ASN H 397 ASN H 485 GLN H1020 GLN H1296 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31312 Z= 0.213 Angle : 0.693 8.006 42588 Z= 0.351 Chirality : 0.040 0.181 5196 Planarity : 0.005 0.060 5116 Dihedral : 5.166 62.944 4204 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.19 % Favored : 97.70 % Rotamer: Outliers : 0.37 % Allowed : 4.84 % Favored : 94.79 % 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: 0.34 (0.13), residues: 3832 helix: 0.68 (0.09), residues: 3184 sheet: None (None), residues: 0 loop : -1.65 (0.25), residues: 648 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 596 time to evaluate : 4.066 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 outliers start: 12 outliers final: 4 residues processed: 604 average time/residue: 0.3839 time to fit residues: 386.2118 Evaluate side-chains 384 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 380 time to evaluate : 3.809 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.0910 time to fit residues: 10.2328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 0.0770 chunk 109 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 239 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 381 optimal weight: 0.9990 chunk 314 optimal weight: 0.9980 chunk 350 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN B 397 ASN B1020 GLN D 262 ASN D 397 ASN D1020 GLN F 262 ASN F 397 ASN F1020 GLN H 262 ASN H 397 ASN H1020 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31312 Z= 0.196 Angle : 0.625 8.036 42588 Z= 0.320 Chirality : 0.038 0.160 5196 Planarity : 0.005 0.055 5116 Dihedral : 4.832 53.816 4204 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3832 helix: 1.23 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 640 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 566 average time/residue: 0.3759 time to fit residues: 360.9084 Evaluate side-chains 350 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 3.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 335 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31312 Z= 0.348 Angle : 0.733 8.085 42588 Z= 0.375 Chirality : 0.042 0.183 5196 Planarity : 0.005 0.075 5116 Dihedral : 5.119 53.234 4204 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.13), residues: 3832 helix: 1.18 (0.09), residues: 3180 sheet: None (None), residues: 0 loop : -1.06 (0.27), residues: 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 3.626 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.3609 time to fit residues: 269.0166 Evaluate side-chains 270 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 3.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 0.6980 chunk 212 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 320 optimal weight: 0.4980 chunk 259 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 485 GLN ** H 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31312 Z= 0.315 Angle : 0.695 8.024 42588 Z= 0.358 Chirality : 0.040 0.219 5196 Planarity : 0.005 0.069 5116 Dihedral : 5.092 50.698 4204 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 3832 helix: 1.24 (0.09), residues: 3212 sheet: None (None), residues: 0 loop : -1.22 (0.28), residues: 620 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 450 time to evaluate : 3.256 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.4052 time to fit residues: 314.2523 Evaluate side-chains 282 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 375 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS B 262 ASN B 397 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN C 175 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 GLN E 175 HIS F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 427 GLN G 175 HIS H 262 ASN ** H 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31312 Z= 0.193 Angle : 0.640 8.050 42588 Z= 0.320 Chirality : 0.039 0.206 5196 Planarity : 0.005 0.068 5116 Dihedral : 4.845 47.190 4204 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.43 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 1.69 (0.14), residues: 3832 helix: 1.56 (0.09), residues: 3164 sheet: None (None), residues: 0 loop : -0.90 (0.28), residues: 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 3.964 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 outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.3411 time to fit residues: 297.0747 Evaluate side-chains 317 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 3.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 274 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 373 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 227 optimal weight: 0.0570 chunk 172 optimal weight: 7.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 397 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H 426 ASN ** 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: 0.7755 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31312 Z= 0.187 Angle : 0.659 10.049 42588 Z= 0.323 Chirality : 0.039 0.198 5196 Planarity : 0.005 0.064 5116 Dihedral : 4.782 45.254 4204 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.17 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 1.71 (0.14), residues: 3832 helix: 1.59 (0.09), residues: 3176 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 656 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 3.580 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.3508 time to fit residues: 290.3801 Evaluate side-chains 304 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 223 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 254 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS B 397 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS H 397 ASN ** H 426 ASN ** 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: 0.7771 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31312 Z= 0.225 Angle : 0.664 8.422 42588 Z= 0.329 Chirality : 0.039 0.203 5196 Planarity : 0.005 0.067 5116 Dihedral : 4.763 48.737 4204 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.71 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 1.75 (0.14), residues: 3832 helix: 1.63 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 664 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 4.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.3581 time to fit residues: 276.4622 Evaluate side-chains 288 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 3.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 6.9990 chunk 358 optimal weight: 4.9990 chunk 326 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 314 optimal weight: 2.9990 chunk 329 optimal weight: 4.9990 chunk 347 optimal weight: 0.0170 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31312 Z= 0.352 Angle : 0.760 8.367 42588 Z= 0.386 Chirality : 0.043 0.213 5196 Planarity : 0.005 0.085 5116 Dihedral : 5.044 54.478 4204 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.14), residues: 3832 helix: 1.36 (0.09), residues: 3176 sheet: None (None), residues: 0 loop : -0.79 (0.28), residues: 656 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 4.053 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.3169 time to fit residues: 230.9418 Evaluate side-chains 271 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 0.6980 chunk 368 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 256 optimal weight: 0.9980 chunk 386 optimal weight: 0.9990 chunk 355 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN F 397 ASN F 426 ASN ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1098 HIS ** 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: 0.7801 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31312 Z= 0.227 Angle : 0.679 8.078 42588 Z= 0.337 Chirality : 0.039 0.187 5196 Planarity : 0.005 0.076 5116 Dihedral : 4.850 55.455 4204 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 0.03 % Allowed : 0.58 % Favored : 99.39 % 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: 1.74 (0.14), residues: 3832 helix: 1.59 (0.09), residues: 3156 sheet: None (None), residues: 0 loop : -0.80 (0.27), residues: 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 428 time to evaluate : 5.502 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 429 average time/residue: 0.3899 time to fit residues: 291.5991 Evaluate side-chains 278 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 3.632 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2610 time to fit residues: 5.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 129 optimal weight: 0.4980 chunk 316 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN B 426 ASN ** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 426 ASN ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1245 ASN E 153 ASN F 397 ASN F 426 ASN ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1245 ASN H 397 ASN H 426 ASN ** H1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.094588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078442 restraints weight = 111557.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077800 restraints weight = 97982.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078624 restraints weight = 92438.573| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6666 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: