Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 9 02:53:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/05_2023/7b05_11957_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 13760 2.51 5 N 3452 2.21 5 O 3716 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ARG 710": "NH1" <-> "NH2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "A TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 707": "OE1" <-> "OE2" Residue "B ARG 710": "NH1" <-> "NH2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "B TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 438": "OD1" <-> "OD2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 594": "OE1" <-> "OE2" Residue "C PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 629": "OD1" <-> "OD2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 707": "OE1" <-> "OE2" Residue "C ARG 710": "NH1" <-> "NH2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C ASP 741": "OD1" <-> "OD2" Residue "C TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D ASP 438": "OD1" <-> "OD2" Residue "D TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "D PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 629": "OD1" <-> "OD2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 707": "OE1" <-> "OE2" Residue "D ARG 710": "NH1" <-> "NH2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ASP 741": "OD1" <-> "OD2" Residue "D TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 21056 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5215 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 623} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5215 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 623} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5215 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 623} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5215 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 623} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 10.53, per 1000 atoms: 0.50 Number of scatterers: 21056 At special positions: 0 Unit cell: (141.05, 141.05, 138.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 4 19.99 Cl 4 17.00 S 108 16.00 P 4 15.00 F 8 9.00 O 3716 8.00 N 3452 7.00 C 13760 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: 8.41 Conformation dependent library (CDL) restraints added in 2.9 seconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 0 sheets defined 67.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 46 through 58 removed outlier: 4.062A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.507A pdb=" N SER A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 removed outlier: 4.690A pdb=" N LEU A 100 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.660A pdb=" N LEU A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 257 Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.619A pdb=" N ILE A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.646A pdb=" N ARG A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 360' Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 401 through 424 removed outlier: 4.042A pdb=" N LEU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 433 through 458 removed outlier: 3.633A pdb=" N LEU A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 445 " --> pdb=" O MET A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 498 removed outlier: 3.702A pdb=" N ARG A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 514 through 541 removed outlier: 3.850A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 576 removed outlier: 4.145A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 593 through 610 removed outlier: 3.559A pdb=" N ALA A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 628 removed outlier: 3.779A pdb=" N ASN A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 646 removed outlier: 3.980A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 719 removed outlier: 3.582A pdb=" N GLU A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 732 through 753 Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 46 through 58 removed outlier: 4.062A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.507A pdb=" N SER B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 removed outlier: 4.690A pdb=" N LEU B 100 " --> pdb=" O GLY B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 155 through 164 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.660A pdb=" N LEU B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 257 Processing helix chain 'B' and resid 262 through 270 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.619A pdb=" N ILE B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 337 " --> pdb=" O CYS B 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.646A pdb=" N ARG B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 360' Processing helix chain 'B' and resid 362 through 383 Processing helix chain 'B' and resid 401 through 424 removed outlier: 4.042A pdb=" N LEU B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 433 through 458 removed outlier: 3.633A pdb=" N LEU B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 445 " --> pdb=" O MET B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 498 removed outlier: 3.702A pdb=" N ARG B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 511 Processing helix chain 'B' and resid 514 through 541 removed outlier: 3.850A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN B 536 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR B 540 " --> pdb=" O GLN B 536 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 576 removed outlier: 4.145A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 593 through 610 removed outlier: 3.559A pdb=" N ALA B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 628 removed outlier: 3.779A pdb=" N ASN B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 646 removed outlier: 3.980A pdb=" N PHE B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 719 removed outlier: 3.582A pdb=" N GLU B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 732 through 753 Processing helix chain 'C' and resid 33 through 42 Processing helix chain 'C' and resid 46 through 58 removed outlier: 4.062A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 91 removed outlier: 3.507A pdb=" N SER C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 removed outlier: 4.690A pdb=" N LEU C 100 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 155 through 164 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 216 through 233 removed outlier: 3.660A pdb=" N LEU C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 257 Processing helix chain 'C' and resid 262 through 270 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 326 through 349 removed outlier: 3.619A pdb=" N ILE C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.646A pdb=" N ARG C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 362 through 383 Processing helix chain 'C' and resid 401 through 424 removed outlier: 4.042A pdb=" N LEU C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 433 through 458 removed outlier: 3.633A pdb=" N LEU C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 445 " --> pdb=" O MET C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 498 removed outlier: 3.702A pdb=" N ARG C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 514 through 541 removed outlier: 3.850A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 537 " --> pdb=" O GLY C 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 576 removed outlier: 4.145A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 593 through 610 removed outlier: 3.559A pdb=" N ALA C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 628 removed outlier: 3.779A pdb=" N ASN C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN C 625 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 removed outlier: 3.980A pdb=" N PHE C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 719 removed outlier: 3.582A pdb=" N GLU C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 727 No H-bonds generated for 'chain 'C' and resid 725 through 727' Processing helix chain 'C' and resid 732 through 753 Processing helix chain 'D' and resid 33 through 42 Processing helix chain 'D' and resid 46 through 58 removed outlier: 4.062A pdb=" N ILE D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 Processing helix chain 'D' and resid 83 through 91 removed outlier: 3.507A pdb=" N SER D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 removed outlier: 4.690A pdb=" N LEU D 100 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 116 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 216 through 233 removed outlier: 3.660A pdb=" N LEU D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 257 Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 304 through 315 Processing helix chain 'D' and resid 326 through 349 removed outlier: 3.619A pdb=" N ILE D 336 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY D 337 " --> pdb=" O CYS D 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 341 - end of helix Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.646A pdb=" N ARG D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 360' Processing helix chain 'D' and resid 362 through 383 Processing helix chain 'D' and resid 401 through 424 removed outlier: 4.042A pdb=" N LEU D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Proline residue: D 408 - end of helix Processing helix chain 'D' and resid 433 through 458 removed outlier: 3.633A pdb=" N LEU D 444 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 498 removed outlier: 3.702A pdb=" N ARG D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE D 493 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA D 498 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 514 through 541 removed outlier: 3.850A pdb=" N LYS D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN D 536 " --> pdb=" O ASN D 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 537 " --> pdb=" O GLY D 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR D 540 " --> pdb=" O GLN D 536 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 576 removed outlier: 4.145A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 593 through 610 removed outlier: 3.559A pdb=" N ALA D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 628 removed outlier: 3.779A pdb=" N ASN D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 646 removed outlier: 3.980A pdb=" N PHE D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 719 removed outlier: 3.582A pdb=" N GLU D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 732 through 753 1080 hydrogen bonds defined for protein. 3168 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: 5.78 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3308 1.30 - 1.43: 5944 1.43 - 1.56: 12124 1.56 - 1.68: 4 1.68 - 1.81: 180 Bond restraints: 21560 Sorted by residual: bond pdb=" CAV SJQ C1001 " pdb=" OAW SJQ C1001 " ideal model delta sigma weight residual 1.185 1.396 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CAV SJQ D1001 " pdb=" OAW SJQ D1001 " ideal model delta sigma weight residual 1.185 1.396 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CAV SJQ B1001 " pdb=" OAW SJQ B1001 " ideal model delta sigma weight residual 1.185 1.396 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CAV SJQ A1001 " pdb=" OAW SJQ A1001 " ideal model delta sigma weight residual 1.185 1.396 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CAV SJQ A1001 " pdb=" NAS SJQ A1001 " ideal model delta sigma weight residual 1.489 1.387 0.102 2.00e-02 2.50e+03 2.61e+01 ... (remaining 21555 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.80: 348 105.80 - 112.85: 11752 112.85 - 119.91: 7644 119.91 - 126.97: 9192 126.97 - 134.02: 292 Bond angle restraints: 29228 Sorted by residual: angle pdb=" N VAL A 610 " pdb=" CA VAL A 610 " pdb=" C VAL A 610 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 angle pdb=" N VAL B 610 " pdb=" CA VAL B 610 " pdb=" C VAL B 610 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 angle pdb=" N VAL D 610 " pdb=" CA VAL D 610 " pdb=" C VAL D 610 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 angle pdb=" N VAL C 610 " pdb=" CA VAL C 610 " pdb=" C VAL C 610 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 angle pdb=" C SJQ C1001 " pdb=" NAJ SJQ C1001 " pdb=" CAK SJQ C1001 " ideal model delta sigma weight residual 110.65 122.18 -11.53 3.00e+00 1.11e-01 1.48e+01 ... (remaining 29223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11324 17.95 - 35.90: 1096 35.90 - 53.85: 244 53.85 - 71.80: 32 71.80 - 89.75: 32 Dihedral angle restraints: 12728 sinusoidal: 5104 harmonic: 7624 Sorted by residual: dihedral pdb=" CA TYR D 538 " pdb=" C TYR D 538 " pdb=" N PHE D 539 " pdb=" CA PHE D 539 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR C 538 " pdb=" C TYR C 538 " pdb=" N PHE C 539 " pdb=" CA PHE C 539 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR A 538 " pdb=" C TYR A 538 " pdb=" N PHE A 539 " pdb=" CA PHE A 539 " ideal model delta harmonic sigma weight residual 180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 12725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1812 0.034 - 0.067: 1104 0.067 - 0.101: 304 0.101 - 0.135: 52 0.135 - 0.169: 16 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CA GLU A 53 " pdb=" N GLU A 53 " pdb=" C GLU A 53 " pdb=" CB GLU A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA GLU D 53 " pdb=" N GLU D 53 " pdb=" C GLU D 53 " pdb=" CB GLU D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA GLU C 53 " pdb=" N GLU C 53 " pdb=" C GLU C 53 " pdb=" CB GLU C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 3285 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N SJQ C1001 " -0.082 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" CA SJQ C1001 " 0.028 2.00e-02 2.50e+03 pdb=" CAL SJQ C1001 " 0.027 2.00e-02 2.50e+03 pdb=" CAP SJQ C1001 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SJQ D1001 " -0.082 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" CA SJQ D1001 " 0.028 2.00e-02 2.50e+03 pdb=" CAL SJQ D1001 " 0.027 2.00e-02 2.50e+03 pdb=" CAP SJQ D1001 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SJQ B1001 " 0.082 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" CA SJQ B1001 " -0.028 2.00e-02 2.50e+03 pdb=" CAL SJQ B1001 " -0.027 2.00e-02 2.50e+03 pdb=" CAP SJQ B1001 " -0.028 2.00e-02 2.50e+03 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5684 2.79 - 3.32: 22248 3.32 - 3.85: 33006 3.85 - 4.37: 36548 4.37 - 4.90: 62600 Nonbonded interactions: 160086 Sorted by model distance: nonbonded pdb=" O LEU A 88 " pdb=" OG SER A 91 " model vdw 2.267 2.440 nonbonded pdb=" O LEU B 88 " pdb=" OG SER B 91 " model vdw 2.267 2.440 nonbonded pdb=" O LEU D 88 " pdb=" OG SER D 91 " model vdw 2.267 2.440 nonbonded pdb=" O LEU C 88 " pdb=" OG SER C 91 " model vdw 2.267 2.440 nonbonded pdb=" O ASN D 117 " pdb=" ND1 HIS D 118 " model vdw 2.285 2.520 ... (remaining 160081 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 'B' selection = chain 'C' 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 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.800 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 49.930 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 0.009 0.211 21560 Z= 0.573 Angle : 0.825 11.526 29228 Z= 0.429 Chirality : 0.045 0.169 3288 Planarity : 0.004 0.047 3616 Dihedral : 15.439 89.752 7768 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 0.00 % 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: -0.12 (0.17), residues: 2532 helix: 0.72 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.759 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3027 time to fit residues: 130.7425 Evaluate side-chains 216 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 103 optimal weight: 0.0570 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 21560 Z= 0.176 Angle : 0.624 9.245 29228 Z= 0.303 Chirality : 0.037 0.163 3288 Planarity : 0.004 0.033 3616 Dihedral : 6.606 60.764 2852 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2532 helix: 1.14 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 2.582 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 262 average time/residue: 0.2923 time to fit residues: 125.1215 Evaluate side-chains 238 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2251 time to fit residues: 8.1322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 230 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 21560 Z= 0.214 Angle : 0.564 8.463 29228 Z= 0.281 Chirality : 0.037 0.161 3288 Planarity : 0.004 0.034 3616 Dihedral : 5.912 47.269 2852 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 1.60 % 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: 0.64 (0.18), residues: 2532 helix: 1.32 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -1.99 (0.24), residues: 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 2.375 Fit side-chains outliers start: 36 outliers final: 24 residues processed: 256 average time/residue: 0.2752 time to fit residues: 118.1769 Evaluate side-chains 248 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 2.564 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2028 time to fit residues: 12.5505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 21560 Z= 0.313 Angle : 0.607 9.102 29228 Z= 0.301 Chirality : 0.039 0.156 3288 Planarity : 0.004 0.035 3616 Dihedral : 5.859 45.657 2852 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer Outliers : 1.42 % 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: 0.64 (0.17), residues: 2532 helix: 1.37 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : -2.07 (0.24), residues: 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 2.534 Fit side-chains outliers start: 32 outliers final: 18 residues processed: 244 average time/residue: 0.2546 time to fit residues: 106.8897 Evaluate side-chains 240 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1780 time to fit residues: 9.2544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2333 > 50: distance: 39 - 43: 5.551 distance: 43 - 44: 5.579 distance: 44 - 45: 4.802 distance: 45 - 46: 7.027 distance: 45 - 47: 6.042 distance: 46 - 71: 14.373 distance: 47 - 48: 8.964 distance: 47 - 53: 8.969 distance: 48 - 49: 5.482 distance: 48 - 51: 15.812 distance: 49 - 50: 4.790 distance: 49 - 54: 6.839 distance: 50 - 79: 7.189 distance: 51 - 52: 11.785 distance: 52 - 53: 16.095 distance: 54 - 55: 11.324 distance: 55 - 56: 13.626 distance: 55 - 58: 14.198 distance: 56 - 57: 3.977 distance: 56 - 62: 3.818 distance: 57 - 85: 37.423 distance: 58 - 59: 12.093 distance: 59 - 60: 7.285 distance: 59 - 61: 12.997 distance: 62 - 63: 10.367 distance: 63 - 64: 8.411 distance: 63 - 66: 5.138 distance: 64 - 65: 14.332 distance: 64 - 71: 4.245 distance: 65 - 93: 17.604 distance: 66 - 67: 11.186 distance: 67 - 68: 4.547 distance: 68 - 69: 8.517 distance: 68 - 70: 16.132 distance: 71 - 72: 12.100 distance: 72 - 73: 6.722 distance: 72 - 75: 8.974 distance: 73 - 74: 9.853 distance: 73 - 79: 7.495 distance: 74 - 97: 19.510 distance: 75 - 76: 12.419 distance: 75 - 77: 14.076 distance: 76 - 78: 8.566 distance: 79 - 80: 29.676 distance: 80 - 81: 15.217 distance: 80 - 83: 10.602 distance: 81 - 82: 7.251 distance: 81 - 85: 40.545 distance: 83 - 84: 22.711 distance: 85 - 86: 10.532 distance: 86 - 87: 18.573 distance: 86 - 89: 9.481 distance: 87 - 88: 19.252 distance: 87 - 93: 8.044 distance: 89 - 90: 27.031 distance: 90 - 91: 14.973 distance: 90 - 92: 32.153 distance: 93 - 94: 5.323 distance: 94 - 95: 13.139 distance: 95 - 96: 19.613 distance: 95 - 97: 17.792 distance: 97 - 98: 7.473 distance: 98 - 99: 10.450 distance: 98 - 101: 4.590 distance: 99 - 100: 16.005 distance: 99 - 108: 19.396 distance: 101 - 102: 6.736 distance: 102 - 103: 11.254 distance: 103 - 104: 4.976 distance: 104 - 105: 9.127 distance: 105 - 106: 25.220 distance: 105 - 107: 12.776 distance: 108 - 109: 15.949 distance: 109 - 110: 11.601 distance: 109 - 112: 20.717 distance: 110 - 111: 6.752 distance: 110 - 116: 12.930 distance: 112 - 113: 15.941 distance: 113 - 114: 16.678 distance: 114 - 115: 17.150