Starting phenix.real_space_refine on Mon Mar 18 13:32:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_11957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_11957.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_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_11957/03_2024/7b05_11957_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_11957_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_11957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_11957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_11957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b05_11957/03_2024/7b05_11957_updated.pdb" } resolution = 3.8 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: 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.10, per 1000 atoms: 0.48 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: 8.48 Conformation dependent library (CDL) restraints added in 3.6 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: 4.40 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: 5.77 Time building geometry restraints manager: 9.10 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: 11336 17.95 - 35.90: 1100 35.90 - 53.85: 244 53.85 - 71.80: 36 71.80 - 89.75: 32 Dihedral angle restraints: 12748 sinusoidal: 5124 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 12745 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: 1.300 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: 5.890 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 54.120 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.410 ------------------------------------------------------------------------------- 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 : 15.497 89.752 7788 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 % Allowed : 0.53 % Favored : 99.47 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 415 HIS 0.005 0.001 HIS C 172 PHE 0.020 0.002 PHE D 539 TYR 0.022 0.002 TYR D 36 ARG 0.010 0.001 ARG B 491 *********************** 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 : 2.610 Fit side-chains REVERT: A 543 ASN cc_start: 0.8217 (t0) cc_final: 0.7970 (t0) REVERT: B 543 ASN cc_start: 0.8213 (t0) cc_final: 0.7967 (t0) REVERT: C 543 ASN cc_start: 0.8215 (t0) cc_final: 0.7969 (t0) REVERT: D 543 ASN cc_start: 0.8212 (t0) cc_final: 0.7970 (t0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2884 time to fit residues: 125.4242 Evaluate side-chains 216 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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: 0.8433 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21560 Z= 0.177 Angle : 0.622 9.235 29228 Z= 0.302 Chirality : 0.038 0.162 3288 Planarity : 0.004 0.033 3616 Dihedral : 7.069 61.286 2872 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.36 % Allowed : 10.21 % Favored : 89.43 % 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: 1.15 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.96 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 635 HIS 0.002 0.001 HIS C 172 PHE 0.016 0.001 PHE B 735 TYR 0.014 0.001 TYR A 523 ARG 0.006 0.000 ARG D 491 *********************** 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 268 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 2.206 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 264 average time/residue: 0.2704 time to fit residues: 116.7928 Evaluate side-chains 236 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21560 Z= 0.217 Angle : 0.569 8.496 29228 Z= 0.282 Chirality : 0.037 0.161 3288 Planarity : 0.004 0.034 3616 Dihedral : 6.408 57.622 2872 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.78 % Allowed : 13.85 % Favored : 84.37 % 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: 0.62 (0.18), residues: 2532 helix: 1.31 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -1.99 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.003 0.001 HIS B 325 PHE 0.016 0.001 PHE A 735 TYR 0.015 0.001 TYR B 523 ARG 0.006 0.000 ARG D 491 *********************** 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: 40 poor density : 240 time to evaluate : 2.477 Fit side-chains REVERT: A 609 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8939 (tt) REVERT: C 609 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8945 (tt) outliers start: 40 outliers final: 26 residues processed: 252 average time/residue: 0.2647 time to fit residues: 111.1854 Evaluate side-chains 248 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 753 MET 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: 0.7980 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 chunk 156 optimal weight: 0.0570 chunk 233 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 122 optimal weight: 0.0970 chunk 221 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 395 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: 0.8392 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21560 Z= 0.137 Angle : 0.535 8.931 29228 Z= 0.261 Chirality : 0.036 0.152 3288 Planarity : 0.004 0.032 3616 Dihedral : 5.998 56.797 2872 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.73 % Rotamer: Outliers : 1.95 % Allowed : 16.70 % Favored : 81.35 % 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: 0.93 (0.18), residues: 2532 helix: 1.60 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.004 0.001 HIS D 325 PHE 0.010 0.001 PHE C 340 TYR 0.014 0.001 TYR B 523 ARG 0.005 0.000 ARG A 491 *********************** 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 308 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 2.762 Fit side-chains REVERT: A 378 PHE cc_start: 0.9008 (t80) cc_final: 0.8652 (t80) REVERT: B 256 LEU cc_start: 0.9336 (tp) cc_final: 0.9136 (tp) REVERT: B 378 PHE cc_start: 0.9006 (t80) cc_final: 0.8651 (t80) REVERT: C 378 PHE cc_start: 0.9002 (t80) cc_final: 0.8647 (t80) REVERT: D 256 LEU cc_start: 0.9341 (tp) cc_final: 0.9139 (tp) REVERT: D 378 PHE cc_start: 0.9004 (t80) cc_final: 0.8649 (t80) outliers start: 44 outliers final: 18 residues processed: 276 average time/residue: 0.2452 time to fit residues: 115.6984 Evaluate side-chains 240 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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: 0.8451 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21560 Z= 0.291 Angle : 0.592 9.851 29228 Z= 0.289 Chirality : 0.039 0.264 3288 Planarity : 0.004 0.035 3616 Dihedral : 6.153 56.808 2872 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.95 % Allowed : 18.16 % Favored : 79.88 % 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: 0.91 (0.18), residues: 2532 helix: 1.59 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -2.03 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.004 0.001 HIS B 325 PHE 0.019 0.001 PHE A 300 TYR 0.014 0.001 TYR A 36 ARG 0.005 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 5 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 266 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 2.407 Fit side-chains REVERT: A 451 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 451 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8947 (tt) REVERT: C 451 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8943 (tt) REVERT: D 451 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8944 (tt) outliers start: 44 outliers final: 32 residues processed: 246 average time/residue: 0.2442 time to fit residues: 103.6870 Evaluate side-chains 256 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 0.0270 chunk 61 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- 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 485 ASN ** 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 485 ASN ** 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 485 ASN ** 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 485 ASN ** 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: 0.8415 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21560 Z= 0.163 Angle : 0.542 9.459 29228 Z= 0.265 Chirality : 0.036 0.173 3288 Planarity : 0.003 0.033 3616 Dihedral : 6.027 56.681 2872 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.75 % Allowed : 17.41 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2532 helix: 1.70 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.96 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 314 HIS 0.004 0.001 HIS A 325 PHE 0.012 0.001 PHE C 340 TYR 0.012 0.001 TYR D 523 ARG 0.004 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 6 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 302 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 240 time to evaluate : 2.461 Fit side-chains REVERT: A 451 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 256 LEU cc_start: 0.9360 (tp) cc_final: 0.9153 (tp) REVERT: B 451 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8948 (tt) REVERT: C 451 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8944 (tt) REVERT: D 256 LEU cc_start: 0.9365 (tp) cc_final: 0.9156 (tp) REVERT: D 451 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8948 (tt) outliers start: 62 outliers final: 37 residues processed: 277 average time/residue: 0.2411 time to fit residues: 114.8237 Evaluate side-chains 271 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 230 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 208 optimal weight: 0.0980 chunk 138 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 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 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** 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 485 ASN ** 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 485 ASN ** 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 485 ASN ** 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: 0.8390 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21560 Z= 0.142 Angle : 0.524 9.520 29228 Z= 0.253 Chirality : 0.035 0.152 3288 Planarity : 0.003 0.033 3616 Dihedral : 5.877 55.496 2872 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.18 % Allowed : 17.85 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2532 helix: 1.78 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 314 HIS 0.004 0.000 HIS B 325 PHE 0.013 0.001 PHE D 340 TYR 0.012 0.001 TYR D 523 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 7 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 296 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 247 time to evaluate : 1.919 Fit side-chains REVERT: A 335 PHE cc_start: 0.8552 (t80) cc_final: 0.8329 (t80) REVERT: A 339 MET cc_start: 0.7916 (ptm) cc_final: 0.7463 (ptm) REVERT: A 378 PHE cc_start: 0.8969 (t80) cc_final: 0.8615 (t80) REVERT: A 451 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8975 (tt) REVERT: B 335 PHE cc_start: 0.8556 (t80) cc_final: 0.8328 (t80) REVERT: B 339 MET cc_start: 0.7928 (ptm) cc_final: 0.7475 (ptm) REVERT: B 378 PHE cc_start: 0.8968 (t80) cc_final: 0.8620 (t80) REVERT: B 451 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8972 (tt) REVERT: C 335 PHE cc_start: 0.8557 (t80) cc_final: 0.8332 (t80) REVERT: C 339 MET cc_start: 0.7908 (ptm) cc_final: 0.7455 (ptm) REVERT: C 378 PHE cc_start: 0.8965 (t80) cc_final: 0.8617 (t80) REVERT: C 451 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8968 (tt) REVERT: D 335 PHE cc_start: 0.8553 (t80) cc_final: 0.8330 (t80) REVERT: D 339 MET cc_start: 0.7907 (ptm) cc_final: 0.7456 (ptm) REVERT: D 378 PHE cc_start: 0.8967 (t80) cc_final: 0.8615 (t80) REVERT: D 451 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8974 (tt) outliers start: 49 outliers final: 31 residues processed: 276 average time/residue: 0.2401 time to fit residues: 113.4551 Evaluate side-chains 266 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 485 ASN ** 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 485 ASN ** 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 485 ASN ** 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 485 ASN ** 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: 0.8403 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21560 Z= 0.170 Angle : 0.552 9.927 29228 Z= 0.262 Chirality : 0.036 0.274 3288 Planarity : 0.003 0.033 3616 Dihedral : 5.895 55.314 2872 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.78 % Allowed : 19.09 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2532 helix: 1.79 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 314 HIS 0.003 0.001 HIS A 325 PHE 0.013 0.001 PHE D 340 TYR 0.012 0.001 TYR A 355 ARG 0.003 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 8 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 260 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 2.319 Fit side-chains REVERT: A 335 PHE cc_start: 0.8558 (t80) cc_final: 0.8268 (t80) REVERT: A 339 MET cc_start: 0.7870 (ptm) cc_final: 0.7349 (ptm) REVERT: A 378 PHE cc_start: 0.8973 (t80) cc_final: 0.8649 (t80) REVERT: A 451 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8966 (tt) REVERT: B 335 PHE cc_start: 0.8570 (t80) cc_final: 0.8318 (t80) REVERT: B 339 MET cc_start: 0.7888 (ptm) cc_final: 0.7410 (ptm) REVERT: B 378 PHE cc_start: 0.8974 (t80) cc_final: 0.8651 (t80) REVERT: B 451 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8963 (tt) REVERT: C 335 PHE cc_start: 0.8562 (t80) cc_final: 0.8269 (t80) REVERT: C 339 MET cc_start: 0.7861 (ptm) cc_final: 0.7343 (ptm) REVERT: C 378 PHE cc_start: 0.8971 (t80) cc_final: 0.8645 (t80) REVERT: C 451 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8959 (tt) REVERT: D 335 PHE cc_start: 0.8558 (t80) cc_final: 0.8267 (t80) REVERT: D 339 MET cc_start: 0.7868 (ptm) cc_final: 0.7351 (ptm) REVERT: D 378 PHE cc_start: 0.8971 (t80) cc_final: 0.8646 (t80) REVERT: D 451 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8964 (tt) outliers start: 40 outliers final: 32 residues processed: 244 average time/residue: 0.2471 time to fit residues: 103.1218 Evaluate side-chains 254 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 215 optimal weight: 0.0060 chunk 229 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 180 optimal weight: 0.0270 chunk 70 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 0.0270 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** 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 485 ASN ** 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 485 ASN ** 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 117 ASN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21560 Z= 0.130 Angle : 0.553 9.729 29228 Z= 0.261 Chirality : 0.035 0.215 3288 Planarity : 0.003 0.032 3616 Dihedral : 5.796 54.499 2872 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.78 % Allowed : 19.89 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2532 helix: 1.82 (0.13), residues: 1812 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 314 HIS 0.004 0.000 HIS B 325 PHE 0.011 0.001 PHE B 340 TYR 0.011 0.001 TYR A 523 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 9 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 266 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 226 time to evaluate : 2.438 Fit side-chains REVERT: A 339 MET cc_start: 0.7755 (ptm) cc_final: 0.7273 (ptm) REVERT: A 378 PHE cc_start: 0.8914 (t80) cc_final: 0.8553 (t80) REVERT: A 451 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8945 (tt) REVERT: A 547 MET cc_start: 0.6785 (mmp) cc_final: 0.6281 (mmp) REVERT: B 335 PHE cc_start: 0.8490 (t80) cc_final: 0.8288 (t80) REVERT: B 339 MET cc_start: 0.7774 (ptm) cc_final: 0.7268 (ptm) REVERT: B 378 PHE cc_start: 0.8914 (t80) cc_final: 0.8555 (t80) REVERT: B 451 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8947 (tt) REVERT: B 547 MET cc_start: 0.6772 (mmp) cc_final: 0.6257 (mmp) REVERT: C 335 PHE cc_start: 0.8492 (t80) cc_final: 0.8289 (t80) REVERT: C 339 MET cc_start: 0.7744 (ptm) cc_final: 0.7268 (ptm) REVERT: C 378 PHE cc_start: 0.8911 (t80) cc_final: 0.8553 (t80) REVERT: C 451 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8940 (tt) REVERT: C 547 MET cc_start: 0.6766 (mmp) cc_final: 0.6256 (mmp) REVERT: D 335 PHE cc_start: 0.8489 (t80) cc_final: 0.8285 (t80) REVERT: D 339 MET cc_start: 0.7749 (ptm) cc_final: 0.7245 (ptm) REVERT: D 378 PHE cc_start: 0.8912 (t80) cc_final: 0.8553 (t80) REVERT: D 451 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8947 (tt) REVERT: D 547 MET cc_start: 0.6761 (mmp) cc_final: 0.6238 (mmp) outliers start: 40 outliers final: 33 residues processed: 256 average time/residue: 0.2456 time to fit residues: 107.6696 Evaluate side-chains 261 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 chunk 255 optimal weight: 0.8980 chunk 234 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 0.0670 chunk 124 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- 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 485 ASN ** 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: 0.8365 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21560 Z= 0.139 Angle : 0.539 9.977 29228 Z= 0.261 Chirality : 0.035 0.203 3288 Planarity : 0.004 0.032 3616 Dihedral : 5.755 54.241 2872 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.91 % Allowed : 19.45 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2532 helix: 1.88 (0.13), residues: 1812 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP B 314 HIS 0.003 0.000 HIS C 325 PHE 0.043 0.001 PHE A 335 TYR 0.012 0.001 TYR A 355 ARG 0.003 0.000 ARG B 491 ********************** REFINEMENT MACRO_CYCLE 10 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 273 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 2.540 Fit side-chains REVERT: A 378 PHE cc_start: 0.8909 (t80) cc_final: 0.8544 (t80) REVERT: A 451 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8957 (tt) REVERT: B 335 PHE cc_start: 0.8510 (t80) cc_final: 0.8290 (t80) REVERT: B 339 MET cc_start: 0.7774 (ptm) cc_final: 0.7226 (ptm) REVERT: B 378 PHE cc_start: 0.8911 (t80) cc_final: 0.8548 (t80) REVERT: B 451 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8956 (tt) REVERT: C 335 PHE cc_start: 0.8504 (t80) cc_final: 0.8285 (t80) REVERT: C 339 MET cc_start: 0.7751 (ptm) cc_final: 0.7200 (ptm) REVERT: C 378 PHE cc_start: 0.8910 (t80) cc_final: 0.8545 (t80) REVERT: C 451 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8954 (tt) REVERT: D 335 PHE cc_start: 0.8503 (t80) cc_final: 0.8280 (t80) REVERT: D 339 MET cc_start: 0.7751 (ptm) cc_final: 0.7200 (ptm) REVERT: D 378 PHE cc_start: 0.8909 (t80) cc_final: 0.8544 (t80) REVERT: D 451 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8957 (tt) outliers start: 43 outliers final: 33 residues processed: 265 average time/residue: 0.2398 time to fit residues: 108.9090 Evaluate side-chains 263 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 203 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 117 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.084032 restraints weight = 50802.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.085374 restraints weight = 30655.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085965 restraints weight = 22467.757| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21560 Z= 0.134 Angle : 0.537 10.665 29228 Z= 0.258 Chirality : 0.036 0.176 3288 Planarity : 0.003 0.032 3616 Dihedral : 5.712 53.953 2872 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.78 % Allowed : 19.14 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2532 helix: 1.96 (0.12), residues: 1808 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.000 HIS A 325 PHE 0.013 0.001 PHE A 340 TYR 0.010 0.001 TYR C 523 ARG 0.003 0.000 ARG D 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.05 seconds wall clock time: 61 minutes 9.25 seconds (3669.25 seconds total)