Starting phenix.real_space_refine on Sun Jun 30 04:23:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/06_2024/8iam_35310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/06_2024/8iam_35310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/06_2024/8iam_35310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/06_2024/8iam_35310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/06_2024/8iam_35310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/06_2024/8iam_35310_updated.pdb" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 C 12980 2.51 5 N 3358 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "B TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 32": "OD1" <-> "OD2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 331": "OD1" <-> "OD2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B ASP 534": "OD1" <-> "OD2" Residue "B ASP 541": "OD1" <-> "OD2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E ASP 94": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 228": "NH1" <-> "NH2" Residue "E ASP 236": "OD1" <-> "OD2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 342": "OD1" <-> "OD2" Residue "E PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 376": "NH1" <-> "NH2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "E GLU 467": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 509": "NH1" <-> "NH2" Residue "E GLU 517": "OE1" <-> "OE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F ARG 194": "NH1" <-> "NH2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 246": "OD1" <-> "OD2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 331": "OD1" <-> "OD2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 496": "NH1" <-> "NH2" Residue "F TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 517": "OE1" <-> "OE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F ASP 534": "OD1" <-> "OD2" Residue "F ASP 541": "OD1" <-> "OD2" Residue "F GLU 543": "OE1" <-> "OE2" Residue "F GLU 544": "OE1" <-> "OE2" Residue "F GLU 551": "OE1" <-> "OE2" Residue "F ASP 552": "OD1" <-> "OD2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 20192 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3844 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 470} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1225 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 142} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3844 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 470} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1225 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 142} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.00, per 1000 atoms: 0.54 Number of scatterers: 20192 At special positions: 0 Unit cell: (171.72, 109.08, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 3738 8.00 N 3358 7.00 C 12980 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 3.9 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 14 sheets defined 46.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 116 through 119 No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 218 through 225 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 335 through 338 No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 343 through 346 No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 409 through 426 Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 535 through 553 Processing helix chain 'B' and resid 21 through 27 Processing helix chain 'B' and resid 58 through 84 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.569A pdb=" N ASP B 119 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASP B 120 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 225 through 236 removed outlier: 4.728A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.581A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 421 through 443 removed outlier: 3.550A pdb=" N ALA B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 475 removed outlier: 3.689A pdb=" N MET B 466 " --> pdb=" O PRO B 463 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 505 through 521 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 542 through 554 Proline residue: B 550 - end of helix removed outlier: 4.900A pdb=" N LYS B 554 " --> pdb=" O PRO B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 80 through 98 removed outlier: 3.810A pdb=" N ILE D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 Processing helix chain 'D' and resid 141 through 147 removed outlier: 6.478A pdb=" N ASN D 146 " --> pdb=" O TRP D 142 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 172 Proline residue: D 162 - end of helix removed outlier: 4.385A pdb=" N GLN D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 28 through 44 Processing helix chain 'C' and resid 53 through 74 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 90 through 99 Processing helix chain 'E' and resid 116 through 119 No H-bonds generated for 'chain 'E' and resid 116 through 119' Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 218 through 225 Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 261 through 278 Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 335 through 338 No H-bonds generated for 'chain 'E' and resid 335 through 338' Processing helix chain 'E' and resid 343 through 346 No H-bonds generated for 'chain 'E' and resid 343 through 346' Processing helix chain 'E' and resid 369 through 378 Processing helix chain 'E' and resid 380 through 383 No H-bonds generated for 'chain 'E' and resid 380 through 383' Processing helix chain 'E' and resid 390 through 404 Processing helix chain 'E' and resid 409 through 426 Processing helix chain 'E' and resid 451 through 457 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'E' and resid 483 through 503 Processing helix chain 'E' and resid 535 through 553 Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 58 through 84 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.569A pdb=" N ASP F 119 " --> pdb=" O MET F 116 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP F 120 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 185 Processing helix chain 'F' and resid 201 through 214 Processing helix chain 'F' and resid 225 through 236 removed outlier: 4.728A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 removed outlier: 3.580A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 285 Processing helix chain 'F' and resid 314 through 324 Processing helix chain 'F' and resid 346 through 350 Processing helix chain 'F' and resid 379 through 388 Processing helix chain 'F' and resid 391 through 394 No H-bonds generated for 'chain 'F' and resid 391 through 394' Processing helix chain 'F' and resid 400 through 414 Processing helix chain 'F' and resid 421 through 443 removed outlier: 3.550A pdb=" N ALA F 430 " --> pdb=" O LEU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 475 removed outlier: 3.689A pdb=" N MET F 466 " --> pdb=" O PRO F 463 " (cutoff:3.500A) Proline residue: F 467 - end of helix Processing helix chain 'F' and resid 505 through 521 Processing helix chain 'F' and resid 529 through 531 No H-bonds generated for 'chain 'F' and resid 529 through 531' Processing helix chain 'F' and resid 542 through 554 Proline residue: F 550 - end of helix removed outlier: 4.900A pdb=" N LYS F 554 " --> pdb=" O PRO F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 558 No H-bonds generated for 'chain 'F' and resid 556 through 558' Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 80 through 98 removed outlier: 3.810A pdb=" N ILE H 85 " --> pdb=" O TRP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 121 Processing helix chain 'H' and resid 141 through 147 removed outlier: 6.478A pdb=" N ASN H 146 " --> pdb=" O TRP H 142 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 172 Proline residue: H 162 - end of helix removed outlier: 4.385A pdb=" N GLN H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR H 172 " --> pdb=" O ILE H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 190 Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'G' and resid 53 through 74 Processing sheet with id= A, first strand: chain 'A' and resid 207 through 211 removed outlier: 4.009A pdb=" N PHE A 364 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 231 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL A 289 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 233 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N GLU A 291 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR A 252 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA A 234 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR A 254 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 444 through 447 removed outlier: 4.099A pdb=" N LEU A 447 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 132 through 137 removed outlier: 7.183A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG A 137 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS A 143 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 133 through 137 Processing sheet with id= E, first strand: chain 'B' and resid 139 through 142 removed outlier: 3.699A pdb=" N TYR B 147 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.638A pdb=" N GLY B 373 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 242 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS B 300 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 244 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLU B 302 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ASP B 246 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 263 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER B 245 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 265 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 455 through 459 removed outlier: 3.685A pdb=" N ARG B 494 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 481 " --> pdb=" O ARG B 496 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 207 through 211 removed outlier: 4.009A pdb=" N PHE E 364 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL E 231 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL E 289 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL E 233 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N GLU E 291 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR E 252 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA E 234 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR E 254 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 444 through 447 removed outlier: 4.099A pdb=" N LEU E 447 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 132 through 137 removed outlier: 7.183A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG E 137 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS E 143 " --> pdb=" O ARG E 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= L, first strand: chain 'F' and resid 139 through 142 removed outlier: 3.698A pdb=" N TYR F 147 " --> pdb=" O HIS F 142 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 218 through 222 removed outlier: 3.638A pdb=" N GLY F 373 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU F 242 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS F 300 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 244 " --> pdb=" O CYS F 300 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLU F 302 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ASP F 246 " --> pdb=" O GLU F 302 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA F 263 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER F 245 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG F 265 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.685A pdb=" N ARG F 494 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL F 481 " --> pdb=" O ARG F 496 " (cutoff:3.500A) 836 hydrogen bonds defined for protein. 2418 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: 6.09 Time building geometry restraints manager: 8.77 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: 6422 1.34 - 1.46: 3882 1.46 - 1.58: 10158 1.58 - 1.69: 2 1.69 - 1.81: 174 Bond restraints: 20638 Sorted by residual: bond pdb=" C14 Z1T D 301 " pdb=" C15 Z1T D 301 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" C14 Z1T H 301 " pdb=" C15 Z1T H 301 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" C13 Z1T H 301 " pdb=" C14 Z1T H 301 " ideal model delta sigma weight residual 1.494 1.529 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C13 Z1T D 301 " pdb=" C14 Z1T D 301 " ideal model delta sigma weight residual 1.494 1.529 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.10e-02 8.26e+03 2.95e+00 ... (remaining 20633 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.93: 490 105.93 - 112.95: 11074 112.95 - 119.97: 7097 119.97 - 126.99: 9092 126.99 - 134.00: 217 Bond angle restraints: 27970 Sorted by residual: angle pdb=" N ASN E 257 " pdb=" CA ASN E 257 " pdb=" C ASN E 257 " ideal model delta sigma weight residual 112.57 126.71 -14.14 1.13e+00 7.83e-01 1.57e+02 angle pdb=" N ASN A 257 " pdb=" CA ASN A 257 " pdb=" C ASN A 257 " ideal model delta sigma weight residual 112.57 126.68 -14.11 1.13e+00 7.83e-01 1.56e+02 angle pdb=" N GLY H 133 " pdb=" CA GLY H 133 " pdb=" C GLY H 133 " ideal model delta sigma weight residual 112.50 106.19 6.31 1.16e+00 7.43e-01 2.96e+01 angle pdb=" N GLY D 133 " pdb=" CA GLY D 133 " pdb=" C GLY D 133 " ideal model delta sigma weight residual 112.50 106.23 6.27 1.16e+00 7.43e-01 2.92e+01 angle pdb=" N LYS A 79 " pdb=" CA LYS A 79 " pdb=" C LYS A 79 " ideal model delta sigma weight residual 113.38 119.93 -6.55 1.23e+00 6.61e-01 2.83e+01 ... (remaining 27965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 11524 21.03 - 42.06: 776 42.06 - 63.10: 96 63.10 - 84.13: 18 84.13 - 105.16: 6 Dihedral angle restraints: 12420 sinusoidal: 5020 harmonic: 7400 Sorted by residual: dihedral pdb=" CA SER F 306 " pdb=" C SER F 306 " pdb=" N MET F 307 " pdb=" CA MET F 307 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA SER B 306 " pdb=" C SER B 306 " pdb=" N MET B 307 " pdb=" CA MET B 307 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PRO F 19 " pdb=" C PRO F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 12417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3074 0.103 - 0.206: 90 0.206 - 0.309: 4 0.309 - 0.412: 0 0.412 - 0.516: 2 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CA ASN E 257 " pdb=" N ASN E 257 " pdb=" C ASN E 257 " pdb=" CB ASN E 257 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA ASN A 257 " pdb=" N ASN A 257 " pdb=" C ASN A 257 " pdb=" CB ASN A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA LYS A 79 " pdb=" N LYS A 79 " pdb=" C LYS A 79 " pdb=" CB LYS A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3167 not shown) Planarity restraints: 3548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 256 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE A 256 " -0.057 2.00e-02 2.50e+03 pdb=" O PHE A 256 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 257 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 256 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE E 256 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE E 256 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN E 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 82 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO E 83 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " -0.037 5.00e-02 4.00e+02 ... (remaining 3545 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 260 2.66 - 3.22: 18432 3.22 - 3.78: 28929 3.78 - 4.34: 40682 4.34 - 4.90: 70174 Nonbonded interactions: 158477 Sorted by model distance: nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 80 " model vdw 2.098 2.440 nonbonded pdb=" O LYS A 79 " pdb=" OG SER A 80 " model vdw 2.098 2.440 nonbonded pdb=" OH TYR E 460 " pdb=" OE1 GLU E 488 " model vdw 2.114 2.440 nonbonded pdb=" OH TYR A 460 " pdb=" OE1 GLU A 488 " model vdw 2.114 2.440 nonbonded pdb=" OG SER A 417 " pdb=" O SER A 442 " model vdw 2.158 2.440 ... (remaining 158472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.290 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 54.980 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.004 0.199 20638 Z= 0.270 Angle : 0.720 14.137 27970 Z= 0.414 Chirality : 0.047 0.516 3170 Planarity : 0.005 0.068 3548 Dihedral : 13.959 105.161 7656 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.56 % Favored : 94.12 % Rotamer: Outliers : 0.27 % Allowed : 0.94 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2516 helix: 1.50 (0.15), residues: 1212 sheet: -0.41 (0.35), residues: 224 loop : -1.94 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 294 HIS 0.008 0.001 HIS F 78 PHE 0.019 0.001 PHE G 62 TYR 0.015 0.001 TYR F 510 ARG 0.003 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 2.352 Fit side-chains REVERT: B 119 ASP cc_start: 0.7841 (t70) cc_final: 0.7267 (t0) REVERT: B 158 MET cc_start: 0.8765 (ttp) cc_final: 0.8457 (ttm) REVERT: D 143 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8322 (mt-10) REVERT: F 119 ASP cc_start: 0.7807 (t70) cc_final: 0.7232 (t0) REVERT: F 158 MET cc_start: 0.8750 (ttp) cc_final: 0.8443 (ttm) REVERT: H 143 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8312 (mt-10) outliers start: 6 outliers final: 0 residues processed: 257 average time/residue: 0.2920 time to fit residues: 118.8315 Evaluate side-chains 206 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS B 90 HIS B 96 HIS B 145 ASN D 62 ASN D 110 ASN E 421 HIS F 90 HIS F 96 HIS F 145 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20638 Z= 0.329 Angle : 0.642 12.314 27970 Z= 0.329 Chirality : 0.045 0.174 3170 Planarity : 0.005 0.060 3548 Dihedral : 7.668 98.168 2846 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.44 % Favored : 93.40 % Rotamer: Outliers : 1.30 % Allowed : 7.80 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2516 helix: 1.50 (0.15), residues: 1208 sheet: -0.18 (0.34), residues: 240 loop : -2.00 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 294 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE A 256 TYR 0.020 0.002 TYR B 510 ARG 0.003 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 2.428 Fit side-chains REVERT: B 119 ASP cc_start: 0.7879 (t70) cc_final: 0.7289 (t0) REVERT: D 111 MET cc_start: 0.7371 (mmt) cc_final: 0.7061 (mmt) REVERT: D 189 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7775 (mp) REVERT: F 119 ASP cc_start: 0.7873 (t70) cc_final: 0.7279 (t0) REVERT: H 111 MET cc_start: 0.7396 (mmt) cc_final: 0.7040 (mmt) outliers start: 29 outliers final: 17 residues processed: 226 average time/residue: 0.2973 time to fit residues: 106.8389 Evaluate side-chains 219 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 388 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain G residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 0.0970 chunk 243 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN D 62 ASN H 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20638 Z= 0.134 Angle : 0.513 10.158 27970 Z= 0.262 Chirality : 0.041 0.200 3170 Planarity : 0.004 0.054 3548 Dihedral : 7.247 98.499 2846 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 0.99 % Allowed : 9.99 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2516 helix: 1.79 (0.15), residues: 1208 sheet: -0.24 (0.32), residues: 274 loop : -1.72 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 294 HIS 0.002 0.001 HIS B 76 PHE 0.013 0.001 PHE E 256 TYR 0.013 0.001 TYR F 510 ARG 0.002 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 2.369 Fit side-chains REVERT: A 477 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: B 119 ASP cc_start: 0.7784 (t70) cc_final: 0.7220 (t0) REVERT: B 158 MET cc_start: 0.8725 (ttp) cc_final: 0.8215 (ttm) REVERT: D 111 MET cc_start: 0.7386 (mmt) cc_final: 0.7060 (mmt) REVERT: C 51 MET cc_start: 0.8864 (mtt) cc_final: 0.8639 (mtt) REVERT: E 477 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: F 119 ASP cc_start: 0.7777 (t70) cc_final: 0.7199 (t0) REVERT: F 158 MET cc_start: 0.8729 (ttp) cc_final: 0.8222 (ttm) REVERT: H 111 MET cc_start: 0.7410 (mmt) cc_final: 0.7117 (mmt) REVERT: G 51 MET cc_start: 0.8861 (mtt) cc_final: 0.8617 (mtt) outliers start: 22 outliers final: 11 residues processed: 254 average time/residue: 0.2969 time to fit residues: 118.5797 Evaluate side-chains 224 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.7243 > 50: distance: 49 - 51: 4.796 distance: 51 - 52: 18.100 distance: 52 - 53: 9.796 distance: 52 - 55: 7.620 distance: 53 - 54: 15.071 distance: 53 - 59: 9.424 distance: 55 - 56: 6.196 distance: 56 - 57: 8.060 distance: 56 - 58: 14.071 distance: 59 - 60: 18.555 distance: 60 - 61: 19.844 distance: 60 - 63: 5.224 distance: 61 - 62: 27.782 distance: 61 - 67: 14.124 distance: 63 - 64: 5.228 distance: 64 - 65: 18.016 distance: 64 - 66: 23.351 distance: 67 - 68: 15.180 distance: 68 - 69: 14.803 distance: 68 - 71: 10.868 distance: 69 - 70: 13.143 distance: 69 - 72: 12.906 distance: 72 - 73: 13.155 distance: 72 - 78: 25.007 distance: 73 - 74: 28.213 distance: 73 - 76: 18.783 distance: 74 - 75: 25.966 distance: 74 - 79: 20.477 distance: 76 - 77: 16.506 distance: 77 - 78: 4.017 distance: 79 - 80: 10.406 distance: 80 - 81: 6.656 distance: 80 - 83: 9.531 distance: 81 - 82: 16.598 distance: 81 - 87: 10.926 distance: 82 - 111: 27.653 distance: 83 - 84: 5.641 distance: 84 - 85: 14.093 distance: 84 - 86: 5.212 distance: 87 - 88: 4.293 distance: 87 - 93: 6.735 distance: 88 - 89: 3.214 distance: 88 - 91: 4.914 distance: 89 - 90: 7.949 distance: 89 - 94: 8.580 distance: 90 - 118: 9.077 distance: 91 - 92: 3.593 distance: 92 - 93: 7.265 distance: 94 - 95: 8.337 distance: 95 - 96: 3.824 distance: 95 - 98: 5.385 distance: 96 - 97: 8.393 distance: 96 - 103: 3.993 distance: 97 - 127: 9.145 distance: 98 - 99: 8.149 distance: 99 - 100: 11.057 distance: 100 - 101: 14.655 distance: 100 - 102: 15.940 distance: 103 - 104: 3.715 distance: 104 - 105: 3.829 distance: 104 - 107: 5.765 distance: 105 - 111: 5.726 distance: 106 - 135: 6.963 distance: 107 - 108: 10.090 distance: 108 - 109: 6.750 distance: 108 - 110: 6.203 distance: 111 - 112: 9.022 distance: 112 - 113: 7.688 distance: 113 - 114: 3.127 distance: 113 - 118: 7.088 distance: 114 - 144: 8.668 distance: 115 - 117: 4.114 distance: 118 - 119: 4.259 distance: 119 - 122: 4.797 distance: 121 - 152: 4.660 distance: 122 - 123: 8.084 distance: 123 - 124: 4.389 distance: 124 - 125: 6.438 distance: 125 - 126: 6.038