Starting phenix.real_space_refine on Fri Feb 23 10:48:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kns_20016/02_2024/7kns_20016_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kns_20016/02_2024/7kns_20016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kns_20016/02_2024/7kns_20016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kns_20016/02_2024/7kns_20016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kns_20016/02_2024/7kns_20016_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kns_20016/02_2024/7kns_20016_updated.pdb" } resolution = 2.77 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ni 6 6.56 5 P 6 5.49 5 S 216 5.16 5 C 23876 2.51 5 N 6638 2.21 5 O 7292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A ASP 652": "OD1" <-> "OD2" Residue "A ASP 664": "OD1" <-> "OD2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A ASP 771": "OD1" <-> "OD2" Residue "A ASP 810": "OD1" <-> "OD2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B ASP 361": "OD1" <-> "OD2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ASP 459": "OD1" <-> "OD2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 556": "OD1" <-> "OD2" Residue "B ARG 575": "NH1" <-> "NH2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 674": "NH1" <-> "NH2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 730": "OD1" <-> "OD2" Residue "B GLU 742": "OE1" <-> "OE2" Residue "B ASP 771": "OD1" <-> "OD2" Residue "B ASP 810": "OD1" <-> "OD2" Residue "B ASP 819": "OD1" <-> "OD2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C ASP 361": "OD1" <-> "OD2" Residue "C ASP 374": "OD1" <-> "OD2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ASP 583": "OD1" <-> "OD2" Residue "C ASP 596": "OD1" <-> "OD2" Residue "C ASP 652": "OD1" <-> "OD2" Residue "C PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 674": "NH1" <-> "NH2" Residue "C PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C GLU 742": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D ASP 361": "OD1" <-> "OD2" Residue "D ASP 374": "OD1" <-> "OD2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ASP 459": "OD1" <-> "OD2" Residue "D PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D ARG 575": "NH1" <-> "NH2" Residue "D ASP 583": "OD1" <-> "OD2" Residue "D GLU 601": "OE1" <-> "OE2" Residue "D PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 674": "NH1" <-> "NH2" Residue "D PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 742": "OE1" <-> "OE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E ARG 439": "NH1" <-> "NH2" Residue "E PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 493": "OE1" <-> "OE2" Residue "E ASP 494": "OD1" <-> "OD2" Residue "E GLU 510": "OE1" <-> "OE2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E GLU 547": "OE1" <-> "OE2" Residue "E ARG 575": "NH1" <-> "NH2" Residue "E PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 674": "NH1" <-> "NH2" Residue "E PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 742": "OE1" <-> "OE2" Residue "E ASP 810": "OD1" <-> "OD2" Residue "E GLU 812": "OE1" <-> "OE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 141": "OD1" <-> "OD2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "F ASP 323": "OD1" <-> "OD2" Residue "F ASP 374": "OD1" <-> "OD2" Residue "F ARG 439": "NH1" <-> "NH2" Residue "F PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 556": "OD1" <-> "OD2" Residue "F ARG 575": "NH1" <-> "NH2" Residue "F ASP 583": "OD1" <-> "OD2" Residue "F GLU 601": "OE1" <-> "OE2" Residue "F ASP 602": "OD1" <-> "OD2" Residue "F GLU 618": "OE1" <-> "OE2" Residue "F PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 674": "NH1" <-> "NH2" Residue "F PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 730": "OD1" <-> "OD2" Residue "F GLU 742": "OE1" <-> "OE2" Residue "F ASP 771": "OD1" <-> "OD2" Residue "F ASP 810": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38034 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6337 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6330 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6330 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6334 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6330 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 6337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6337 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.46, per 1000 atoms: 0.51 Number of scatterers: 38034 At special positions: 0 Unit cell: (142.76, 145.25, 151.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 6 28.00 S 216 16.00 P 6 15.00 O 7292 8.00 N 6638 7.00 C 23876 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: 15.95 Conformation dependent library (CDL) restraints added in 7.0 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 76 sheets defined 29.1% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.92 Creating SS restraints... Processing helix chain 'A' and resid 5 through 26 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 54 through 62 removed outlier: 4.146A pdb=" N GLN A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 234 through 247 Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 436 through 440 removed outlier: 3.805A pdb=" N ALA A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 440' Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 529 through 536 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.943A pdb=" N ASP A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 658 removed outlier: 3.935A pdb=" N VAL A 643 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE A 644 " --> pdb=" O GLY A 641 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 645 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A 646 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN A 657 " --> pdb=" O MET A 654 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A 658 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 679 removed outlier: 3.652A pdb=" N LYS A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'A' and resid 750 through 752 No H-bonds generated for 'chain 'A' and resid 750 through 752' Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 774 through 777 No H-bonds generated for 'chain 'A' and resid 774 through 777' Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 32 through 49 Processing helix chain 'B' and resid 54 through 62 removed outlier: 4.165A pdb=" N GLN B 62 " --> pdb=" O MET B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 234 through 247 Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.583A pdb=" N SER B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.722A pdb=" N ALA B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'B' and resid 581 through 592 Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.594A pdb=" N ASP B 619 " --> pdb=" O ILE B 615 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 658 removed outlier: 3.930A pdb=" N VAL B 643 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE B 644 " --> pdb=" O GLY B 641 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 645 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B 646 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 657 " --> pdb=" O MET B 654 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 658 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 679 removed outlier: 3.651A pdb=" N LYS B 679 " --> pdb=" O ARG B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'B' and resid 750 through 752 No H-bonds generated for 'chain 'B' and resid 750 through 752' Processing helix chain 'B' and resid 767 through 771 Processing helix chain 'B' and resid 774 through 777 No H-bonds generated for 'chain 'B' and resid 774 through 777' Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'C' and resid 5 through 26 Processing helix chain 'C' and resid 32 through 49 Processing helix chain 'C' and resid 54 through 62 removed outlier: 4.147A pdb=" N GLN C 62 " --> pdb=" O MET C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 74 through 77 No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 234 through 247 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 414 through 422 Processing helix chain 'C' and resid 436 through 440 removed outlier: 3.901A pdb=" N ALA C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 436 through 440' Processing helix chain 'C' and resid 447 through 458 removed outlier: 3.604A pdb=" N ASP C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 499 through 512 Processing helix chain 'C' and resid 529 through 536 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 572 through 574 No H-bonds generated for 'chain 'C' and resid 572 through 574' Processing helix chain 'C' and resid 581 through 592 Processing helix chain 'C' and resid 600 through 609 Processing helix chain 'C' and resid 612 through 624 Processing helix chain 'C' and resid 640 through 658 removed outlier: 4.001A pdb=" N VAL C 643 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE C 644 " --> pdb=" O GLY C 641 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 645 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG C 646 " --> pdb=" O VAL C 643 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 657 " --> pdb=" O MET C 654 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 658 " --> pdb=" O LYS C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 679 removed outlier: 3.689A pdb=" N LYS C 679 " --> pdb=" O ARG C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 688 Processing helix chain 'C' and resid 710 through 712 No H-bonds generated for 'chain 'C' and resid 710 through 712' Processing helix chain 'C' and resid 750 through 752 No H-bonds generated for 'chain 'C' and resid 750 through 752' Processing helix chain 'C' and resid 767 through 771 Processing helix chain 'C' and resid 774 through 777 No H-bonds generated for 'chain 'C' and resid 774 through 777' Processing helix chain 'C' and resid 795 through 797 No H-bonds generated for 'chain 'C' and resid 795 through 797' Processing helix chain 'D' and resid 5 through 26 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 54 through 62 removed outlier: 4.141A pdb=" N GLN D 62 " --> pdb=" O MET D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 74 through 77 No H-bonds generated for 'chain 'D' and resid 74 through 77' Processing helix chain 'D' and resid 107 through 110 No H-bonds generated for 'chain 'D' and resid 107 through 110' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 436 through 439 No H-bonds generated for 'chain 'D' and resid 436 through 439' Processing helix chain 'D' and resid 447 through 458 removed outlier: 3.557A pdb=" N ASP D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 499 through 512 Processing helix chain 'D' and resid 529 through 536 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 572 through 574 No H-bonds generated for 'chain 'D' and resid 572 through 574' Processing helix chain 'D' and resid 581 through 593 Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 612 through 624 removed outlier: 3.577A pdb=" N ASP D 619 " --> pdb=" O ILE D 615 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 656 removed outlier: 3.968A pdb=" N VAL D 643 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE D 644 " --> pdb=" O GLY D 641 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER D 645 " --> pdb=" O GLU D 642 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG D 646 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 679 removed outlier: 3.687A pdb=" N LYS D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 688 Processing helix chain 'D' and resid 710 through 712 No H-bonds generated for 'chain 'D' and resid 710 through 712' Processing helix chain 'D' and resid 750 through 752 No H-bonds generated for 'chain 'D' and resid 750 through 752' Processing helix chain 'D' and resid 757 through 760 removed outlier: 3.715A pdb=" N LEU D 760 " --> pdb=" O GLY D 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 757 through 760' Processing helix chain 'D' and resid 767 through 771 Processing helix chain 'D' and resid 774 through 777 No H-bonds generated for 'chain 'D' and resid 774 through 777' Processing helix chain 'D' and resid 795 through 797 No H-bonds generated for 'chain 'D' and resid 795 through 797' Processing helix chain 'E' and resid 5 through 26 removed outlier: 3.509A pdb=" N GLU E 9 " --> pdb=" O PRO E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 49 Processing helix chain 'E' and resid 54 through 62 removed outlier: 4.159A pdb=" N GLN E 62 " --> pdb=" O MET E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 74 through 77 No H-bonds generated for 'chain 'E' and resid 74 through 77' Processing helix chain 'E' and resid 107 through 110 No H-bonds generated for 'chain 'E' and resid 107 through 110' Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 234 through 247 Processing helix chain 'E' and resid 276 through 283 Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 436 through 440 removed outlier: 3.781A pdb=" N ALA E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 436 through 440' Processing helix chain 'E' and resid 447 through 456 Processing helix chain 'E' and resid 476 through 483 Processing helix chain 'E' and resid 499 through 512 Processing helix chain 'E' and resid 529 through 536 Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 572 through 574 No H-bonds generated for 'chain 'E' and resid 572 through 574' Processing helix chain 'E' and resid 581 through 593 Processing helix chain 'E' and resid 600 through 609 Processing helix chain 'E' and resid 612 through 624 Processing helix chain 'E' and resid 640 through 658 removed outlier: 3.963A pdb=" N VAL E 643 " --> pdb=" O VAL E 640 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE E 644 " --> pdb=" O GLY E 641 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER E 645 " --> pdb=" O GLU E 642 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG E 646 " --> pdb=" O VAL E 643 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN E 657 " --> pdb=" O MET E 654 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR E 658 " --> pdb=" O LYS E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 678 Processing helix chain 'E' and resid 683 through 688 Processing helix chain 'E' and resid 710 through 712 No H-bonds generated for 'chain 'E' and resid 710 through 712' Processing helix chain 'E' and resid 750 through 752 No H-bonds generated for 'chain 'E' and resid 750 through 752' Processing helix chain 'E' and resid 758 through 760 No H-bonds generated for 'chain 'E' and resid 758 through 760' Processing helix chain 'E' and resid 767 through 771 Processing helix chain 'E' and resid 774 through 777 No H-bonds generated for 'chain 'E' and resid 774 through 777' Processing helix chain 'E' and resid 795 through 797 No H-bonds generated for 'chain 'E' and resid 795 through 797' Processing helix chain 'F' and resid 5 through 25 Processing helix chain 'F' and resid 32 through 49 Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.173A pdb=" N GLN F 62 " --> pdb=" O MET F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 69 No H-bonds generated for 'chain 'F' and resid 67 through 69' Processing helix chain 'F' and resid 74 through 77 No H-bonds generated for 'chain 'F' and resid 74 through 77' Processing helix chain 'F' and resid 107 through 110 No H-bonds generated for 'chain 'F' and resid 107 through 110' Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 234 through 247 Processing helix chain 'F' and resid 276 through 283 Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.561A pdb=" N SER F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 440 removed outlier: 3.737A pdb=" N ALA F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 436 through 440' Processing helix chain 'F' and resid 447 through 456 Processing helix chain 'F' and resid 476 through 483 Processing helix chain 'F' and resid 499 through 512 Processing helix chain 'F' and resid 529 through 536 Processing helix chain 'F' and resid 556 through 562 Processing helix chain 'F' and resid 572 through 574 No H-bonds generated for 'chain 'F' and resid 572 through 574' Processing helix chain 'F' and resid 581 through 593 Processing helix chain 'F' and resid 600 through 609 Processing helix chain 'F' and resid 612 through 624 removed outlier: 3.638A pdb=" N ASP F 619 " --> pdb=" O ILE F 615 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 620 " --> pdb=" O ALA F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 658 removed outlier: 3.922A pdb=" N VAL F 643 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE F 644 " --> pdb=" O GLY F 641 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER F 645 " --> pdb=" O GLU F 642 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG F 646 " --> pdb=" O VAL F 643 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN F 657 " --> pdb=" O MET F 654 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR F 658 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 679 removed outlier: 3.663A pdb=" N LYS F 679 " --> pdb=" O ARG F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 688 Processing helix chain 'F' and resid 750 through 752 No H-bonds generated for 'chain 'F' and resid 750 through 752' Processing helix chain 'F' and resid 758 through 760 No H-bonds generated for 'chain 'F' and resid 758 through 760' Processing helix chain 'F' and resid 767 through 771 Processing helix chain 'F' and resid 774 through 777 No H-bonds generated for 'chain 'F' and resid 774 through 777' Processing helix chain 'F' and resid 795 through 797 No H-bonds generated for 'chain 'F' and resid 795 through 797' Processing sheet with id= A, first strand: chain 'A' and resid 80 through 87 Processing sheet with id= B, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.762A pdb=" N THR A 272 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 258 through 261 removed outlier: 3.729A pdb=" N SER A 258 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS A 151 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 165 through 168 Processing sheet with id= E, first strand: chain 'A' and resid 290 through 292 Processing sheet with id= F, first strand: chain 'A' and resid 390 through 393 removed outlier: 6.166A pdb=" N LYS A 360 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.693A pdb=" N ALA A 401 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LYS A 722 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 463 through 466 removed outlier: 7.030A pdb=" N ALA A 403 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 427 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP A 405 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY A 429 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 541 through 543 Processing sheet with id= J, first strand: chain 'A' and resid 569 through 571 removed outlier: 6.435A pdb=" N ILE A 629 " --> pdb=" O SER A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 762 through 765 removed outlier: 6.637A pdb=" N ARG A 783 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 765 " --> pdb=" O ARG A 783 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU A 785 " --> pdb=" O VAL A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 807 through 809 Processing sheet with id= M, first strand: chain 'B' and resid 80 through 87 Processing sheet with id= N, first strand: chain 'B' and resid 143 through 146 removed outlier: 4.714A pdb=" N THR B 272 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 258 through 261 removed outlier: 3.697A pdb=" N SER B 258 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LYS B 151 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 165 through 168 Processing sheet with id= Q, first strand: chain 'B' and resid 290 through 292 Processing sheet with id= R, first strand: chain 'B' and resid 390 through 393 removed outlier: 6.169A pdb=" N LYS B 360 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 344 through 348 Processing sheet with id= T, first strand: chain 'B' and resid 397 through 401 removed outlier: 5.911A pdb=" N LYS B 722 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL B 726 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 463 through 466 removed outlier: 7.063A pdb=" N ALA B 403 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU B 427 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP B 405 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY B 429 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 541 through 543 Processing sheet with id= W, first strand: chain 'B' and resid 569 through 571 removed outlier: 6.372A pdb=" N ILE B 629 " --> pdb=" O SER B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'B' and resid 762 through 765 removed outlier: 6.666A pdb=" N ARG B 783 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL B 765 " --> pdb=" O ARG B 783 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B 785 " --> pdb=" O VAL B 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'B' and resid 807 through 809 Processing sheet with id= Z, first strand: chain 'C' and resid 80 through 87 Processing sheet with id= AA, first strand: chain 'C' and resid 143 through 146 removed outlier: 4.733A pdb=" N THR C 272 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 258 through 261 removed outlier: 3.688A pdb=" N SER C 258 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS C 151 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 165 through 168 Processing sheet with id= AD, first strand: chain 'C' and resid 290 through 292 Processing sheet with id= AE, first strand: chain 'C' and resid 390 through 393 removed outlier: 6.136A pdb=" N LYS C 360 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 344 through 347 Processing sheet with id= AG, first strand: chain 'C' and resid 397 through 401 removed outlier: 3.754A pdb=" N MET C 719 " --> pdb=" O MET C 707 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS C 722 " --> pdb=" O VAL C 726 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL C 726 " --> pdb=" O LYS C 722 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 463 through 466 removed outlier: 7.040A pdb=" N ALA C 403 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU C 427 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP C 405 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLY C 429 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 541 through 543 Processing sheet with id= AJ, first strand: chain 'C' and resid 569 through 571 removed outlier: 6.421A pdb=" N ILE C 629 " --> pdb=" O SER C 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'C' and resid 762 through 765 removed outlier: 6.643A pdb=" N ARG C 783 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL C 765 " --> pdb=" O ARG C 783 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU C 785 " --> pdb=" O VAL C 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'C' and resid 807 through 809 Processing sheet with id= AM, first strand: chain 'D' and resid 80 through 87 Processing sheet with id= AN, first strand: chain 'D' and resid 143 through 146 removed outlier: 4.741A pdb=" N THR D 272 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'D' and resid 258 through 261 removed outlier: 3.762A pdb=" N SER D 258 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS D 151 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 165 through 168 Processing sheet with id= AQ, first strand: chain 'D' and resid 290 through 292 Processing sheet with id= AR, first strand: chain 'D' and resid 390 through 393 removed outlier: 6.109A pdb=" N LYS D 360 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'D' and resid 344 through 347 Processing sheet with id= AT, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.689A pdb=" N MET D 719 " --> pdb=" O MET D 707 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS D 722 " --> pdb=" O VAL D 726 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL D 726 " --> pdb=" O LYS D 722 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 463 through 466 removed outlier: 7.057A pdb=" N ALA D 403 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D 427 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP D 405 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY D 429 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'D' and resid 541 through 543 Processing sheet with id= AW, first strand: chain 'D' and resid 569 through 571 removed outlier: 6.381A pdb=" N ILE D 629 " --> pdb=" O SER D 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'D' and resid 762 through 765 removed outlier: 6.649A pdb=" N ARG D 783 " --> pdb=" O ALA D 763 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL D 765 " --> pdb=" O ARG D 783 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU D 785 " --> pdb=" O VAL D 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'D' and resid 807 through 809 Processing sheet with id= AZ, first strand: chain 'E' and resid 80 through 87 Processing sheet with id= BA, first strand: chain 'E' and resid 143 through 146 removed outlier: 4.748A pdb=" N THR E 272 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'E' and resid 258 through 261 removed outlier: 3.730A pdb=" N SER E 258 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS E 151 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'E' and resid 165 through 168 Processing sheet with id= BD, first strand: chain 'E' and resid 290 through 292 Processing sheet with id= BE, first strand: chain 'E' and resid 390 through 393 removed outlier: 6.169A pdb=" N LYS E 360 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'E' and resid 351 through 355 removed outlier: 4.695A pdb=" N ALA E 401 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS E 722 " --> pdb=" O VAL E 726 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'E' and resid 463 through 466 removed outlier: 7.029A pdb=" N ALA E 403 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU E 427 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP E 405 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY E 429 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'E' and resid 541 through 543 Processing sheet with id= BI, first strand: chain 'E' and resid 569 through 571 removed outlier: 6.405A pdb=" N ILE E 629 " --> pdb=" O SER E 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'E' and resid 762 through 765 removed outlier: 6.661A pdb=" N ARG E 783 " --> pdb=" O ALA E 763 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL E 765 " --> pdb=" O ARG E 783 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU E 785 " --> pdb=" O VAL E 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'E' and resid 807 through 809 Processing sheet with id= BL, first strand: chain 'F' and resid 80 through 87 Processing sheet with id= BM, first strand: chain 'F' and resid 143 through 146 removed outlier: 4.710A pdb=" N THR F 272 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'F' and resid 258 through 261 removed outlier: 3.714A pdb=" N SER F 258 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS F 151 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'F' and resid 165 through 168 Processing sheet with id= BP, first strand: chain 'F' and resid 290 through 292 Processing sheet with id= BQ, first strand: chain 'F' and resid 390 through 393 removed outlier: 6.168A pdb=" N LYS F 360 " --> pdb=" O ILE F 364 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'F' and resid 344 through 348 Processing sheet with id= BS, first strand: chain 'F' and resid 397 through 401 removed outlier: 5.917A pdb=" N LYS F 722 " --> pdb=" O VAL F 726 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL F 726 " --> pdb=" O LYS F 722 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'F' and resid 463 through 466 removed outlier: 7.044A pdb=" N ALA F 403 " --> pdb=" O THR F 425 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU F 427 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP F 405 " --> pdb=" O LEU F 427 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY F 429 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'F' and resid 541 through 543 Processing sheet with id= BV, first strand: chain 'F' and resid 569 through 571 removed outlier: 6.391A pdb=" N ILE F 629 " --> pdb=" O SER F 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'F' and resid 762 through 765 removed outlier: 6.668A pdb=" N ARG F 783 " --> pdb=" O ALA F 763 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL F 765 " --> pdb=" O ARG F 783 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU F 785 " --> pdb=" O VAL F 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= BW Processing sheet with id= BX, first strand: chain 'F' and resid 807 through 809 1143 hydrogen bonds defined for protein. 3021 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: 16.79 Time building geometry restraints manager: 16.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12418 1.34 - 1.46: 5156 1.46 - 1.58: 20814 1.58 - 1.69: 0 1.69 - 1.81: 342 Bond restraints: 38730 Sorted by residual: bond pdb=" NZ KCX C 490 " pdb=" CX KCX C 490 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" NZ KCX B 490 " pdb=" CX KCX B 490 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" NZ KCX E 490 " pdb=" CX KCX E 490 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" NZ KCX D 490 " pdb=" CX KCX D 490 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" NZ KCX F 490 " pdb=" CX KCX F 490 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 38725 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.76: 1268 106.76 - 113.62: 21655 113.62 - 120.47: 14686 120.47 - 127.33: 14443 127.33 - 134.18: 447 Bond angle restraints: 52499 Sorted by residual: angle pdb=" N THR B 740 " pdb=" CA THR B 740 " pdb=" C THR B 740 " ideal model delta sigma weight residual 109.81 119.39 -9.58 2.21e+00 2.05e-01 1.88e+01 angle pdb=" N THR F 740 " pdb=" CA THR F 740 " pdb=" C THR F 740 " ideal model delta sigma weight residual 109.81 119.29 -9.48 2.21e+00 2.05e-01 1.84e+01 angle pdb=" N THR D 740 " pdb=" CA THR D 740 " pdb=" C THR D 740 " ideal model delta sigma weight residual 109.81 119.12 -9.31 2.21e+00 2.05e-01 1.78e+01 angle pdb=" N THR E 740 " pdb=" CA THR E 740 " pdb=" C THR E 740 " ideal model delta sigma weight residual 109.81 119.02 -9.21 2.21e+00 2.05e-01 1.74e+01 angle pdb=" N THR A 740 " pdb=" CA THR A 740 " pdb=" C THR A 740 " ideal model delta sigma weight residual 109.81 118.89 -9.08 2.21e+00 2.05e-01 1.69e+01 ... (remaining 52494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 21127 17.07 - 34.13: 1892 34.13 - 51.20: 269 51.20 - 68.27: 86 68.27 - 85.33: 27 Dihedral angle restraints: 23401 sinusoidal: 9169 harmonic: 14232 Sorted by residual: dihedral pdb=" CA TRP B 708 " pdb=" C TRP B 708 " pdb=" N LYS B 709 " pdb=" CA LYS B 709 " ideal model delta harmonic sigma weight residual 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG A 163 " pdb=" C ARG A 163 " pdb=" N PRO A 164 " pdb=" CA PRO A 164 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TRP C 708 " pdb=" C TRP C 708 " pdb=" N LYS C 709 " pdb=" CA LYS C 709 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 23398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4161 0.043 - 0.086: 1241 0.086 - 0.129: 521 0.129 - 0.172: 84 0.172 - 0.215: 11 Chirality restraints: 6018 Sorted by residual: chirality pdb=" CA ASN D 572 " pdb=" N ASN D 572 " pdb=" C ASN D 572 " pdb=" CB ASN D 572 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 572 " pdb=" N ASN A 572 " pdb=" C ASN A 572 " pdb=" CB ASN A 572 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASN B 572 " pdb=" N ASN B 572 " pdb=" C ASN B 572 " pdb=" CB ASN B 572 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 6015 not shown) Planarity restraints: 6857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 651 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ALA A 651 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA A 651 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP A 652 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 649 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C GLN A 649 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 649 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 650 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 649 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C GLN E 649 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN E 649 " -0.011 2.00e-02 2.50e+03 pdb=" N THR E 650 " -0.010 2.00e-02 2.50e+03 ... (remaining 6854 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 151 2.45 - 3.07: 25060 3.07 - 3.68: 59825 3.68 - 4.29: 99270 4.29 - 4.90: 162749 Nonbonded interactions: 347055 Sorted by model distance: nonbonded pdb="NI NI E 901 " pdb=" O1 PO4 E 902 " model vdw 1.842 2.180 nonbonded pdb="NI NI D 901 " pdb=" O1 PO4 D 902 " model vdw 1.846 2.180 nonbonded pdb="NI NI B 901 " pdb=" O3 PO4 B 902 " model vdw 1.854 2.180 nonbonded pdb="NI NI C 901 " pdb=" O4 PO4 C 902 " model vdw 1.894 2.180 nonbonded pdb=" OQ1 KCX E 490 " pdb="NI NI E 901 " model vdw 1.897 2.180 ... (remaining 347050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 or (resid 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 840 or resid 901 through 902 \ )) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 1 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 840 or resid 901 through 902)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 or (resid 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 840 or resid 901 through 902 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 13.850 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 104.410 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 38730 Z= 0.335 Angle : 0.731 9.583 52499 Z= 0.379 Chirality : 0.049 0.215 6018 Planarity : 0.004 0.043 6857 Dihedral : 13.498 85.332 14305 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.78 (0.11), residues: 4980 helix: -0.18 (0.13), residues: 1476 sheet: -0.27 (0.19), residues: 636 loop : -0.70 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 708 HIS 0.016 0.002 HIS A 519 PHE 0.019 0.002 PHE A 528 TYR 0.026 0.001 TYR E 544 ARG 0.018 0.001 ARG F 609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 4.675 Fit side-chains REVERT: A 632 SER cc_start: 0.8473 (p) cc_final: 0.8198 (p) REVERT: C 632 SER cc_start: 0.8492 (p) cc_final: 0.8242 (p) REVERT: D 632 SER cc_start: 0.8502 (p) cc_final: 0.8253 (p) REVERT: F 812 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6894 (mm-30) outliers start: 0 outliers final: 2 residues processed: 560 average time/residue: 1.5681 time to fit residues: 1055.2995 Evaluate side-chains 449 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 447 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain F residue 508 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 0.8980 chunk 377 optimal weight: 0.9990 chunk 209 optimal weight: 0.0770 chunk 128 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 452 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN B 511 HIS C 82 GLN C 511 HIS C 517 ASN D 82 GLN D 511 HIS E 82 GLN F 82 GLN F 511 HIS F 585 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38730 Z= 0.198 Angle : 0.517 8.975 52499 Z= 0.274 Chirality : 0.046 0.213 6018 Planarity : 0.004 0.041 6857 Dihedral : 4.929 38.651 5398 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.81 % Allowed : 6.25 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.58 (0.11), residues: 4980 helix: -0.07 (0.13), residues: 1512 sheet: -0.21 (0.18), residues: 762 loop : -0.54 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 708 HIS 0.006 0.001 HIS E 479 PHE 0.009 0.001 PHE D 838 TYR 0.014 0.001 TYR E 544 ARG 0.003 0.000 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 480 time to evaluate : 4.070 Fit side-chains REVERT: A 82 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: A 122 ASP cc_start: 0.7630 (m-30) cc_final: 0.7382 (m-30) REVERT: A 163 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8100 (ptt-90) REVERT: B 277 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8540 (mtmm) REVERT: C 82 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8655 (mt0) REVERT: C 618 GLU cc_start: 0.8018 (tt0) cc_final: 0.7716 (tt0) REVERT: D 82 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: E 163 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8157 (ptt-90) REVERT: F 277 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (mtmm) outliers start: 74 outliers final: 35 residues processed: 509 average time/residue: 1.4645 time to fit residues: 910.2664 Evaluate side-chains 479 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 437 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 547 GLU Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 830 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 376 optimal weight: 2.9990 chunk 307 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 453 optimal weight: 2.9990 chunk 489 optimal weight: 0.8980 chunk 403 optimal weight: 0.4980 chunk 449 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 363 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 82 GLN B 504 ASN B 511 HIS C 511 HIS F 82 GLN F 504 ASN F 511 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38730 Z= 0.229 Angle : 0.514 8.756 52499 Z= 0.271 Chirality : 0.046 0.211 6018 Planarity : 0.004 0.045 6857 Dihedral : 4.843 40.295 5398 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.53 % Allowed : 8.07 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.52 (0.12), residues: 4980 helix: -0.08 (0.13), residues: 1548 sheet: -0.07 (0.18), residues: 762 loop : -0.50 (0.12), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 708 HIS 0.006 0.001 HIS F 519 PHE 0.011 0.001 PHE C 838 TYR 0.012 0.001 TYR E 544 ARG 0.005 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 456 time to evaluate : 4.746 Fit side-chains REVERT: A 82 GLN cc_start: 0.8780 (mp10) cc_final: 0.8538 (mt0) REVERT: A 122 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: A 252 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: A 587 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7621 (t0) REVERT: A 618 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6436 (pt0) REVERT: B 277 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8539 (mtmm) REVERT: C 252 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: D 58 MET cc_start: 0.8836 (mtp) cc_final: 0.8554 (mtt) REVERT: D 252 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: E 584 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: F 277 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8546 (mtmm) outliers start: 103 outliers final: 55 residues processed: 511 average time/residue: 1.4568 time to fit residues: 910.1775 Evaluate side-chains 498 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 434 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 821 LYS Chi-restraints excluded: chain F residue 830 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 0.3980 chunk 340 optimal weight: 6.9990 chunk 235 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 304 optimal weight: 0.8980 chunk 454 optimal weight: 4.9990 chunk 481 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 430 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN B 511 HIS B 585 HIS C 511 HIS F 82 GLN F 511 HIS F 585 HIS F 657 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38730 Z= 0.227 Angle : 0.507 8.610 52499 Z= 0.267 Chirality : 0.046 0.215 6018 Planarity : 0.004 0.049 6857 Dihedral : 4.811 41.672 5398 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.60 % Allowed : 9.71 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.42 (0.12), residues: 4980 helix: 0.00 (0.13), residues: 1536 sheet: 0.05 (0.18), residues: 762 loop : -0.46 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 708 HIS 0.007 0.001 HIS F 519 PHE 0.011 0.001 PHE B 838 TYR 0.010 0.001 TYR E 544 ARG 0.004 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 454 time to evaluate : 4.473 Fit side-chains REVERT: A 252 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: A 480 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 618 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6518 (pt0) REVERT: C 252 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: D 156 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8191 (tptm) REVERT: D 252 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: E 82 GLN cc_start: 0.8859 (mp10) cc_final: 0.8558 (mt0) REVERT: E 252 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: E 480 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: E 584 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7748 (tt0) outliers start: 106 outliers final: 61 residues processed: 511 average time/residue: 1.4708 time to fit residues: 921.8225 Evaluate side-chains 501 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 431 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 821 LYS Chi-restraints excluded: chain F residue 830 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 358 optimal weight: 0.0170 chunk 198 optimal weight: 0.5980 chunk 410 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 432 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN B 511 HIS C 511 HIS F 82 GLN F 511 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38730 Z= 0.152 Angle : 0.470 8.101 52499 Z= 0.247 Chirality : 0.044 0.212 6018 Planarity : 0.004 0.050 6857 Dihedral : 4.550 41.532 5398 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.21 % Allowed : 11.03 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.23 (0.12), residues: 4980 helix: 0.16 (0.13), residues: 1536 sheet: 0.23 (0.18), residues: 702 loop : -0.35 (0.12), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 708 HIS 0.005 0.001 HIS C 511 PHE 0.007 0.001 PHE A 690 TYR 0.007 0.001 TYR E 680 ARG 0.003 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 465 time to evaluate : 4.387 Fit side-chains REVERT: A 252 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: A 263 LYS cc_start: 0.7817 (mttp) cc_final: 0.7522 (mttm) REVERT: A 480 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: B 586 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8334 (tp) REVERT: C 252 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: D 252 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: E 82 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: E 480 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: E 618 GLU cc_start: 0.7931 (tt0) cc_final: 0.7716 (tt0) REVERT: F 586 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8356 (tp) outliers start: 90 outliers final: 53 residues processed: 516 average time/residue: 1.4335 time to fit residues: 905.1995 Evaluate side-chains 494 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 433 time to evaluate : 4.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 740 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 5.9990 chunk 433 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 481 optimal weight: 0.0670 chunk 399 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS B 504 ASN B 511 HIS E 275 HIS F 504 ASN F 511 HIS F 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38730 Z= 0.213 Angle : 0.495 8.608 52499 Z= 0.260 Chirality : 0.045 0.209 6018 Planarity : 0.004 0.050 6857 Dihedral : 4.637 42.607 5398 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.33 % Allowed : 11.67 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.21 (0.12), residues: 4980 helix: 0.13 (0.13), residues: 1542 sheet: 0.29 (0.18), residues: 702 loop : -0.32 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 708 HIS 0.007 0.001 HIS F 519 PHE 0.011 0.001 PHE E 838 TYR 0.009 0.001 TYR E 680 ARG 0.004 0.000 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 432 time to evaluate : 4.475 Fit side-chains REVERT: A 82 GLN cc_start: 0.8882 (mp10) cc_final: 0.8577 (mt0) REVERT: A 252 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: A 263 LYS cc_start: 0.7765 (mttp) cc_final: 0.7445 (mttm) REVERT: A 480 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 586 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8357 (tp) REVERT: C 252 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: D 252 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: E 82 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: E 252 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: E 480 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: F 252 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: F 586 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8376 (tp) outliers start: 95 outliers final: 58 residues processed: 487 average time/residue: 1.4446 time to fit residues: 862.6892 Evaluate side-chains 491 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 423 time to evaluate : 4.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 274 optimal weight: 0.8980 chunk 351 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 405 optimal weight: 0.4980 chunk 269 optimal weight: 2.9990 chunk 479 optimal weight: 0.7980 chunk 300 optimal weight: 8.9990 chunk 292 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS F 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38730 Z= 0.194 Angle : 0.486 8.293 52499 Z= 0.255 Chirality : 0.045 0.209 6018 Planarity : 0.004 0.051 6857 Dihedral : 4.606 42.774 5398 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.28 % Allowed : 12.09 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.17 (0.12), residues: 4980 helix: 0.16 (0.13), residues: 1542 sheet: 0.33 (0.19), residues: 702 loop : -0.30 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 708 HIS 0.006 0.001 HIS F 519 PHE 0.009 0.001 PHE E 838 TYR 0.008 0.001 TYR E 680 ARG 0.004 0.000 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 429 time to evaluate : 4.613 Fit side-chains REVERT: A 82 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: A 252 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: A 263 LYS cc_start: 0.7778 (mttp) cc_final: 0.7464 (mttm) REVERT: A 480 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: B 586 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 252 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: D 252 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: E 82 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: E 252 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: E 480 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: F 586 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8375 (tp) outliers start: 93 outliers final: 64 residues processed: 482 average time/residue: 1.4425 time to fit residues: 853.0458 Evaluate side-chains 497 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 423 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 6.9990 chunk 191 optimal weight: 0.0980 chunk 286 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 305 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 377 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS B 836 ASN D 275 HIS F 511 HIS F 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38730 Z= 0.199 Angle : 0.488 8.498 52499 Z= 0.256 Chirality : 0.045 0.206 6018 Planarity : 0.004 0.051 6857 Dihedral : 4.607 43.562 5398 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.33 % Allowed : 12.41 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.15 (0.12), residues: 4980 helix: 0.17 (0.13), residues: 1542 sheet: 0.37 (0.19), residues: 702 loop : -0.29 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 708 HIS 0.006 0.001 HIS A 511 PHE 0.010 0.001 PHE E 838 TYR 0.008 0.001 TYR E 680 ARG 0.004 0.000 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 427 time to evaluate : 4.977 Fit side-chains REVERT: A 82 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8681 (mt0) REVERT: A 252 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: A 263 LYS cc_start: 0.7766 (mttp) cc_final: 0.7449 (mttm) REVERT: A 480 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: B 586 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8358 (tp) REVERT: B 657 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: C 156 LYS cc_start: 0.8385 (tptm) cc_final: 0.8115 (tptt) REVERT: C 252 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: D 252 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: E 82 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8640 (mt0) REVERT: E 252 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: E 480 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 586 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (tp) outliers start: 95 outliers final: 69 residues processed: 488 average time/residue: 1.4689 time to fit residues: 883.4345 Evaluate side-chains 501 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 421 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 4.9990 chunk 459 optimal weight: 0.9980 chunk 419 optimal weight: 0.6980 chunk 447 optimal weight: 0.9990 chunk 269 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 404 optimal weight: 7.9990 chunk 423 optimal weight: 1.9990 chunk 445 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS E 511 HIS F 511 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38730 Z= 0.193 Angle : 0.486 8.296 52499 Z= 0.255 Chirality : 0.045 0.207 6018 Planarity : 0.004 0.051 6857 Dihedral : 4.593 43.997 5398 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.21 % Allowed : 12.53 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.14 (0.12), residues: 4980 helix: 0.18 (0.13), residues: 1542 sheet: 0.37 (0.18), residues: 768 loop : -0.30 (0.12), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 708 HIS 0.006 0.001 HIS F 519 PHE 0.009 0.001 PHE E 838 TYR 0.008 0.001 TYR F 171 ARG 0.004 0.000 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 428 time to evaluate : 4.718 Fit side-chains REVERT: A 82 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8674 (mt0) REVERT: A 252 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: A 263 LYS cc_start: 0.7754 (mttp) cc_final: 0.7440 (mttm) REVERT: A 480 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 586 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8356 (tp) REVERT: B 657 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: C 156 LYS cc_start: 0.8388 (tptm) cc_final: 0.8120 (tptt) REVERT: C 252 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: D 252 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: E 82 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8673 (mt0) REVERT: E 252 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: E 480 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 586 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8408 (tp) outliers start: 90 outliers final: 71 residues processed: 485 average time/residue: 1.4390 time to fit residues: 854.1240 Evaluate side-chains 504 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 422 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 0.9980 chunk 472 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 496 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 395 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 242 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS C 275 HIS E 511 HIS F 511 HIS F 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 38730 Z= 0.275 Angle : 0.523 8.658 52499 Z= 0.274 Chirality : 0.047 0.208 6018 Planarity : 0.004 0.049 6857 Dihedral : 4.808 48.452 5398 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.23 % Allowed : 12.70 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.23 (0.12), residues: 4980 helix: 0.15 (0.13), residues: 1512 sheet: 0.37 (0.18), residues: 762 loop : -0.41 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 708 HIS 0.008 0.001 HIS F 519 PHE 0.014 0.001 PHE C 838 TYR 0.009 0.001 TYR E 680 ARG 0.005 0.000 ARG F 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 430 time to evaluate : 4.682 Fit side-chains REVERT: A 82 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: A 122 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: A 252 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: A 263 LYS cc_start: 0.7753 (mttp) cc_final: 0.7431 (mttm) REVERT: A 480 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: B 480 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 586 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8378 (tp) REVERT: C 156 LYS cc_start: 0.8417 (tptm) cc_final: 0.8139 (tptt) REVERT: C 252 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: D 252 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: E 82 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8617 (mt0) REVERT: E 252 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: E 480 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: E 603 LEU cc_start: 0.7835 (mt) cc_final: 0.7444 (mt) REVERT: F 586 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8415 (tp) outliers start: 91 outliers final: 67 residues processed: 490 average time/residue: 1.4256 time to fit residues: 856.1106 Evaluate side-chains 500 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 421 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 830 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 2.9990 chunk 420 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 364 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 0.0570 chunk 395 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS B 657 GLN E 511 HIS F 511 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.093510 restraints weight = 44404.950| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.42 r_work: 0.2810 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38730 Z= 0.155 Angle : 0.472 8.048 52499 Z= 0.248 Chirality : 0.044 0.209 6018 Planarity : 0.004 0.052 6857 Dihedral : 4.537 45.358 5398 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.77 % Allowed : 13.21 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.09 (0.12), residues: 4980 helix: 0.23 (0.13), residues: 1536 sheet: 0.45 (0.18), residues: 768 loop : -0.29 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 708 HIS 0.005 0.001 HIS E 511 PHE 0.007 0.001 PHE A 690 TYR 0.009 0.001 TYR B 171 ARG 0.004 0.000 ARG F 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13619.32 seconds wall clock time: 243 minutes 34.37 seconds (14614.37 seconds total)