Starting phenix.real_space_refine on Thu Mar 21 16:04:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/03_2024/5yke_6831_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/03_2024/5yke_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_6831/03_2024/5yke_6831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/03_2024/5yke_6831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/03_2024/5yke_6831_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yke_6831/03_2024/5yke_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 15.30, per 1000 atoms: 0.50 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: 11.56 Conformation dependent library (CDL) restraints added in 5.2 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: 6.32 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: 9.66 Time building geometry restraints manager: 12.62 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 - 16.66: 16888 16.66 - 33.32: 1056 33.32 - 49.99: 344 49.99 - 66.65: 104 66.65 - 83.31: 24 Dihedral angle restraints: 18416 sinusoidal: 6960 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 18413 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: 1.690 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: 7.840 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 75.840 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.490 ------------------------------------------------------------------------------- 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 : 13.613 83.309 10932 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1037 HIS 0.011 0.001 HIS E 175 PHE 0.034 0.002 PHE A 168 TYR 0.014 0.002 TYR D 378 ARG 0.002 0.000 ARG B 598 *********************** 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 : 3.483 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 REVERT: A 47 LYS cc_start: 0.7945 (tptt) cc_final: 0.6949 (mptt) REVERT: A 91 TRP cc_start: 0.9116 (t60) cc_final: 0.8852 (t-100) REVERT: A 152 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8635 (tp40) REVERT: A 176 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7260 (mtt180) REVERT: A 177 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.6761 (ttp-170) REVERT: B 51 TRP cc_start: 0.7652 (t60) cc_final: 0.6543 (m-10) REVERT: B 79 PHE cc_start: 0.8932 (m-80) cc_final: 0.8666 (m-10) REVERT: B 136 LEU cc_start: 0.8057 (mt) cc_final: 0.7532 (pp) REVERT: B 157 PHE cc_start: 0.7468 (t80) cc_final: 0.6640 (t80) REVERT: B 158 TYR cc_start: 0.8838 (t80) cc_final: 0.8619 (t80) REVERT: B 181 MET cc_start: 0.9001 (mtp) cc_final: 0.8522 (mmt) REVERT: B 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8689 (tt) REVERT: B 186 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7759 (tp30) REVERT: B 233 MET cc_start: 0.9260 (mmm) cc_final: 0.9004 (mmm) REVERT: B 374 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9085 (mm-40) REVERT: B 382 GLU cc_start: 0.8066 (tt0) cc_final: 0.7679 (tt0) REVERT: B 441 MET cc_start: 0.9035 (tpp) cc_final: 0.8739 (tpt) REVERT: B 570 ASP cc_start: 0.7538 (m-30) cc_final: 0.6976 (t70) REVERT: B 1031 ASP cc_start: 0.8795 (m-30) cc_final: 0.8487 (p0) REVERT: B 1064 TYR cc_start: 0.7670 (m-80) cc_final: 0.7445 (m-80) REVERT: B 1148 LEU cc_start: 0.8954 (mt) cc_final: 0.8600 (tp) REVERT: B 1168 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8031 (tp) REVERT: B 1171 LEU cc_start: 0.8464 (mt) cc_final: 0.8261 (pp) REVERT: B 1246 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8774 (mmp80) REVERT: B 1252 MET cc_start: 0.9034 (ttm) cc_final: 0.8721 (mmt) REVERT: C 91 TRP cc_start: 0.9116 (t60) cc_final: 0.8852 (t-100) REVERT: C 131 ILE cc_start: 0.8712 (pt) cc_final: 0.8497 (mt) REVERT: C 152 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8629 (tp40) REVERT: C 176 ARG cc_start: 0.7544 (mmt180) cc_final: 0.7261 (mtt180) REVERT: C 177 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.6759 (ttp-170) REVERT: D 51 TRP cc_start: 0.7654 (t60) cc_final: 0.6547 (m-10) REVERT: D 79 PHE cc_start: 0.8932 (m-80) cc_final: 0.8664 (m-10) REVERT: D 136 LEU cc_start: 0.8059 (mt) cc_final: 0.7529 (pp) REVERT: D 157 PHE cc_start: 0.7467 (t80) cc_final: 0.6639 (t80) REVERT: D 158 TYR cc_start: 0.8839 (t80) cc_final: 0.8617 (t80) REVERT: D 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8523 (mmt) REVERT: D 184 LEU cc_start: 0.9346 (mt) cc_final: 0.8691 (tt) REVERT: D 186 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7760 (tp30) REVERT: D 233 MET cc_start: 0.9261 (mmm) cc_final: 0.9006 (mmm) REVERT: D 374 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9082 (mm-40) REVERT: D 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7670 (tt0) REVERT: D 441 MET cc_start: 0.9032 (tpp) cc_final: 0.8735 (tpt) REVERT: D 570 ASP cc_start: 0.7539 (m-30) cc_final: 0.6980 (t70) REVERT: D 1031 ASP cc_start: 0.8797 (m-30) cc_final: 0.8486 (p0) REVERT: D 1064 TYR cc_start: 0.7668 (m-80) cc_final: 0.7445 (m-80) REVERT: D 1148 LEU cc_start: 0.8956 (mt) cc_final: 0.8602 (tp) REVERT: D 1168 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8029 (tp) REVERT: D 1171 LEU cc_start: 0.8465 (mt) cc_final: 0.8262 (pp) REVERT: D 1246 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8775 (mmp80) REVERT: D 1252 MET cc_start: 0.9036 (ttm) cc_final: 0.8723 (mmt) REVERT: E 91 TRP cc_start: 0.9119 (t60) cc_final: 0.8852 (t-100) REVERT: E 152 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8631 (tp40) REVERT: E 176 ARG cc_start: 0.7543 (mmt180) cc_final: 0.7255 (mtt180) REVERT: E 177 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: F 51 TRP cc_start: 0.7650 (t60) cc_final: 0.6544 (m-10) REVERT: F 79 PHE cc_start: 0.8930 (m-80) cc_final: 0.8663 (m-10) REVERT: F 136 LEU cc_start: 0.8064 (mt) cc_final: 0.7535 (pp) REVERT: F 157 PHE cc_start: 0.7469 (t80) cc_final: 0.6644 (t80) REVERT: F 158 TYR cc_start: 0.8840 (t80) cc_final: 0.8620 (t80) REVERT: F 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8525 (mmt) REVERT: F 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8691 (tt) REVERT: F 186 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7757 (tp30) REVERT: F 233 MET cc_start: 0.9255 (mmm) cc_final: 0.9003 (mmm) REVERT: F 320 ILE cc_start: 0.8992 (mt) cc_final: 0.8792 (mt) REVERT: F 374 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9083 (mm-40) REVERT: F 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7672 (tt0) REVERT: F 441 MET cc_start: 0.9031 (tpp) cc_final: 0.8733 (tpt) REVERT: F 570 ASP cc_start: 0.7538 (m-30) cc_final: 0.6979 (t70) REVERT: F 1031 ASP cc_start: 0.8795 (m-30) cc_final: 0.8483 (p0) REVERT: F 1064 TYR cc_start: 0.7669 (m-80) cc_final: 0.7448 (m-80) REVERT: F 1148 LEU cc_start: 0.8958 (mt) cc_final: 0.8602 (tp) REVERT: F 1168 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8036 (tp) REVERT: F 1171 LEU cc_start: 0.8465 (mt) cc_final: 0.8263 (pp) REVERT: F 1246 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8775 (mmp80) REVERT: F 1252 MET cc_start: 0.9033 (ttm) cc_final: 0.8721 (mmt) REVERT: G 91 TRP cc_start: 0.9115 (t60) cc_final: 0.8847 (t-100) REVERT: G 131 ILE cc_start: 0.8714 (pt) cc_final: 0.8507 (mt) REVERT: G 152 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8626 (tp40) REVERT: G 176 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7256 (mtt180) REVERT: G 177 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.6760 (ttp-170) REVERT: H 51 TRP cc_start: 0.7653 (t60) cc_final: 0.6545 (m-10) REVERT: H 79 PHE cc_start: 0.8930 (m-80) cc_final: 0.8665 (m-10) REVERT: H 136 LEU cc_start: 0.8062 (mt) cc_final: 0.7537 (pp) REVERT: H 157 PHE cc_start: 0.7469 (t80) cc_final: 0.6642 (t80) REVERT: H 158 TYR cc_start: 0.8839 (t80) cc_final: 0.8618 (t80) REVERT: H 181 MET cc_start: 0.9000 (mtp) cc_final: 0.8522 (mmt) REVERT: H 184 LEU cc_start: 0.9344 (mt) cc_final: 0.8691 (tt) REVERT: H 186 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7759 (tp30) REVERT: H 233 MET cc_start: 0.9257 (mmm) cc_final: 0.9003 (mmm) REVERT: H 374 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.9084 (mm-40) REVERT: H 382 GLU cc_start: 0.8068 (tt0) cc_final: 0.7673 (tt0) REVERT: H 441 MET cc_start: 0.9036 (tpp) cc_final: 0.8738 (tpt) REVERT: H 570 ASP cc_start: 0.7534 (m-30) cc_final: 0.6975 (t70) REVERT: H 1031 ASP cc_start: 0.8798 (m-30) cc_final: 0.8483 (p0) REVERT: H 1064 TYR cc_start: 0.7670 (m-80) cc_final: 0.7449 (m-80) REVERT: H 1148 LEU cc_start: 0.8953 (mt) cc_final: 0.8597 (tp) REVERT: H 1168 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8036 (tp) REVERT: H 1171 LEU cc_start: 0.8467 (mt) cc_final: 0.8264 (pp) REVERT: H 1246 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8776 (mmp80) REVERT: H 1252 MET cc_start: 0.9036 (ttm) cc_final: 0.8724 (mmt) outliers start: 248 outliers final: 48 residues processed: 1114 average time/residue: 0.3981 time to fit residues: 715.5529 Evaluate side-chains 536 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 472 time to evaluate : 3.673 ------------------------------------------------------------------------------- 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: 0.9980 chunk 294 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 304 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 352 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 326 HIS D 397 ASN D 485 GLN D1020 GLN D1296 ASN 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: 0.7646 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31312 Z= 0.218 Angle : 0.687 7.691 42588 Z= 0.349 Chirality : 0.040 0.160 5196 Planarity : 0.005 0.060 5116 Dihedral : 5.681 62.514 4236 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.19 % Favored : 97.70 % Rotamer: Outliers : 0.12 % Allowed : 4.04 % Favored : 95.83 % 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: 0.39 (0.13), residues: 3832 helix: 0.70 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 232 HIS 0.006 0.001 HIS D 36 PHE 0.029 0.002 PHE G 168 TYR 0.012 0.001 TYR B 123 ARG 0.005 0.000 ARG F 306 *********************** 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 629 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 625 time to evaluate : 3.742 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 47 LYS cc_start: 0.7892 (tptt) cc_final: 0.7103 (mptt) REVERT: A 158 MET cc_start: 0.8407 (mmt) cc_final: 0.8142 (tmm) REVERT: A 163 MET cc_start: 0.8630 (ttt) cc_final: 0.8160 (ppp) REVERT: B 51 TRP cc_start: 0.7782 (t60) cc_final: 0.6384 (m-10) REVERT: B 79 PHE cc_start: 0.8920 (m-80) cc_final: 0.8634 (m-10) REVERT: B 104 LEU cc_start: 0.8372 (mt) cc_final: 0.7794 (mt) REVERT: B 108 MET cc_start: 0.9029 (tpp) cc_final: 0.8392 (mpp) REVERT: B 157 PHE cc_start: 0.7578 (t80) cc_final: 0.6722 (t80) REVERT: B 184 LEU cc_start: 0.9411 (mt) cc_final: 0.8787 (tt) REVERT: B 319 CYS cc_start: 0.7496 (m) cc_final: 0.7142 (t) REVERT: B 507 LYS cc_start: 0.8442 (tptt) cc_final: 0.8218 (mmtm) REVERT: B 570 ASP cc_start: 0.7551 (m-30) cc_final: 0.6935 (t70) REVERT: B 1110 MET cc_start: 0.4263 (mmt) cc_final: 0.3989 (mmt) REVERT: B 1146 SER cc_start: 0.8614 (m) cc_final: 0.8138 (p) REVERT: B 1298 MET cc_start: 0.8621 (ttt) cc_final: 0.8245 (ttt) REVERT: C 91 TRP cc_start: 0.9004 (t60) cc_final: 0.8298 (t60) REVERT: C 158 MET cc_start: 0.8403 (mmt) cc_final: 0.8137 (tmm) REVERT: C 163 MET cc_start: 0.8631 (ttt) cc_final: 0.8167 (ppp) REVERT: D 51 TRP cc_start: 0.7786 (t60) cc_final: 0.6397 (m-10) REVERT: D 79 PHE cc_start: 0.8921 (m-80) cc_final: 0.8635 (m-10) REVERT: D 104 LEU cc_start: 0.8372 (mt) cc_final: 0.7791 (mt) REVERT: D 108 MET cc_start: 0.9030 (tpp) cc_final: 0.8393 (mpp) REVERT: D 157 PHE cc_start: 0.7576 (t80) cc_final: 0.6697 (t80) REVERT: D 184 LEU cc_start: 0.9410 (mt) cc_final: 0.8788 (tt) REVERT: D 319 CYS cc_start: 0.7493 (m) cc_final: 0.7140 (t) REVERT: D 507 LYS cc_start: 0.8441 (tptt) cc_final: 0.8217 (mmtm) REVERT: D 570 ASP cc_start: 0.7557 (m-30) cc_final: 0.6942 (t70) REVERT: D 1110 MET cc_start: 0.4256 (mmt) cc_final: 0.3982 (mmt) REVERT: D 1146 SER cc_start: 0.8619 (m) cc_final: 0.8140 (p) REVERT: D 1298 MET cc_start: 0.8626 (ttt) cc_final: 0.8249 (ttt) REVERT: E 158 MET cc_start: 0.8400 (mmt) cc_final: 0.8134 (tmm) REVERT: E 163 MET cc_start: 0.8621 (ttt) cc_final: 0.8166 (ppp) REVERT: F 51 TRP cc_start: 0.7783 (t60) cc_final: 0.6387 (m-10) REVERT: F 79 PHE cc_start: 0.8922 (m-80) cc_final: 0.8637 (m-10) REVERT: F 104 LEU cc_start: 0.8375 (mt) cc_final: 0.7799 (mt) REVERT: F 108 MET cc_start: 0.9026 (tpp) cc_final: 0.8394 (mpp) REVERT: F 157 PHE cc_start: 0.7575 (t80) cc_final: 0.6705 (t80) REVERT: F 184 LEU cc_start: 0.9409 (mt) cc_final: 0.8785 (tt) REVERT: F 319 CYS cc_start: 0.7475 (m) cc_final: 0.7106 (t) REVERT: F 507 LYS cc_start: 0.8440 (tptt) cc_final: 0.8218 (mmtm) REVERT: F 570 ASP cc_start: 0.7554 (m-30) cc_final: 0.6940 (t70) REVERT: F 1110 MET cc_start: 0.4259 (mmt) cc_final: 0.3981 (mmt) REVERT: F 1146 SER cc_start: 0.8618 (m) cc_final: 0.8132 (p) REVERT: F 1298 MET cc_start: 0.8628 (ttt) cc_final: 0.8248 (ttt) REVERT: G 137 MET cc_start: 0.7473 (mmm) cc_final: 0.6674 (tmm) REVERT: G 158 MET cc_start: 0.8393 (mmt) cc_final: 0.8109 (tmm) REVERT: G 163 MET cc_start: 0.8624 (ttt) cc_final: 0.8167 (ppp) REVERT: H 51 TRP cc_start: 0.7790 (t60) cc_final: 0.6402 (m-10) REVERT: H 79 PHE cc_start: 0.8921 (m-80) cc_final: 0.8635 (m-10) REVERT: H 104 LEU cc_start: 0.8371 (mt) cc_final: 0.7791 (mt) REVERT: H 108 MET cc_start: 0.9027 (tpp) cc_final: 0.8390 (mpp) REVERT: H 157 PHE cc_start: 0.7584 (t80) cc_final: 0.6709 (t80) REVERT: H 184 LEU cc_start: 0.9409 (mt) cc_final: 0.8785 (tt) REVERT: H 319 CYS cc_start: 0.7492 (m) cc_final: 0.7135 (t) REVERT: H 507 LYS cc_start: 0.8444 (tptt) cc_final: 0.8217 (mmtm) REVERT: H 570 ASP cc_start: 0.7549 (m-30) cc_final: 0.6932 (t70) REVERT: H 1110 MET cc_start: 0.4261 (mmt) cc_final: 0.3987 (mmt) REVERT: H 1146 SER cc_start: 0.8614 (m) cc_final: 0.8129 (p) REVERT: H 1298 MET cc_start: 0.8625 (ttt) cc_final: 0.8248 (ttt) outliers start: 4 outliers final: 0 residues processed: 629 average time/residue: 0.3605 time to fit residues: 378.1719 Evaluate side-chains 411 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.301 ------------------------------------------------------------------------------- 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: 0.9990 chunk 109 optimal weight: 0.8980 chunk 293 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 chunk 381 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN D 397 ASN D1020 GLN F 397 ASN H 397 ASN H1020 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31312 Z= 0.238 Angle : 0.651 8.118 42588 Z= 0.332 Chirality : 0.039 0.157 5196 Planarity : 0.005 0.053 5116 Dihedral : 5.300 52.336 4236 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.73 % 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: 1.32 (0.14), residues: 3832 helix: 1.33 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 90 HIS 0.008 0.001 HIS F 326 PHE 0.038 0.002 PHE A 168 TYR 0.019 0.001 TYR D 230 ARG 0.005 0.000 ARG G 136 *********************** 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 526 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 521 time to evaluate : 3.526 Fit side-chains REVERT: A 47 LYS cc_start: 0.8295 (tptt) cc_final: 0.7436 (mptt) REVERT: A 81 CYS cc_start: 0.8298 (t) cc_final: 0.8090 (t) REVERT: B 104 LEU cc_start: 0.8758 (mt) cc_final: 0.7972 (mt) REVERT: B 108 MET cc_start: 0.9018 (tpp) cc_final: 0.8005 (mpp) REVERT: B 112 MET cc_start: 0.9375 (mmm) cc_final: 0.9129 (mmm) REVERT: B 136 LEU cc_start: 0.7864 (mt) cc_final: 0.7207 (pp) REVERT: B 157 PHE cc_start: 0.7701 (t80) cc_final: 0.7053 (t80) REVERT: B 181 MET cc_start: 0.9217 (mmm) cc_final: 0.8943 (mmm) REVERT: B 184 LEU cc_start: 0.9387 (mt) cc_final: 0.8778 (tt) REVERT: B 319 CYS cc_start: 0.7394 (m) cc_final: 0.7001 (t) REVERT: B 417 ILE cc_start: 0.9528 (mt) cc_final: 0.9201 (mt) REVERT: B 507 LYS cc_start: 0.8333 (tptt) cc_final: 0.8052 (mptt) REVERT: B 570 ASP cc_start: 0.7601 (m-30) cc_final: 0.7131 (t0) REVERT: B 583 PHE cc_start: 0.9576 (m-10) cc_final: 0.9353 (m-80) REVERT: B 1110 MET cc_start: 0.4723 (mmt) cc_final: 0.3201 (mmt) REVERT: C 81 CYS cc_start: 0.8297 (t) cc_final: 0.8088 (t) REVERT: C 163 MET cc_start: 0.8620 (ttt) cc_final: 0.8368 (ttt) REVERT: D 104 LEU cc_start: 0.8763 (mt) cc_final: 0.7975 (mt) REVERT: D 108 MET cc_start: 0.9006 (tpp) cc_final: 0.7997 (mpp) REVERT: D 112 MET cc_start: 0.9383 (mmm) cc_final: 0.9140 (mmm) REVERT: D 136 LEU cc_start: 0.7866 (mt) cc_final: 0.7210 (pp) REVERT: D 157 PHE cc_start: 0.7708 (t80) cc_final: 0.7058 (t80) REVERT: D 181 MET cc_start: 0.9219 (mmm) cc_final: 0.8946 (mmm) REVERT: D 184 LEU cc_start: 0.9386 (mt) cc_final: 0.8778 (tt) REVERT: D 319 CYS cc_start: 0.7391 (m) cc_final: 0.7003 (t) REVERT: D 417 ILE cc_start: 0.9535 (mt) cc_final: 0.9202 (mt) REVERT: D 507 LYS cc_start: 0.8335 (tptt) cc_final: 0.8054 (mptt) REVERT: D 570 ASP cc_start: 0.7600 (m-30) cc_final: 0.7135 (t0) REVERT: D 583 PHE cc_start: 0.9576 (m-10) cc_final: 0.9352 (m-80) REVERT: D 1110 MET cc_start: 0.4721 (mmt) cc_final: 0.3203 (mmt) REVERT: E 81 CYS cc_start: 0.8305 (t) cc_final: 0.8091 (t) REVERT: E 163 MET cc_start: 0.8603 (ttt) cc_final: 0.8370 (ttt) REVERT: E 168 PHE cc_start: 0.7043 (t80) cc_final: 0.6799 (t80) REVERT: F 104 LEU cc_start: 0.8760 (mt) cc_final: 0.7977 (mt) REVERT: F 108 MET cc_start: 0.9015 (tpp) cc_final: 0.8002 (mpp) REVERT: F 112 MET cc_start: 0.9380 (mmm) cc_final: 0.9137 (mmm) REVERT: F 136 LEU cc_start: 0.7869 (mt) cc_final: 0.7211 (pp) REVERT: F 157 PHE cc_start: 0.7699 (t80) cc_final: 0.7050 (t80) REVERT: F 181 MET cc_start: 0.9220 (mmm) cc_final: 0.8946 (mmm) REVERT: F 184 LEU cc_start: 0.9388 (mt) cc_final: 0.8777 (tt) REVERT: F 319 CYS cc_start: 0.7415 (m) cc_final: 0.7029 (t) REVERT: F 417 ILE cc_start: 0.9535 (mt) cc_final: 0.9203 (mt) REVERT: F 507 LYS cc_start: 0.8334 (tptt) cc_final: 0.8054 (mptt) REVERT: F 570 ASP cc_start: 0.7599 (m-30) cc_final: 0.7132 (t0) REVERT: F 583 PHE cc_start: 0.9576 (m-10) cc_final: 0.9372 (m-80) REVERT: F 1110 MET cc_start: 0.4716 (mmt) cc_final: 0.3200 (mmt) REVERT: G 81 CYS cc_start: 0.8297 (t) cc_final: 0.8074 (t) REVERT: G 163 MET cc_start: 0.8651 (ttt) cc_final: 0.8324 (ppp) REVERT: H 104 LEU cc_start: 0.8756 (mt) cc_final: 0.7971 (mt) REVERT: H 108 MET cc_start: 0.9015 (tpp) cc_final: 0.8000 (mpp) REVERT: H 112 MET cc_start: 0.9377 (mmm) cc_final: 0.9136 (mmm) REVERT: H 136 LEU cc_start: 0.7864 (mt) cc_final: 0.7207 (pp) REVERT: H 157 PHE cc_start: 0.7707 (t80) cc_final: 0.7054 (t80) REVERT: H 181 MET cc_start: 0.9218 (mmm) cc_final: 0.8945 (mmm) REVERT: H 184 LEU cc_start: 0.9386 (mt) cc_final: 0.8777 (tt) REVERT: H 319 CYS cc_start: 0.7392 (m) cc_final: 0.6999 (t) REVERT: H 417 ILE cc_start: 0.9529 (mt) cc_final: 0.9199 (mt) REVERT: H 507 LYS cc_start: 0.8338 (tptt) cc_final: 0.8054 (mptt) REVERT: H 570 ASP cc_start: 0.7594 (m-30) cc_final: 0.7126 (t0) REVERT: H 583 PHE cc_start: 0.9576 (m-10) cc_final: 0.9351 (m-80) REVERT: H 1110 MET cc_start: 0.4722 (mmt) cc_final: 0.3201 (mmt) outliers start: 5 outliers final: 0 residues processed: 523 average time/residue: 0.3424 time to fit residues: 307.6669 Evaluate side-chains 350 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 3.479 ------------------------------------------------------------------------------- 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: 2.9990 chunk 265 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 354 optimal weight: 7.9990 chunk 375 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 335 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 397 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31312 Z= 0.263 Angle : 0.651 7.584 42588 Z= 0.329 Chirality : 0.039 0.176 5196 Planarity : 0.005 0.077 5116 Dihedral : 5.317 50.332 4236 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.38 % 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: 1.62 (0.14), residues: 3832 helix: 1.52 (0.09), residues: 3196 sheet: None (None), residues: 0 loop : -1.08 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 90 HIS 0.007 0.001 HIS F 326 PHE 0.031 0.002 PHE A 168 TYR 0.013 0.002 TYR D 124 ARG 0.006 0.000 ARG G 136 *********************** 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 457 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 455 time to evaluate : 3.375 Fit side-chains REVERT: A 47 LYS cc_start: 0.8403 (tptt) cc_final: 0.7538 (mptt) REVERT: B 104 LEU cc_start: 0.8596 (mt) cc_final: 0.7980 (mt) REVERT: B 108 MET cc_start: 0.9051 (tpp) cc_final: 0.8182 (tpp) REVERT: B 112 MET cc_start: 0.9341 (mmm) cc_final: 0.9111 (mmm) REVERT: B 181 MET cc_start: 0.9272 (mmm) cc_final: 0.9068 (mmm) REVERT: B 184 LEU cc_start: 0.9424 (mt) cc_final: 0.8815 (tt) REVERT: B 319 CYS cc_start: 0.7601 (m) cc_final: 0.7390 (t) REVERT: B 507 LYS cc_start: 0.8468 (tptt) cc_final: 0.8250 (mmtm) REVERT: B 570 ASP cc_start: 0.7608 (m-30) cc_final: 0.7147 (t70) REVERT: B 583 PHE cc_start: 0.9593 (m-10) cc_final: 0.9330 (m-10) REVERT: B 1110 MET cc_start: 0.4705 (mmt) cc_final: 0.4157 (mmt) REVERT: B 1298 MET cc_start: 0.8884 (ttt) cc_final: 0.8648 (ttt) REVERT: C 168 PHE cc_start: 0.7639 (t80) cc_final: 0.7357 (t80) REVERT: D 104 LEU cc_start: 0.8597 (mt) cc_final: 0.7976 (mt) REVERT: D 108 MET cc_start: 0.9047 (tpp) cc_final: 0.8179 (tpp) REVERT: D 112 MET cc_start: 0.9349 (mmm) cc_final: 0.9114 (mmm) REVERT: D 181 MET cc_start: 0.9276 (mmm) cc_final: 0.9071 (mmm) REVERT: D 184 LEU cc_start: 0.9424 (mt) cc_final: 0.8811 (tt) REVERT: D 319 CYS cc_start: 0.7592 (m) cc_final: 0.7388 (t) REVERT: D 507 LYS cc_start: 0.8465 (tptt) cc_final: 0.8248 (mmtm) REVERT: D 570 ASP cc_start: 0.7604 (m-30) cc_final: 0.7148 (t70) REVERT: D 583 PHE cc_start: 0.9594 (m-10) cc_final: 0.9330 (m-10) REVERT: D 1110 MET cc_start: 0.4710 (mmt) cc_final: 0.4160 (mmt) REVERT: D 1298 MET cc_start: 0.8885 (ttt) cc_final: 0.8650 (ttt) REVERT: F 104 LEU cc_start: 0.8602 (mt) cc_final: 0.7990 (mt) REVERT: F 108 MET cc_start: 0.9050 (tpp) cc_final: 0.8183 (tpp) REVERT: F 112 MET cc_start: 0.9344 (mmm) cc_final: 0.9111 (mmm) REVERT: F 181 MET cc_start: 0.9278 (mmm) cc_final: 0.9070 (mmm) REVERT: F 184 LEU cc_start: 0.9423 (mt) cc_final: 0.8813 (tt) REVERT: F 507 LYS cc_start: 0.8467 (tptt) cc_final: 0.8250 (mmtm) REVERT: F 570 ASP cc_start: 0.7601 (m-30) cc_final: 0.7145 (t70) REVERT: F 583 PHE cc_start: 0.9595 (m-10) cc_final: 0.9331 (m-10) REVERT: F 1110 MET cc_start: 0.4703 (mmt) cc_final: 0.4159 (mmt) REVERT: F 1298 MET cc_start: 0.8886 (ttt) cc_final: 0.8648 (ttt) REVERT: H 104 LEU cc_start: 0.8589 (mt) cc_final: 0.7973 (mt) REVERT: H 108 MET cc_start: 0.9049 (tpp) cc_final: 0.8182 (tpp) REVERT: H 112 MET cc_start: 0.9342 (mmm) cc_final: 0.9108 (mmm) REVERT: H 181 MET cc_start: 0.9275 (mmm) cc_final: 0.9068 (mmm) REVERT: H 184 LEU cc_start: 0.9423 (mt) cc_final: 0.8811 (tt) REVERT: H 319 CYS cc_start: 0.7594 (m) cc_final: 0.7390 (t) REVERT: H 507 LYS cc_start: 0.8471 (tptt) cc_final: 0.8251 (mmtm) REVERT: H 570 ASP cc_start: 0.7606 (m-30) cc_final: 0.7148 (t70) REVERT: H 583 PHE cc_start: 0.9596 (m-10) cc_final: 0.9330 (m-10) REVERT: H 1110 MET cc_start: 0.4712 (mmt) cc_final: 0.4160 (mmt) REVERT: H 1298 MET cc_start: 0.8889 (ttt) cc_final: 0.8654 (ttt) outliers start: 2 outliers final: 0 residues processed: 455 average time/residue: 0.3333 time to fit residues: 261.5678 Evaluate side-chains 303 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 3.328 ------------------------------------------------------------------------------- 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: 4.9990 chunk 212 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 320 optimal weight: 0.4980 chunk 259 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 427 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 397 ASN D 427 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN F 397 ASN F 427 GLN H 262 ASN H 397 ASN H 427 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31312 Z= 0.222 Angle : 0.623 7.688 42588 Z= 0.315 Chirality : 0.037 0.149 5196 Planarity : 0.005 0.068 5116 Dihedral : 5.170 46.015 4236 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 1.59 (0.09), residues: 3180 sheet: None (None), residues: 0 loop : -0.84 (0.28), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1037 HIS 0.009 0.001 HIS H 326 PHE 0.042 0.002 PHE E 168 TYR 0.013 0.001 TYR D 158 ARG 0.005 0.000 ARG A 136 *********************** 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 456 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8440 (tptt) cc_final: 0.7625 (mptt) REVERT: A 110 CYS cc_start: 0.7955 (m) cc_final: 0.7715 (m) REVERT: B 104 LEU cc_start: 0.8673 (mt) cc_final: 0.7998 (mt) REVERT: B 108 MET cc_start: 0.9013 (tpp) cc_final: 0.8187 (tpp) REVERT: B 112 MET cc_start: 0.9366 (mmm) cc_final: 0.9134 (mmm) REVERT: B 136 LEU cc_start: 0.8133 (mm) cc_final: 0.7324 (pp) REVERT: B 181 MET cc_start: 0.9322 (mmm) cc_final: 0.9118 (mmm) REVERT: B 184 LEU cc_start: 0.9431 (mt) cc_final: 0.8887 (tt) REVERT: B 319 CYS cc_start: 0.7289 (m) cc_final: 0.7061 (t) REVERT: B 506 MET cc_start: 0.6184 (ptm) cc_final: 0.5951 (ptm) REVERT: B 570 ASP cc_start: 0.7574 (m-30) cc_final: 0.7190 (t70) REVERT: B 583 PHE cc_start: 0.9596 (m-10) cc_final: 0.9347 (m-10) REVERT: B 1110 MET cc_start: 0.4849 (mmt) cc_final: 0.4330 (mmt) REVERT: C 81 CYS cc_start: 0.8484 (t) cc_final: 0.8278 (t) REVERT: C 110 CYS cc_start: 0.7979 (m) cc_final: 0.7709 (m) REVERT: C 118 SER cc_start: 0.8981 (m) cc_final: 0.8775 (p) REVERT: D 104 LEU cc_start: 0.8683 (mt) cc_final: 0.8001 (mt) REVERT: D 108 MET cc_start: 0.9013 (tpp) cc_final: 0.8187 (tpp) REVERT: D 112 MET cc_start: 0.9374 (mmm) cc_final: 0.9139 (mmm) REVERT: D 136 LEU cc_start: 0.8136 (mm) cc_final: 0.7324 (pp) REVERT: D 181 MET cc_start: 0.9323 (mmm) cc_final: 0.9119 (mmm) REVERT: D 184 LEU cc_start: 0.9431 (mt) cc_final: 0.8883 (tt) REVERT: D 319 CYS cc_start: 0.7279 (m) cc_final: 0.7062 (t) REVERT: D 506 MET cc_start: 0.6180 (ptm) cc_final: 0.5956 (ptm) REVERT: D 570 ASP cc_start: 0.7569 (m-30) cc_final: 0.7187 (t70) REVERT: D 583 PHE cc_start: 0.9598 (m-10) cc_final: 0.9348 (m-10) REVERT: D 1110 MET cc_start: 0.4849 (mmt) cc_final: 0.4333 (mmt) REVERT: E 81 CYS cc_start: 0.8490 (t) cc_final: 0.8288 (t) REVERT: E 110 CYS cc_start: 0.7956 (m) cc_final: 0.7709 (m) REVERT: F 104 LEU cc_start: 0.8684 (mt) cc_final: 0.8006 (mt) REVERT: F 108 MET cc_start: 0.9014 (tpp) cc_final: 0.8184 (tpp) REVERT: F 112 MET cc_start: 0.9367 (mmm) cc_final: 0.9134 (mmm) REVERT: F 136 LEU cc_start: 0.8137 (mm) cc_final: 0.7327 (pp) REVERT: F 181 MET cc_start: 0.9326 (mmm) cc_final: 0.9120 (mmm) REVERT: F 184 LEU cc_start: 0.9433 (mt) cc_final: 0.8886 (tt) REVERT: F 506 MET cc_start: 0.6191 (ptm) cc_final: 0.5963 (ptm) REVERT: F 570 ASP cc_start: 0.7569 (m-30) cc_final: 0.7186 (t70) REVERT: F 583 PHE cc_start: 0.9599 (m-10) cc_final: 0.9349 (m-10) REVERT: F 1110 MET cc_start: 0.4858 (mmt) cc_final: 0.4330 (mmt) REVERT: G 81 CYS cc_start: 0.8481 (t) cc_final: 0.8272 (t) REVERT: G 110 CYS cc_start: 0.7986 (m) cc_final: 0.7742 (m) REVERT: H 104 LEU cc_start: 0.8671 (mt) cc_final: 0.7994 (mt) REVERT: H 108 MET cc_start: 0.9017 (tpp) cc_final: 0.8187 (tpp) REVERT: H 112 MET cc_start: 0.9367 (mmm) cc_final: 0.9134 (mmm) REVERT: H 136 LEU cc_start: 0.8131 (mm) cc_final: 0.7326 (pp) REVERT: H 181 MET cc_start: 0.9321 (mmm) cc_final: 0.9119 (mmm) REVERT: H 184 LEU cc_start: 0.9431 (mt) cc_final: 0.8881 (tt) REVERT: H 319 CYS cc_start: 0.7276 (m) cc_final: 0.7061 (t) REVERT: H 506 MET cc_start: 0.6188 (ptm) cc_final: 0.5962 (ptm) REVERT: H 570 ASP cc_start: 0.7574 (m-30) cc_final: 0.7188 (t70) REVERT: H 583 PHE cc_start: 0.9600 (m-10) cc_final: 0.9348 (m-10) REVERT: H 1110 MET cc_start: 0.4853 (mmt) cc_final: 0.4323 (mmt) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.3394 time to fit residues: 267.5857 Evaluate side-chains 318 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.409 ------------------------------------------------------------------------------- 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: 0.9990 chunk 220 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 375 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 D 262 ASN D 397 ASN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN F 397 ASN H 262 ASN H 397 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31312 Z= 0.187 Angle : 0.603 7.378 42588 Z= 0.302 Chirality : 0.037 0.183 5196 Planarity : 0.005 0.066 5116 Dihedral : 4.986 43.294 4236 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.40 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 1.93 (0.14), residues: 3832 helix: 1.71 (0.09), residues: 3164 sheet: None (None), residues: 0 loop : -0.68 (0.28), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F1037 HIS 0.008 0.001 HIS H 326 PHE 0.031 0.002 PHE G 75 TYR 0.012 0.001 TYR D 158 ARG 0.005 0.000 ARG B 495 *********************** 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 462 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8441 (tptt) cc_final: 0.7668 (mptt) REVERT: A 81 CYS cc_start: 0.8508 (t) cc_final: 0.8276 (t) REVERT: A 110 CYS cc_start: 0.8043 (m) cc_final: 0.7803 (m) REVERT: B 88 GLU cc_start: 0.9223 (tp30) cc_final: 0.8973 (tp30) REVERT: B 104 LEU cc_start: 0.8655 (mt) cc_final: 0.7999 (mt) REVERT: B 108 MET cc_start: 0.8998 (tpp) cc_final: 0.8153 (tpp) REVERT: B 112 MET cc_start: 0.9332 (mmm) cc_final: 0.9123 (mmm) REVERT: B 136 LEU cc_start: 0.8162 (mm) cc_final: 0.7355 (pp) REVERT: B 181 MET cc_start: 0.9354 (mmm) cc_final: 0.9122 (tpt) REVERT: B 184 LEU cc_start: 0.9425 (mt) cc_final: 0.8890 (tt) REVERT: B 507 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8243 (mttt) REVERT: B 570 ASP cc_start: 0.7575 (m-30) cc_final: 0.7233 (t70) REVERT: B 583 PHE cc_start: 0.9608 (m-10) cc_final: 0.9378 (m-80) REVERT: C 81 CYS cc_start: 0.8503 (t) cc_final: 0.8264 (t) REVERT: C 110 CYS cc_start: 0.8024 (m) cc_final: 0.7608 (m) REVERT: C 118 SER cc_start: 0.9023 (m) cc_final: 0.8814 (p) REVERT: C 168 PHE cc_start: 0.7173 (t80) cc_final: 0.6279 (t80) REVERT: C 170 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8211 (ttpp) REVERT: D 88 GLU cc_start: 0.9219 (tp30) cc_final: 0.8973 (tp30) REVERT: D 104 LEU cc_start: 0.8660 (mt) cc_final: 0.8000 (mt) REVERT: D 108 MET cc_start: 0.8994 (tpp) cc_final: 0.8154 (tpp) REVERT: D 112 MET cc_start: 0.9338 (mmm) cc_final: 0.9130 (mmm) REVERT: D 136 LEU cc_start: 0.8167 (mm) cc_final: 0.7360 (pp) REVERT: D 181 MET cc_start: 0.9354 (mmm) cc_final: 0.9123 (tpt) REVERT: D 184 LEU cc_start: 0.9427 (mt) cc_final: 0.8885 (tt) REVERT: D 507 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8242 (mttt) REVERT: D 570 ASP cc_start: 0.7571 (m-30) cc_final: 0.7230 (t70) REVERT: D 583 PHE cc_start: 0.9610 (m-10) cc_final: 0.9378 (m-80) REVERT: D 1298 MET cc_start: 0.8835 (ttt) cc_final: 0.8559 (ttt) REVERT: E 81 CYS cc_start: 0.8505 (t) cc_final: 0.8255 (t) REVERT: E 110 CYS cc_start: 0.7981 (m) cc_final: 0.7752 (m) REVERT: F 88 GLU cc_start: 0.9216 (tp30) cc_final: 0.8971 (tp30) REVERT: F 104 LEU cc_start: 0.8660 (mt) cc_final: 0.8004 (mt) REVERT: F 108 MET cc_start: 0.8996 (tpp) cc_final: 0.8155 (tpp) REVERT: F 112 MET cc_start: 0.9333 (mmm) cc_final: 0.9124 (mmm) REVERT: F 136 LEU cc_start: 0.8168 (mm) cc_final: 0.7364 (pp) REVERT: F 181 MET cc_start: 0.9357 (mmm) cc_final: 0.9121 (tpt) REVERT: F 184 LEU cc_start: 0.9429 (mt) cc_final: 0.8889 (tt) REVERT: F 507 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8242 (mttt) REVERT: F 570 ASP cc_start: 0.7570 (m-30) cc_final: 0.7231 (t70) REVERT: F 583 PHE cc_start: 0.9612 (m-10) cc_final: 0.9381 (m-80) REVERT: F 1298 MET cc_start: 0.8816 (ttt) cc_final: 0.8554 (ttt) REVERT: G 81 CYS cc_start: 0.8511 (t) cc_final: 0.8259 (t) REVERT: G 110 CYS cc_start: 0.8031 (m) cc_final: 0.7812 (m) REVERT: H 88 GLU cc_start: 0.9217 (tp30) cc_final: 0.8970 (tp30) REVERT: H 104 LEU cc_start: 0.8656 (mt) cc_final: 0.7994 (mt) REVERT: H 108 MET cc_start: 0.9001 (tpp) cc_final: 0.8155 (tpp) REVERT: H 112 MET cc_start: 0.9331 (mmm) cc_final: 0.9124 (mmm) REVERT: H 136 LEU cc_start: 0.8163 (mm) cc_final: 0.7362 (pp) REVERT: H 181 MET cc_start: 0.9355 (mmm) cc_final: 0.9123 (tpt) REVERT: H 184 LEU cc_start: 0.9427 (mt) cc_final: 0.8886 (tt) REVERT: H 507 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8245 (mttt) REVERT: H 570 ASP cc_start: 0.7574 (m-30) cc_final: 0.7232 (t70) REVERT: H 583 PHE cc_start: 0.9611 (m-10) cc_final: 0.9380 (m-80) REVERT: H 1298 MET cc_start: 0.8900 (ttt) cc_final: 0.8693 (ttt) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3347 time to fit residues: 266.5500 Evaluate side-chains 307 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.163 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 373 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5861 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= 0.311 Angle : 0.678 7.404 42588 Z= 0.345 Chirality : 0.039 0.150 5196 Planarity : 0.005 0.065 5116 Dihedral : 5.141 45.542 4236 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 1.57 (0.09), residues: 3136 sheet: None (None), residues: 0 loop : -0.85 (0.27), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 232 HIS 0.008 0.001 HIS F 326 PHE 0.036 0.002 PHE G 168 TYR 0.020 0.002 TYR B 124 ARG 0.008 0.001 ARG E 136 *********************** 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 408 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 3.488 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8393 (tptt) cc_final: 0.7702 (mptt) REVERT: A 81 CYS cc_start: 0.8591 (t) cc_final: 0.8341 (t) REVERT: A 137 MET cc_start: 0.7857 (mmm) cc_final: 0.7574 (tpp) REVERT: A 141 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 88 GLU cc_start: 0.9194 (tp30) cc_final: 0.8966 (tp30) REVERT: B 108 MET cc_start: 0.9005 (tpp) cc_final: 0.8141 (tpp) REVERT: B 112 MET cc_start: 0.9342 (mmm) cc_final: 0.9140 (mmm) REVERT: B 136 LEU cc_start: 0.8156 (mm) cc_final: 0.7304 (pp) REVERT: B 181 MET cc_start: 0.9395 (mmm) cc_final: 0.9154 (tpt) REVERT: B 184 LEU cc_start: 0.9497 (mt) cc_final: 0.8978 (tt) REVERT: B 570 ASP cc_start: 0.7640 (m-30) cc_final: 0.7338 (t70) REVERT: C 81 CYS cc_start: 0.8606 (t) cc_final: 0.8372 (t) REVERT: C 137 MET cc_start: 0.7957 (mmm) cc_final: 0.7643 (tpp) REVERT: C 170 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8445 (ttmm) REVERT: D 88 GLU cc_start: 0.9191 (tp30) cc_final: 0.8966 (tp30) REVERT: D 108 MET cc_start: 0.9004 (tpp) cc_final: 0.8135 (tpp) REVERT: D 112 MET cc_start: 0.9353 (mmm) cc_final: 0.9144 (mmm) REVERT: D 136 LEU cc_start: 0.8155 (mm) cc_final: 0.7304 (pp) REVERT: D 181 MET cc_start: 0.9400 (mmm) cc_final: 0.9158 (tpt) REVERT: D 184 LEU cc_start: 0.9498 (mt) cc_final: 0.8975 (tt) REVERT: D 530 MET cc_start: 0.8182 (mmt) cc_final: 0.7735 (mmt) REVERT: D 570 ASP cc_start: 0.7637 (m-30) cc_final: 0.7338 (t70) REVERT: E 81 CYS cc_start: 0.8583 (t) cc_final: 0.8348 (t) REVERT: E 137 MET cc_start: 0.7914 (mmm) cc_final: 0.7627 (tpp) REVERT: E 141 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7750 (tm-30) REVERT: F 88 GLU cc_start: 0.9185 (tp30) cc_final: 0.8964 (tp30) REVERT: F 108 MET cc_start: 0.9004 (tpp) cc_final: 0.8141 (tpp) REVERT: F 112 MET cc_start: 0.9346 (mmm) cc_final: 0.9140 (mmm) REVERT: F 136 LEU cc_start: 0.8159 (mm) cc_final: 0.7307 (pp) REVERT: F 181 MET cc_start: 0.9396 (mmm) cc_final: 0.9157 (tpt) REVERT: F 184 LEU cc_start: 0.9500 (mt) cc_final: 0.8976 (tt) REVERT: F 530 MET cc_start: 0.8186 (mmt) cc_final: 0.7734 (mmt) REVERT: F 570 ASP cc_start: 0.7634 (m-30) cc_final: 0.7337 (t70) REVERT: G 65 ASP cc_start: 0.8016 (t70) cc_final: 0.7814 (t0) REVERT: G 81 CYS cc_start: 0.8605 (t) cc_final: 0.8355 (t) REVERT: G 110 CYS cc_start: 0.8051 (m) cc_final: 0.7791 (m) REVERT: H 88 GLU cc_start: 0.9189 (tp30) cc_final: 0.8964 (tp30) REVERT: H 108 MET cc_start: 0.9010 (tpp) cc_final: 0.8144 (tpp) REVERT: H 112 MET cc_start: 0.9346 (mmm) cc_final: 0.9140 (mmm) REVERT: H 136 LEU cc_start: 0.8157 (mm) cc_final: 0.7305 (pp) REVERT: H 181 MET cc_start: 0.9397 (mmm) cc_final: 0.9156 (tpt) REVERT: H 184 LEU cc_start: 0.9497 (mt) cc_final: 0.8972 (tt) REVERT: H 570 ASP cc_start: 0.7638 (m-30) cc_final: 0.7340 (t70) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3650 time to fit residues: 253.0377 Evaluate side-chains 284 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 3.778 ------------------------------------------------------------------------------- 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: 9.9990 chunk 149 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 293 optimal weight: 0.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31312 Z= 0.210 Angle : 0.626 7.659 42588 Z= 0.313 Chirality : 0.038 0.142 5196 Planarity : 0.005 0.068 5116 Dihedral : 4.966 45.101 4236 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 1.97 (0.14), residues: 3832 helix: 1.75 (0.09), residues: 3156 sheet: None (None), residues: 0 loop : -0.76 (0.28), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1037 HIS 0.009 0.001 HIS H 326 PHE 0.028 0.002 PHE G 168 TYR 0.017 0.001 TYR B 123 ARG 0.009 0.000 ARG B 526 *********************** 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 422 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8387 (tptt) cc_final: 0.7737 (mptt) REVERT: A 81 CYS cc_start: 0.8631 (t) cc_final: 0.8413 (t) REVERT: A 110 CYS cc_start: 0.8149 (m) cc_final: 0.7853 (m) REVERT: A 137 MET cc_start: 0.7731 (mmm) cc_final: 0.7501 (tpp) REVERT: B 88 GLU cc_start: 0.9166 (tp30) cc_final: 0.8942 (tp30) REVERT: B 108 MET cc_start: 0.8978 (tpp) cc_final: 0.8112 (tpp) REVERT: B 112 MET cc_start: 0.9306 (mmm) cc_final: 0.9103 (mmm) REVERT: B 136 LEU cc_start: 0.8112 (mm) cc_final: 0.7353 (pp) REVERT: B 181 MET cc_start: 0.9382 (mmm) cc_final: 0.9104 (tpt) REVERT: B 184 LEU cc_start: 0.9446 (mt) cc_final: 0.8935 (tt) REVERT: B 570 ASP cc_start: 0.7589 (m-30) cc_final: 0.7298 (t70) REVERT: C 137 MET cc_start: 0.7759 (mmm) cc_final: 0.7540 (tpp) REVERT: C 170 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8492 (ttmm) REVERT: D 88 GLU cc_start: 0.9164 (tp30) cc_final: 0.8938 (tp30) REVERT: D 108 MET cc_start: 0.8978 (tpp) cc_final: 0.8110 (tpp) REVERT: D 112 MET cc_start: 0.9318 (mmm) cc_final: 0.9102 (mmm) REVERT: D 136 LEU cc_start: 0.8112 (mm) cc_final: 0.7357 (pp) REVERT: D 181 MET cc_start: 0.9385 (mmm) cc_final: 0.9107 (tpt) REVERT: D 184 LEU cc_start: 0.9449 (mt) cc_final: 0.8932 (tt) REVERT: D 530 MET cc_start: 0.8143 (mmt) cc_final: 0.7774 (mmt) REVERT: D 570 ASP cc_start: 0.7587 (m-30) cc_final: 0.7298 (t70) REVERT: E 110 CYS cc_start: 0.8138 (m) cc_final: 0.7746 (m) REVERT: E 137 MET cc_start: 0.7768 (mmm) cc_final: 0.7558 (tpp) REVERT: F 88 GLU cc_start: 0.9160 (tp30) cc_final: 0.8936 (tp30) REVERT: F 108 MET cc_start: 0.8982 (tpp) cc_final: 0.8113 (tpp) REVERT: F 112 MET cc_start: 0.9306 (mmm) cc_final: 0.9097 (mmm) REVERT: F 136 LEU cc_start: 0.8115 (mm) cc_final: 0.7359 (pp) REVERT: F 181 MET cc_start: 0.9383 (mmm) cc_final: 0.9105 (tpt) REVERT: F 184 LEU cc_start: 0.9452 (mt) cc_final: 0.8935 (tt) REVERT: F 530 MET cc_start: 0.8146 (mmt) cc_final: 0.7770 (mmt) REVERT: F 570 ASP cc_start: 0.7585 (m-30) cc_final: 0.7296 (t70) REVERT: F 1305 MET cc_start: 0.7830 (mmm) cc_final: 0.7611 (mmm) REVERT: H 88 GLU cc_start: 0.9163 (tp30) cc_final: 0.8937 (tp30) REVERT: H 108 MET cc_start: 0.8987 (tpp) cc_final: 0.8119 (tpp) REVERT: H 112 MET cc_start: 0.9306 (mmm) cc_final: 0.9099 (mmm) REVERT: H 136 LEU cc_start: 0.8111 (mm) cc_final: 0.7357 (pp) REVERT: H 181 MET cc_start: 0.9383 (mmm) cc_final: 0.9105 (tpt) REVERT: H 184 LEU cc_start: 0.9447 (mt) cc_final: 0.8930 (tt) REVERT: H 570 ASP cc_start: 0.7587 (m-30) cc_final: 0.7298 (t70) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.3414 time to fit residues: 247.2436 Evaluate side-chains 299 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.581 ------------------------------------------------------------------------------- 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: 0.9990 chunk 358 optimal weight: 0.1980 chunk 326 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 314 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 347 optimal weight: 9.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31312 Z= 0.263 Angle : 0.658 8.288 42588 Z= 0.333 Chirality : 0.039 0.152 5196 Planarity : 0.005 0.083 5116 Dihedral : 4.958 46.511 4236 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 1.91 (0.14), residues: 3832 helix: 1.70 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -0.78 (0.28), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 232 HIS 0.009 0.001 HIS F 326 PHE 0.050 0.002 PHE E 168 TYR 0.030 0.002 TYR B 123 ARG 0.006 0.000 ARG E 136 *********************** 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 419 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8424 (tptt) cc_final: 0.7798 (mptt) REVERT: A 81 CYS cc_start: 0.8573 (t) cc_final: 0.8341 (t) REVERT: A 110 CYS cc_start: 0.8158 (m) cc_final: 0.7868 (m) REVERT: A 137 MET cc_start: 0.7904 (mmm) cc_final: 0.7658 (tpp) REVERT: B 88 GLU cc_start: 0.9173 (tp30) cc_final: 0.8942 (tp30) REVERT: B 108 MET cc_start: 0.8948 (tpp) cc_final: 0.8113 (tpp) REVERT: B 112 MET cc_start: 0.9314 (mmm) cc_final: 0.9100 (mmm) REVERT: B 136 LEU cc_start: 0.8190 (mm) cc_final: 0.7342 (pp) REVERT: B 181 MET cc_start: 0.9394 (mmm) cc_final: 0.9112 (tpt) REVERT: B 184 LEU cc_start: 0.9459 (mt) cc_final: 0.8942 (tt) REVERT: B 570 ASP cc_start: 0.7631 (m-30) cc_final: 0.7421 (t0) REVERT: C 137 MET cc_start: 0.7867 (mmm) cc_final: 0.7573 (tpp) REVERT: C 170 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8448 (ttmm) REVERT: D 88 GLU cc_start: 0.9167 (tp30) cc_final: 0.8934 (tp30) REVERT: D 108 MET cc_start: 0.8948 (tpp) cc_final: 0.8107 (tpp) REVERT: D 112 MET cc_start: 0.9324 (mmm) cc_final: 0.9097 (mmm) REVERT: D 136 LEU cc_start: 0.8187 (mm) cc_final: 0.7341 (pp) REVERT: D 181 MET cc_start: 0.9396 (mmm) cc_final: 0.9114 (tpt) REVERT: D 184 LEU cc_start: 0.9461 (mt) cc_final: 0.8940 (tt) REVERT: D 530 MET cc_start: 0.8162 (mmt) cc_final: 0.7910 (mmm) REVERT: D 570 ASP cc_start: 0.7634 (m-30) cc_final: 0.7421 (t0) REVERT: D 1290 MET cc_start: 0.8411 (mtm) cc_final: 0.7766 (mtt) REVERT: E 110 CYS cc_start: 0.8192 (m) cc_final: 0.7941 (m) REVERT: E 137 MET cc_start: 0.7915 (mmm) cc_final: 0.7647 (tpp) REVERT: F 88 GLU cc_start: 0.9166 (tp30) cc_final: 0.8932 (tp30) REVERT: F 108 MET cc_start: 0.8954 (tpp) cc_final: 0.8114 (tpp) REVERT: F 112 MET cc_start: 0.9317 (mmm) cc_final: 0.9094 (mmm) REVERT: F 136 LEU cc_start: 0.8190 (mm) cc_final: 0.7342 (pp) REVERT: F 181 MET cc_start: 0.9394 (mmm) cc_final: 0.9111 (tpt) REVERT: F 184 LEU cc_start: 0.9464 (mt) cc_final: 0.8940 (tt) REVERT: F 530 MET cc_start: 0.8165 (mmt) cc_final: 0.7909 (mmm) REVERT: F 570 ASP cc_start: 0.7633 (m-30) cc_final: 0.7422 (t0) REVERT: F 1290 MET cc_start: 0.8449 (mtm) cc_final: 0.7883 (mtt) REVERT: F 1305 MET cc_start: 0.7954 (mmm) cc_final: 0.7671 (mmm) REVERT: G 110 CYS cc_start: 0.8173 (m) cc_final: 0.7921 (m) REVERT: H 88 GLU cc_start: 0.9169 (tp30) cc_final: 0.8934 (tp30) REVERT: H 108 MET cc_start: 0.8954 (tpp) cc_final: 0.8122 (tpp) REVERT: H 112 MET cc_start: 0.9319 (mmm) cc_final: 0.9099 (mmm) REVERT: H 136 LEU cc_start: 0.8189 (mm) cc_final: 0.7345 (pp) REVERT: H 181 MET cc_start: 0.9395 (mmm) cc_final: 0.9115 (tpt) REVERT: H 184 LEU cc_start: 0.9460 (mt) cc_final: 0.8941 (tt) REVERT: H 570 ASP cc_start: 0.7635 (m-30) cc_final: 0.7425 (t0) REVERT: H 1290 MET cc_start: 0.8409 (mtm) cc_final: 0.7886 (mtt) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.3562 time to fit residues: 257.6096 Evaluate side-chains 291 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 3.363 ------------------------------------------------------------------------------- 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: 9.9990 chunk 368 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 386 optimal weight: 8.9990 chunk 355 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1197 GLN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1197 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31312 Z= 0.325 Angle : 0.707 10.683 42588 Z= 0.362 Chirality : 0.041 0.149 5196 Planarity : 0.005 0.075 5116 Dihedral : 5.213 47.827 4236 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 1.78 (0.14), residues: 3832 helix: 1.57 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -0.55 (0.29), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 232 HIS 0.009 0.001 HIS F 326 PHE 0.065 0.002 PHE E 168 TYR 0.042 0.002 TYR D 123 ARG 0.007 0.001 ARG G 136 ********************** 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 413 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8425 (tptt) cc_final: 0.7872 (mptt) REVERT: A 110 CYS cc_start: 0.8186 (m) cc_final: 0.7916 (m) REVERT: B 88 GLU cc_start: 0.9143 (tp30) cc_final: 0.8923 (tp30) REVERT: B 108 MET cc_start: 0.8937 (tpp) cc_final: 0.8015 (tpp) REVERT: B 112 MET cc_start: 0.9337 (mmm) cc_final: 0.9096 (mmm) REVERT: B 136 LEU cc_start: 0.8235 (mm) cc_final: 0.7398 (pp) REVERT: B 181 MET cc_start: 0.9399 (mmm) cc_final: 0.9078 (tpt) REVERT: B 184 LEU cc_start: 0.9500 (mt) cc_final: 0.8995 (tt) REVERT: B 570 ASP cc_start: 0.7750 (m-30) cc_final: 0.7498 (t0) REVERT: B 1290 MET cc_start: 0.8259 (mtt) cc_final: 0.7968 (mtt) REVERT: B 1294 TYR cc_start: 0.8840 (m-10) cc_final: 0.8571 (m-80) REVERT: D 88 GLU cc_start: 0.9140 (tp30) cc_final: 0.8917 (tp30) REVERT: D 108 MET cc_start: 0.8939 (tpp) cc_final: 0.8005 (tpp) REVERT: D 112 MET cc_start: 0.9344 (mmm) cc_final: 0.9099 (mmm) REVERT: D 136 LEU cc_start: 0.8233 (mm) cc_final: 0.7396 (pp) REVERT: D 181 MET cc_start: 0.9398 (mmm) cc_final: 0.9078 (tpt) REVERT: D 184 LEU cc_start: 0.9501 (mt) cc_final: 0.8991 (tt) REVERT: D 530 MET cc_start: 0.8124 (mmt) cc_final: 0.7911 (mmm) REVERT: D 570 ASP cc_start: 0.7756 (m-30) cc_final: 0.7506 (t0) REVERT: D 1294 TYR cc_start: 0.8851 (m-80) cc_final: 0.8378 (m-80) REVERT: E 110 CYS cc_start: 0.8144 (m) cc_final: 0.7918 (m) REVERT: E 137 MET cc_start: 0.7998 (mmm) cc_final: 0.7747 (tpp) REVERT: E 170 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8368 (ttmm) REVERT: F 88 GLU cc_start: 0.9135 (tp30) cc_final: 0.8914 (tp30) REVERT: F 108 MET cc_start: 0.8938 (tpp) cc_final: 0.8018 (tpp) REVERT: F 112 MET cc_start: 0.9339 (mmm) cc_final: 0.9097 (mmm) REVERT: F 136 LEU cc_start: 0.8234 (mm) cc_final: 0.7400 (pp) REVERT: F 181 MET cc_start: 0.9397 (mmm) cc_final: 0.9079 (tpt) REVERT: F 184 LEU cc_start: 0.9504 (mt) cc_final: 0.8992 (tt) REVERT: F 530 MET cc_start: 0.8126 (mmt) cc_final: 0.7914 (mmm) REVERT: F 570 ASP cc_start: 0.7756 (m-30) cc_final: 0.7506 (t0) REVERT: F 1294 TYR cc_start: 0.8867 (m-80) cc_final: 0.8313 (m-80) REVERT: F 1305 MET cc_start: 0.7935 (mmm) cc_final: 0.7653 (mmm) REVERT: G 110 CYS cc_start: 0.8155 (m) cc_final: 0.7916 (m) REVERT: H 88 GLU cc_start: 0.9140 (tp30) cc_final: 0.8918 (tp30) REVERT: H 108 MET cc_start: 0.8939 (tpp) cc_final: 0.8018 (tpp) REVERT: H 112 MET cc_start: 0.9341 (mmm) cc_final: 0.9105 (mmm) REVERT: H 136 LEU cc_start: 0.8226 (mm) cc_final: 0.7398 (pp) REVERT: H 181 MET cc_start: 0.9396 (mmm) cc_final: 0.9080 (tpt) REVERT: H 184 LEU cc_start: 0.9501 (mt) cc_final: 0.8990 (tt) REVERT: H 570 ASP cc_start: 0.7754 (m-30) cc_final: 0.7506 (t0) REVERT: H 1294 TYR cc_start: 0.8874 (m-80) cc_final: 0.8647 (m-80) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.3526 time to fit residues: 250.3956 Evaluate side-chains 273 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 3.603 ------------------------------------------------------------------------------- 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: 8.9990 chunk 327 optimal weight: 0.0670 chunk 94 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 39 optimal weight: 0.0060 chunk 56 optimal weight: 0.0980 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 B1020 GLN D 397 ASN D1020 GLN ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN F1020 GLN H 397 ASN H1020 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.095516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.079389 restraints weight = 109868.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078986 restraints weight = 93723.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079614 restraints weight = 86444.870| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31312 Z= 0.181 Angle : 0.633 11.015 42588 Z= 0.312 Chirality : 0.038 0.232 5196 Planarity : 0.005 0.072 5116 Dihedral : 4.813 48.196 4236 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.09 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.14), residues: 3832 helix: 1.81 (0.09), residues: 3160 sheet: None (None), residues: 0 loop : -0.74 (0.28), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F1037 HIS 0.010 0.001 HIS D 326 PHE 0.032 0.002 PHE H 583 TYR 0.016 0.001 TYR B 158 ARG 0.002 0.000 ARG C 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6004.50 seconds wall clock time: 110 minutes 34.88 seconds (6634.88 seconds total)