Starting phenix.real_space_refine on Fri Feb 16 11:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcv_31532/02_2024/7fcv_31532_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcv_31532/02_2024/7fcv_31532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcv_31532/02_2024/7fcv_31532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcv_31532/02_2024/7fcv_31532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcv_31532/02_2024/7fcv_31532_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcv_31532/02_2024/7fcv_31532_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 92 5.16 5 C 9862 2.51 5 N 2526 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 303": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15143 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3747 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3739 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3743 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3739 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 46 Unusual residues: {' K': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 8.25, per 1000 atoms: 0.54 Number of scatterers: 15143 At special positions: 0 Unit cell: (127.735, 136.395, 123.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 92 16.00 P 4 15.00 O 2656 8.00 N 2526 7.00 C 9862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.83 Conformation dependent library (CDL) restraints added in 2.9 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 10 sheets defined 57.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.983A pdb=" N ILE A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 87 through 108 removed outlier: 5.212A pdb=" N THR A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.863A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TRP A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG A 170 " --> pdb=" O TRP A 166 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 214 Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 264 through 295 removed outlier: 3.534A pdb=" N GLY A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.564A pdb=" N ARG A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.931A pdb=" N TYR A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 346 No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.578A pdb=" N GLU A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 482 through 492 removed outlier: 3.689A pdb=" N HIS A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.593A pdb=" N ILE A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 4.047A pdb=" N ILE B 59 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 87 through 108 removed outlier: 4.964A pdb=" N THR B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 157 through 180 removed outlier: 4.061A pdb=" N LEU B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP B 166 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 214 Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 264 through 295 Processing helix chain 'B' and resid 298 through 316 Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.803A pdb=" N TYR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.542A pdb=" N GLU B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 379 through 387 removed outlier: 3.566A pdb=" N GLU B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 475 removed outlier: 3.536A pdb=" N ILE B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 492 removed outlier: 3.628A pdb=" N HIS B 491 " --> pdb=" O ASN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 509 removed outlier: 3.809A pdb=" N GLU B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.925A pdb=" N ILE C 59 " --> pdb=" O HIS C 55 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 87 through 108 removed outlier: 5.186A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 157 through 180 removed outlier: 4.331A pdb=" N LEU C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 164 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TRP C 166 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ARG C 170 " --> pdb=" O TRP C 166 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 214 Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 264 through 295 Processing helix chain 'C' and resid 298 through 316 Processing helix chain 'C' and resid 320 through 335 removed outlier: 4.053A pdb=" N TYR C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 removed outlier: 4.068A pdb=" N ASP C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 365 through 368 No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 379 through 387 removed outlier: 3.595A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'C' and resid 480 through 494 removed outlier: 3.634A pdb=" N HIS C 491 " --> pdb=" O ASN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 removed outlier: 3.747A pdb=" N GLU C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 81 Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 87 through 106 removed outlier: 5.074A pdb=" N THR D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 136 through 143 removed outlier: 4.062A pdb=" N THR D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 157 through 180 removed outlier: 4.229A pdb=" N LEU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TRP D 166 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG D 170 " --> pdb=" O TRP D 166 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 214 Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 295 Processing helix chain 'D' and resid 298 through 315 Processing helix chain 'D' and resid 320 through 335 removed outlier: 3.875A pdb=" N TYR D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 349 removed outlier: 3.709A pdb=" N GLU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP D 348 " --> pdb=" O GLN D 344 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA D 349 " --> pdb=" O GLU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 379 through 387 removed outlier: 3.506A pdb=" N GLU D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 444 No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 467 through 475 Processing helix chain 'D' and resid 481 through 492 removed outlier: 3.886A pdb=" N HIS D 491 " --> pdb=" O ASN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 removed outlier: 3.712A pdb=" N GLU D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 507 " --> pdb=" O VAL D 503 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.904A pdb=" N LEU A 119 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 389 through 393 Processing sheet with id= C, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.510A pdb=" N SER A 428 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 400 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 456 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP A 398 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 389 through 393 Processing sheet with id= E, first strand: chain 'B' and resid 427 through 429 removed outlier: 3.879A pdb=" N ILE B 400 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR B 456 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 398 " --> pdb=" O THR B 456 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.919A pdb=" N LEU C 119 " --> pdb=" O ASP C 114 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 389 through 393 Processing sheet with id= H, first strand: chain 'C' and resid 453 through 456 removed outlier: 4.191A pdb=" N ARG C 431 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP C 421 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE C 429 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 389 through 393 Processing sheet with id= J, first strand: chain 'D' and resid 397 through 400 removed outlier: 6.629A pdb=" N VAL D 454 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 417 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 431 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP D 421 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE D 429 " --> pdb=" O ASP D 421 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 2133 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: 4.61 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2593 1.32 - 1.45: 4174 1.45 - 1.57: 8567 1.57 - 1.69: 10 1.69 - 1.81: 156 Bond restraints: 15500 Sorted by residual: bond pdb=" C ALA B 349 " pdb=" N LEU B 350 " ideal model delta sigma weight residual 1.331 1.246 0.085 2.83e-02 1.25e+03 9.12e+00 bond pdb=" CA PHE B 109 " pdb=" CB PHE B 109 " ideal model delta sigma weight residual 1.531 1.611 -0.080 3.12e-02 1.03e+03 6.58e+00 bond pdb=" C PRO D 406 " pdb=" N THR D 407 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.40e-02 5.10e+03 5.91e+00 bond pdb=" CA ASP D 122 " pdb=" CB ASP D 122 " ideal model delta sigma weight residual 1.532 1.570 -0.038 1.62e-02 3.81e+03 5.45e+00 bond pdb=" O14 PTY D 901 " pdb=" P1 PTY D 901 " ideal model delta sigma weight residual 1.646 1.602 0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 15495 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.64: 285 105.64 - 112.77: 8055 112.77 - 119.90: 5689 119.90 - 127.03: 6808 127.03 - 134.16: 186 Bond angle restraints: 21023 Sorted by residual: angle pdb=" N PRO B 87 " pdb=" CA PRO B 87 " pdb=" C PRO B 87 " ideal model delta sigma weight residual 110.70 117.76 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" N VAL D 413 " pdb=" CA VAL D 413 " pdb=" C VAL D 413 " ideal model delta sigma weight residual 111.62 107.12 4.50 7.90e-01 1.60e+00 3.25e+01 angle pdb=" C TYR A 256 " pdb=" N GLY A 257 " pdb=" CA GLY A 257 " ideal model delta sigma weight residual 123.30 117.56 5.74 1.06e+00 8.90e-01 2.94e+01 angle pdb=" N PRO C 87 " pdb=" CA PRO C 87 " pdb=" C PRO C 87 " ideal model delta sigma weight residual 110.70 117.19 -6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" N PRO A 87 " pdb=" CA PRO A 87 " pdb=" C PRO A 87 " ideal model delta sigma weight residual 110.70 117.11 -6.41 1.22e+00 6.72e-01 2.76e+01 ... (remaining 21018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.37: 9063 30.37 - 60.73: 128 60.73 - 91.10: 10 91.10 - 121.46: 4 121.46 - 151.83: 4 Dihedral angle restraints: 9209 sinusoidal: 3737 harmonic: 5472 Sorted by residual: dihedral pdb=" CA ASP C 497 " pdb=" C ASP C 497 " pdb=" N PRO C 498 " pdb=" CA PRO C 498 " ideal model delta harmonic sigma weight residual 180.00 -128.24 -51.76 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ASN C 496 " pdb=" C ASN C 496 " pdb=" N ASP C 497 " pdb=" CA ASP C 497 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA MET D 106 " pdb=" C MET D 106 " pdb=" N THR D 107 " pdb=" CA THR D 107 " ideal model delta harmonic sigma weight residual 180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 9206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2143 0.092 - 0.184: 220 0.184 - 0.275: 13 0.275 - 0.367: 0 0.367 - 0.459: 4 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C6 PTY A 901 " pdb=" C1 PTY A 901 " pdb=" C5 PTY A 901 " pdb=" O7 PTY A 901 " both_signs ideal model delta sigma weight residual False 2.49 2.03 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C6 PTY B 901 " pdb=" C1 PTY B 901 " pdb=" C5 PTY B 901 " pdb=" O7 PTY B 901 " both_signs ideal model delta sigma weight residual False 2.49 2.06 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C6 PTY D 901 " pdb=" C1 PTY D 901 " pdb=" C5 PTY D 901 " pdb=" O7 PTY D 901 " both_signs ideal model delta sigma weight residual False 2.49 2.07 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 2377 not shown) Planarity restraints: 2623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 246 " -0.027 2.00e-02 2.50e+03 1.56e-02 6.07e+00 pdb=" CG TRP B 246 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 246 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 246 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP B 246 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 246 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 246 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 246 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 246 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 246 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 260 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO B 261 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 87 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO D 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.035 5.00e-02 4.00e+02 ... (remaining 2620 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.85: 5008 2.85 - 3.42: 16828 3.42 - 3.99: 28284 3.99 - 4.57: 39070 4.57 - 5.14: 56803 Nonbonded interactions: 145993 Sorted by model distance: nonbonded pdb=" OG SER D 359 " pdb=" O VAL D 385 " model vdw 2.271 2.440 nonbonded pdb=" OG SER A 359 " pdb=" O VAL A 385 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR D 371 " pdb=" OE2 GLU D 441 " model vdw 2.282 2.440 nonbonded pdb=" OG SER C 359 " pdb=" O VAL C 385 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR C 371 " pdb=" OE2 GLU C 441 " model vdw 2.292 2.440 ... (remaining 145988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 49 through 343 or (resid 344 through 345 and (name N or na \ me CA or name C or name O or name CB )) or resid 346 through 510 or resid 901)) selection = chain 'B' selection = (chain 'C' and (resid 49 through 343 or (resid 344 through 345 and (name N or na \ me CA or name C or name O or name CB )) or resid 346 through 510 or resid 901)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.010 Extract box with map and model: 7.540 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.690 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.008 0.085 15500 Z= 0.547 Angle : 1.035 10.952 21023 Z= 0.571 Chirality : 0.060 0.459 2380 Planarity : 0.007 0.061 2623 Dihedral : 12.123 151.830 5665 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -3.29 (0.16), residues: 1840 helix: -1.78 (0.12), residues: 1056 sheet: -2.57 (0.49), residues: 84 loop : -2.59 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP A 135 HIS 0.016 0.004 HIS C 294 PHE 0.038 0.003 PHE C 109 TYR 0.032 0.003 TYR B 209 ARG 0.014 0.001 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASN cc_start: 0.8919 (t0) cc_final: 0.8610 (t0) REVERT: B 368 ASP cc_start: 0.8229 (m-30) cc_final: 0.7796 (m-30) REVERT: B 466 ASN cc_start: 0.8954 (t0) cc_final: 0.8737 (t0) REVERT: C 368 ASP cc_start: 0.8475 (m-30) cc_final: 0.8173 (p0) REVERT: C 388 MET cc_start: 0.8742 (mmm) cc_final: 0.8197 (mmm) REVERT: D 96 VAL cc_start: 0.6645 (t) cc_final: 0.6110 (p) REVERT: D 133 ARG cc_start: 0.4106 (mmt180) cc_final: 0.3856 (tmt-80) REVERT: D 510 MET cc_start: 0.5140 (mtm) cc_final: 0.4890 (mtt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 1.1177 time to fit residues: 256.6997 Evaluate side-chains 120 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 343 GLN A 486 ASN A 502 ASN A 509 ASN B 290 ASN B 294 HIS B 311 ASN B 343 GLN B 461 GLN B 486 ASN C 126 GLN C 294 HIS C 311 ASN C 378 ASN C 486 ASN C 502 ASN C 509 ASN D 311 ASN D 343 GLN D 378 ASN D 486 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15500 Z= 0.176 Angle : 0.624 8.354 21023 Z= 0.326 Chirality : 0.041 0.167 2380 Planarity : 0.005 0.051 2623 Dihedral : 10.636 162.051 2184 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.54 % Allowed : 9.04 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1840 helix: 0.20 (0.15), residues: 1056 sheet: -2.30 (0.45), residues: 88 loop : -2.34 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 73 HIS 0.005 0.001 HIS D 294 PHE 0.051 0.001 PHE D 99 TYR 0.018 0.002 TYR A 131 ARG 0.008 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7950 (tmt) REVERT: A 388 MET cc_start: 0.8507 (mmm) cc_final: 0.7959 (mmm) REVERT: A 504 LEU cc_start: 0.9403 (tm) cc_final: 0.9120 (mm) REVERT: B 388 MET cc_start: 0.8840 (mmm) cc_final: 0.8042 (mmm) REVERT: B 466 ASN cc_start: 0.8835 (t0) cc_final: 0.8587 (t0) REVERT: C 388 MET cc_start: 0.8771 (mmm) cc_final: 0.8257 (mmm) REVERT: D 352 LYS cc_start: 0.8974 (tmtm) cc_final: 0.8700 (tppt) REVERT: D 388 MET cc_start: 0.8818 (mmm) cc_final: 0.8526 (mmm) REVERT: D 492 LEU cc_start: 0.9004 (tp) cc_final: 0.8761 (tt) REVERT: D 510 MET cc_start: 0.5301 (mtm) cc_final: 0.4748 (mtt) outliers start: 25 outliers final: 5 residues processed: 162 average time/residue: 1.0817 time to fit residues: 196.9242 Evaluate side-chains 124 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 165 optimal weight: 0.0000 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN B 461 GLN C 126 GLN D 97 ASN D 294 HIS ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15500 Z= 0.203 Angle : 0.609 12.667 21023 Z= 0.314 Chirality : 0.041 0.153 2380 Planarity : 0.005 0.076 2623 Dihedral : 9.939 165.557 2184 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.03 % Allowed : 10.76 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1840 helix: 0.93 (0.16), residues: 1072 sheet: -2.06 (0.46), residues: 88 loop : -2.16 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 73 HIS 0.005 0.001 HIS D 294 PHE 0.020 0.001 PHE C 129 TYR 0.026 0.002 TYR D 283 ARG 0.014 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASN cc_start: 0.8878 (t0) cc_final: 0.8443 (t0) REVERT: B 288 MET cc_start: 0.8849 (tpp) cc_final: 0.8577 (mmm) REVERT: B 388 MET cc_start: 0.8907 (mmm) cc_final: 0.7951 (mmm) REVERT: B 495 MET cc_start: 0.6565 (pmm) cc_final: 0.6162 (pmm) REVERT: B 496 ASN cc_start: 0.7980 (m-40) cc_final: 0.7673 (m-40) REVERT: C 106 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7598 (tmm) REVERT: C 388 MET cc_start: 0.8922 (mmm) cc_final: 0.8200 (mmm) REVERT: C 510 MET cc_start: 0.6565 (mtm) cc_final: 0.5058 (tpt) REVERT: D 388 MET cc_start: 0.8810 (mmm) cc_final: 0.8451 (mmm) REVERT: D 510 MET cc_start: 0.5419 (mtm) cc_final: 0.4884 (mtt) outliers start: 33 outliers final: 13 residues processed: 143 average time/residue: 0.9370 time to fit residues: 153.6359 Evaluate side-chains 125 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 0.4980 chunk 177 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 159 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN D 97 ASN D 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15500 Z= 0.146 Angle : 0.576 12.804 21023 Z= 0.294 Chirality : 0.040 0.163 2380 Planarity : 0.004 0.048 2623 Dihedral : 9.241 158.865 2184 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.15 % Allowed : 11.37 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.07 (0.20), residues: 1840 helix: 1.30 (0.16), residues: 1072 sheet: -1.90 (0.46), residues: 88 loop : -2.04 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 73 HIS 0.007 0.001 HIS D 491 PHE 0.024 0.001 PHE C 129 TYR 0.012 0.001 TYR B 283 ARG 0.004 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 388 MET cc_start: 0.8838 (mmm) cc_final: 0.7965 (mmm) REVERT: B 466 ASN cc_start: 0.8612 (t0) cc_final: 0.8364 (t0) REVERT: B 495 MET cc_start: 0.6758 (pmm) cc_final: 0.6383 (pmm) REVERT: B 496 ASN cc_start: 0.8001 (m-40) cc_final: 0.7711 (m-40) REVERT: C 106 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7587 (tmm) REVERT: C 388 MET cc_start: 0.8921 (mmm) cc_final: 0.8268 (mmm) REVERT: D 106 MET cc_start: 0.4124 (tmt) cc_final: 0.3902 (mtt) REVERT: D 388 MET cc_start: 0.8743 (mmm) cc_final: 0.8516 (mmm) REVERT: D 510 MET cc_start: 0.5355 (mtm) cc_final: 0.4867 (mtt) outliers start: 35 outliers final: 16 residues processed: 149 average time/residue: 0.9192 time to fit residues: 156.9529 Evaluate side-chains 127 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.1980 chunk 100 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 0.0970 chunk 122 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15500 Z= 0.134 Angle : 0.570 10.707 21023 Z= 0.286 Chirality : 0.040 0.169 2380 Planarity : 0.004 0.052 2623 Dihedral : 8.974 152.739 2184 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.41 % Allowed : 13.28 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.09 (0.20), residues: 1840 helix: 1.33 (0.16), residues: 1096 sheet: -1.75 (0.46), residues: 88 loop : -1.93 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 135 HIS 0.003 0.000 HIS B 294 PHE 0.018 0.001 PHE D 136 TYR 0.018 0.001 TYR D 131 ARG 0.006 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 388 MET cc_start: 0.8821 (mmm) cc_final: 0.7972 (mmm) REVERT: B 466 ASN cc_start: 0.8624 (t0) cc_final: 0.8327 (t0) REVERT: B 495 MET cc_start: 0.6645 (pmm) cc_final: 0.6263 (pmm) REVERT: B 496 ASN cc_start: 0.7996 (m-40) cc_final: 0.7689 (m-40) REVERT: C 106 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7550 (tmm) REVERT: D 388 MET cc_start: 0.8701 (mmm) cc_final: 0.8475 (mmm) REVERT: D 510 MET cc_start: 0.5251 (mtm) cc_final: 0.4794 (mtt) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 0.9892 time to fit residues: 156.9621 Evaluate side-chains 126 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 378 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN D 97 ASN D 316 ASN D 343 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 15500 Z= 0.382 Angle : 0.700 12.165 21023 Z= 0.353 Chirality : 0.045 0.154 2380 Planarity : 0.005 0.043 2623 Dihedral : 9.238 144.435 2184 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.03 (0.20), residues: 1840 helix: 1.11 (0.16), residues: 1124 sheet: -1.51 (0.50), residues: 88 loop : -1.76 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 246 HIS 0.006 0.001 HIS C 329 PHE 0.022 0.002 PHE D 269 TYR 0.021 0.002 TYR D 131 ARG 0.007 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8305 (m-30) cc_final: 0.7972 (m-30) REVERT: A 466 ASN cc_start: 0.8997 (t0) cc_final: 0.8507 (t0) REVERT: B 388 MET cc_start: 0.8870 (mmm) cc_final: 0.7982 (mmm) REVERT: B 466 ASN cc_start: 0.8713 (t0) cc_final: 0.8404 (t0) REVERT: B 495 MET cc_start: 0.6783 (pmm) cc_final: 0.6315 (pmm) REVERT: B 496 ASN cc_start: 0.8217 (m-40) cc_final: 0.7942 (m-40) REVERT: C 106 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7969 (tmt) REVERT: D 123 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8014 (p0) REVERT: D 188 TRP cc_start: 0.6788 (m100) cc_final: 0.5356 (t60) REVERT: D 510 MET cc_start: 0.5409 (mtm) cc_final: 0.5036 (mtt) outliers start: 37 outliers final: 19 residues processed: 145 average time/residue: 0.9521 time to fit residues: 157.7591 Evaluate side-chains 129 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN B 343 GLN B 461 GLN D 97 ASN D 343 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15500 Z= 0.163 Angle : 0.592 11.157 21023 Z= 0.297 Chirality : 0.040 0.170 2380 Planarity : 0.004 0.052 2623 Dihedral : 8.918 142.346 2184 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.84 % Allowed : 15.12 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1840 helix: 1.54 (0.16), residues: 1100 sheet: -1.55 (0.48), residues: 88 loop : -1.79 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 73 HIS 0.002 0.001 HIS B 203 PHE 0.010 0.001 PHE D 100 TYR 0.015 0.001 TYR D 131 ARG 0.003 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 ASN cc_start: 0.8950 (t0) cc_final: 0.8515 (t0) REVERT: B 238 MET cc_start: 0.7689 (ttp) cc_final: 0.7196 (tmm) REVERT: B 388 MET cc_start: 0.8744 (mmm) cc_final: 0.7918 (mmm) REVERT: B 466 ASN cc_start: 0.8664 (t0) cc_final: 0.8319 (t0) REVERT: B 495 MET cc_start: 0.6746 (pmm) cc_final: 0.6318 (pmm) REVERT: B 496 ASN cc_start: 0.8211 (m-40) cc_final: 0.7932 (m-40) REVERT: C 388 MET cc_start: 0.8820 (mmm) cc_final: 0.8103 (mmm) REVERT: C 510 MET cc_start: 0.6916 (mtm) cc_final: 0.5380 (tpt) REVERT: D 510 MET cc_start: 0.5304 (mtm) cc_final: 0.4834 (mtt) outliers start: 30 outliers final: 18 residues processed: 137 average time/residue: 0.9357 time to fit residues: 146.8116 Evaluate side-chains 126 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15500 Z= 0.160 Angle : 0.605 11.406 21023 Z= 0.299 Chirality : 0.040 0.166 2380 Planarity : 0.004 0.098 2623 Dihedral : 8.673 138.355 2184 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.84 % Allowed : 14.87 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.46 (0.20), residues: 1840 helix: 1.64 (0.16), residues: 1096 sheet: -1.39 (0.49), residues: 88 loop : -1.83 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 73 HIS 0.002 0.001 HIS B 294 PHE 0.010 0.001 PHE D 100 TYR 0.012 0.001 TYR D 131 ARG 0.024 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 ASN cc_start: 0.8916 (t0) cc_final: 0.8455 (t0) REVERT: A 504 LEU cc_start: 0.9390 (tm) cc_final: 0.9098 (mt) REVERT: B 238 MET cc_start: 0.7651 (ttp) cc_final: 0.7205 (tmm) REVERT: B 388 MET cc_start: 0.8725 (mmm) cc_final: 0.7925 (mmm) REVERT: B 495 MET cc_start: 0.6747 (pmm) cc_final: 0.6407 (pmm) REVERT: B 496 ASN cc_start: 0.8194 (m-40) cc_final: 0.7917 (m-40) REVERT: C 106 MET cc_start: 0.8230 (tmm) cc_final: 0.7959 (tmt) REVERT: D 510 MET cc_start: 0.5297 (mtm) cc_final: 0.4853 (mtt) outliers start: 30 outliers final: 18 residues processed: 133 average time/residue: 0.9825 time to fit residues: 149.2150 Evaluate side-chains 124 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Chi-restraints excluded: chain D residue 471 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 99 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN D 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 15500 Z= 0.151 Angle : 0.606 11.857 21023 Z= 0.297 Chirality : 0.040 0.188 2380 Planarity : 0.004 0.056 2623 Dihedral : 8.501 135.581 2184 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.48 % Allowed : 15.43 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.45 (0.20), residues: 1840 helix: 1.56 (0.16), residues: 1120 sheet: -1.32 (0.49), residues: 88 loop : -1.82 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 73 HIS 0.003 0.000 HIS C 491 PHE 0.024 0.001 PHE B 470 TYR 0.015 0.001 TYR D 283 ARG 0.004 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 ASN cc_start: 0.8906 (t0) cc_final: 0.8448 (t0) REVERT: A 504 LEU cc_start: 0.9345 (tm) cc_final: 0.9085 (mt) REVERT: B 238 MET cc_start: 0.7633 (ttp) cc_final: 0.7215 (tmm) REVERT: B 388 MET cc_start: 0.8695 (mmm) cc_final: 0.7930 (mmm) REVERT: B 495 MET cc_start: 0.6729 (pmm) cc_final: 0.6384 (pmm) REVERT: B 496 ASN cc_start: 0.8201 (m-40) cc_final: 0.7944 (m-40) REVERT: C 106 MET cc_start: 0.8212 (tmm) cc_final: 0.7943 (tmt) REVERT: C 388 MET cc_start: 0.8792 (mmm) cc_final: 0.7935 (mmm) REVERT: C 510 MET cc_start: 0.6960 (mtm) cc_final: 0.5373 (tpt) REVERT: D 510 MET cc_start: 0.5307 (mtm) cc_final: 0.4868 (mtt) outliers start: 24 outliers final: 17 residues processed: 137 average time/residue: 0.9517 time to fit residues: 149.0541 Evaluate side-chains 127 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 0.4980 chunk 145 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15500 Z= 0.162 Angle : 0.618 11.759 21023 Z= 0.301 Chirality : 0.040 0.183 2380 Planarity : 0.004 0.055 2623 Dihedral : 8.344 133.219 2184 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.23 % Allowed : 16.16 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1840 helix: 1.74 (0.16), residues: 1096 sheet: -1.25 (0.50), residues: 88 loop : -1.82 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.002 0.000 HIS C 294 PHE 0.026 0.001 PHE B 470 TYR 0.011 0.001 TYR B 283 ARG 0.004 0.000 ARG C 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 ASN cc_start: 0.8898 (t0) cc_final: 0.8367 (t0) REVERT: A 504 LEU cc_start: 0.9339 (tm) cc_final: 0.9096 (mt) REVERT: B 238 MET cc_start: 0.7617 (ttp) cc_final: 0.7275 (tmm) REVERT: B 388 MET cc_start: 0.8668 (mmm) cc_final: 0.7925 (mmm) REVERT: B 495 MET cc_start: 0.6817 (pmm) cc_final: 0.6464 (pmm) REVERT: B 496 ASN cc_start: 0.8263 (m-40) cc_final: 0.8046 (m-40) REVERT: C 510 MET cc_start: 0.6934 (mtm) cc_final: 0.5326 (tpt) REVERT: D 510 MET cc_start: 0.5310 (mtm) cc_final: 0.4873 (mtt) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.9844 time to fit residues: 143.7677 Evaluate side-chains 120 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN D 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.097408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.074549 restraints weight = 48211.162| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.05 r_work: 0.3272 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15500 Z= 0.155 Angle : 0.602 11.514 21023 Z= 0.296 Chirality : 0.040 0.178 2380 Planarity : 0.004 0.060 2623 Dihedral : 8.223 131.682 2184 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.29 % Allowed : 16.10 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.60 (0.20), residues: 1840 helix: 1.75 (0.16), residues: 1096 sheet: -1.21 (0.50), residues: 88 loop : -1.79 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.002 0.000 HIS C 294 PHE 0.024 0.001 PHE B 470 TYR 0.014 0.001 TYR D 283 ARG 0.005 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4130.79 seconds wall clock time: 75 minutes 0.49 seconds (4500.49 seconds total)