Starting phenix.real_space_refine on Fri Mar 15 19:01:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx5_16308/03_2024/8bx5_16308.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx5_16308/03_2024/8bx5_16308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx5_16308/03_2024/8bx5_16308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx5_16308/03_2024/8bx5_16308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx5_16308/03_2024/8bx5_16308.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx5_16308/03_2024/8bx5_16308.pdb" } resolution = 4.2 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= 0.013 sd= 0.122 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 8303 2.51 5 N 2031 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12527 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2487 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "D" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2489 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.55 Number of scatterers: 12527 At special positions: 0 Unit cell: (92.6016, 91.1547, 125.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2118 8.00 N 2031 7.00 C 8303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 16 sheets defined 38.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 219 through 239 removed outlier: 3.530A pdb=" N TYR A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.643A pdb=" N LYS A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.811A pdb=" N MET A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 441 removed outlier: 4.008A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.935A pdb=" N SER B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.826A pdb=" N ARG B 144 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 removed outlier: 4.698A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.829A pdb=" N LYS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.793A pdb=" N MET B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 442 removed outlier: 3.806A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 219 through 238 removed outlier: 4.147A pdb=" N MET C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.784A pdb=" N LYS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 307 Processing helix chain 'C' and resid 416 through 443 removed outlier: 3.832A pdb=" N ILE C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR C 443 " --> pdb=" O MET C 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 219 through 239 removed outlier: 4.542A pdb=" N MET D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Proline residue: D 228 - end of helix Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.593A pdb=" N LYS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 416 through 441 removed outlier: 3.908A pdb=" N ILE D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.021A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 219 through 239 removed outlier: 5.137A pdb=" N MET E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix removed outlier: 3.526A pdb=" N MET E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.537A pdb=" N LYS E 247 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 307 Processing helix chain 'E' and resid 416 through 441 removed outlier: 3.839A pdb=" N ILE E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 137 removed outlier: 6.478A pdb=" N VAL A 59 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 53 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR A 61 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP A 65 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL A 47 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR A 67 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 45 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 69 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU A 43 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.651A pdb=" N GLY A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 194 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 209 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 211 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 137 removed outlier: 6.437A pdb=" N VAL B 59 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 53 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR B 61 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP B 65 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL B 47 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR B 67 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 45 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLU B 69 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU B 43 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 39 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 169 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 41 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.523A pdb=" N VAL B 119 " --> pdb=" O MET B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 137 removed outlier: 7.054A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 39 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL C 41 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 90 Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.754A pdb=" N GLY C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 209 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C 211 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 137 removed outlier: 6.458A pdb=" N ASN D 63 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL D 50 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N TRP D 65 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 48 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR D 67 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR D 46 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLU D 69 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N GLU D 44 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AB4, first strand: chain 'D' and resid 101 through 102 removed outlier: 6.030A pdb=" N TYR D 205 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D 196 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY D 207 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG D 194 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 209 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY D 211 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 180 " --> pdb=" O VAL D 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 137 removed outlier: 6.403A pdb=" N ASN E 63 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL E 50 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TRP E 65 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL E 48 " --> pdb=" O TRP E 65 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR E 67 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR E 46 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU E 69 " --> pdb=" O GLU E 44 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N GLU E 44 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AB7, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.704A pdb=" N GLY E 207 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG E 194 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE E 209 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY E 211 " --> pdb=" O VAL E 190 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1665 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: 3.73 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3345 1.33 - 1.45: 2459 1.45 - 1.58: 6913 1.58 - 1.70: 0 1.70 - 1.82: 131 Bond restraints: 12848 Sorted by residual: bond pdb=" N VAL B 166 " pdb=" CA VAL B 166 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.23e-02 6.61e+03 1.45e+01 bond pdb=" N VAL A 168 " pdb=" CA VAL A 168 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.37e+01 bond pdb=" N VAL D 166 " pdb=" CA VAL D 166 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N VAL C 166 " pdb=" CA VAL C 166 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N VAL E 168 " pdb=" CA VAL E 168 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 ... (remaining 12843 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.99: 287 105.99 - 113.03: 7231 113.03 - 120.07: 4278 120.07 - 127.11: 5665 127.11 - 134.15: 172 Bond angle restraints: 17633 Sorted by residual: angle pdb=" N VAL A 166 " pdb=" CA VAL A 166 " pdb=" CB VAL A 166 " ideal model delta sigma weight residual 112.45 104.38 8.07 1.12e+00 7.97e-01 5.20e+01 angle pdb=" N VAL E 166 " pdb=" CA VAL E 166 " pdb=" CB VAL E 166 " ideal model delta sigma weight residual 111.23 102.20 9.03 1.65e+00 3.67e-01 2.99e+01 angle pdb=" N VAL C 166 " pdb=" CA VAL C 166 " pdb=" CB VAL C 166 " ideal model delta sigma weight residual 112.44 105.48 6.96 1.68e+00 3.54e-01 1.72e+01 angle pdb=" C MET E 265 " pdb=" N MET E 266 " pdb=" CA MET E 266 " ideal model delta sigma weight residual 121.14 114.03 7.11 1.75e+00 3.27e-01 1.65e+01 angle pdb=" CA VAL C 166 " pdb=" CB VAL C 166 " pdb=" CG1 VAL C 166 " ideal model delta sigma weight residual 110.40 117.18 -6.78 1.70e+00 3.46e-01 1.59e+01 ... (remaining 17628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.44: 6906 19.44 - 38.88: 481 38.88 - 58.31: 88 58.31 - 77.75: 12 77.75 - 97.19: 14 Dihedral angle restraints: 7501 sinusoidal: 2656 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS B 138 " pdb=" SG CYS B 138 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 35.53 57.47 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual -86.00 -29.53 -56.47 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" N VAL E 166 " pdb=" C VAL E 166 " pdb=" CA VAL E 166 " pdb=" CB VAL E 166 " ideal model delta harmonic sigma weight residual 123.40 112.50 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2142 0.146 - 0.292: 17 0.292 - 0.438: 3 0.438 - 0.584: 2 0.584 - 0.730: 3 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB VAL C 166 " pdb=" CA VAL C 166 " pdb=" CG1 VAL C 166 " pdb=" CG2 VAL C 166 " both_signs ideal model delta sigma weight residual False -2.63 -1.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 167 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2164 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.330 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG D 501 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 501 " -0.313 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C7 NAG C 501 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 501 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 501 " 0.490 2.00e-02 2.50e+03 pdb=" O7 NAG C 501 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.295 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG E 501 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.440 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " -0.045 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1552 2.75 - 3.29: 13264 3.29 - 3.83: 21602 3.83 - 4.36: 23739 4.36 - 4.90: 39905 Nonbonded interactions: 100062 Sorted by model distance: nonbonded pdb=" OG1 THR E 123 " pdb=" NZ LYS E 125 " model vdw 2.218 2.520 nonbonded pdb=" O ILE C 242 " pdb=" NH1 ARG C 249 " model vdw 2.247 2.520 nonbonded pdb=" O HOH A 601 " pdb=" O HOH B 501 " model vdw 2.257 2.440 nonbonded pdb=" OG SER A 268 " pdb=" OH TYR B 220 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN C 34 " pdb=" OG SER C 36 " model vdw 2.260 2.440 ... (remaining 100057 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 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 126 or (resid 127 and \ (name N or name CA or name C or name O or name CB )) or resid 128 through 304 o \ r (resid 305 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 06 through 422 or (resid 423 through 424 and (name N or name CA or name C or nam \ e O or name CB )) or resid 425 through 443)) selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 126 or (resid 127 and \ (name N or name CA or name C or name O or name CB )) or resid 128 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE )) or resid 271 through 306 or (resid 307 and (name N or nam \ e CA or name C or name O or name CB )) or resid 414 through 422 or (resid 423 th \ rough 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 443)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 126 or (resid 127 and (name N or n \ ame CA or name C or name O or name CB )) or resid 128 through 443)) selection = (chain 'D' and (resid 12 through 422 or (resid 423 through 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 through 443)) selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 126 or (resid 127 and (name N or n \ ame CA or name C or name O or name CB )) or resid 128 through 422 or (resid 423 \ through 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 443)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.940 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.920 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.050 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.003 0.047 12848 Z= 0.231 Angle : 0.784 9.027 17633 Z= 0.409 Chirality : 0.059 0.730 2167 Planarity : 0.012 0.288 2122 Dihedral : 14.220 97.188 4356 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.63 % Allowed : 0.16 % Favored : 99.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.69 % 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: -0.69 (0.21), residues: 1610 helix: 1.11 (0.23), residues: 520 sheet: -0.58 (0.28), residues: 350 loop : -1.55 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 159 HIS 0.004 0.001 HIS E 131 PHE 0.035 0.002 PHE A 289 TYR 0.028 0.002 TYR E 252 ARG 0.004 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 456 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8037 (mtpt) REVERT: A 128 TRP cc_start: 0.7447 (t60) cc_final: 0.6475 (t60) REVERT: A 161 HIS cc_start: 0.7680 (p90) cc_final: 0.7129 (p90) REVERT: A 173 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8101 (tp-100) REVERT: A 234 PHE cc_start: 0.8644 (t80) cc_final: 0.8367 (t80) REVERT: A 241 PHE cc_start: 0.8703 (m-80) cc_final: 0.8112 (m-10) REVERT: A 287 TYR cc_start: 0.8909 (t80) cc_final: 0.8454 (t80) REVERT: A 305 MET cc_start: 0.7784 (ppp) cc_final: 0.6773 (mmt) REVERT: B 29 ILE cc_start: 0.7954 (mt) cc_final: 0.7641 (mm) REVERT: B 85 LEU cc_start: 0.9053 (tp) cc_final: 0.8805 (pp) REVERT: B 127 MET cc_start: 0.6870 (mmt) cc_final: 0.5777 (tpt) REVERT: B 227 MET cc_start: 0.8115 (ttm) cc_final: 0.7109 (tpp) REVERT: B 256 LEU cc_start: 0.9370 (mm) cc_final: 0.9169 (mm) REVERT: B 287 TYR cc_start: 0.8743 (t80) cc_final: 0.8322 (t80) REVERT: B 301 MET cc_start: 0.8903 (mmp) cc_final: 0.8323 (ptm) REVERT: C 62 THR cc_start: 0.9011 (p) cc_final: 0.8791 (p) REVERT: C 151 MET cc_start: 0.7088 (ttp) cc_final: 0.6859 (ttm) REVERT: C 166 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8369 (m) REVERT: C 231 LEU cc_start: 0.8957 (mt) cc_final: 0.8570 (mt) REVERT: C 234 PHE cc_start: 0.9301 (t80) cc_final: 0.8747 (t80) REVERT: C 266 MET cc_start: 0.9012 (ptp) cc_final: 0.8641 (ptm) REVERT: C 269 ASP cc_start: 0.8311 (m-30) cc_final: 0.8049 (m-30) REVERT: C 287 TYR cc_start: 0.8846 (t80) cc_final: 0.8006 (t80) REVERT: C 301 MET cc_start: 0.9088 (mmp) cc_final: 0.8701 (mmm) REVERT: D 103 PHE cc_start: 0.8142 (m-80) cc_final: 0.7678 (m-80) REVERT: D 137 PHE cc_start: 0.8343 (m-10) cc_final: 0.8135 (m-80) REVERT: D 266 MET cc_start: 0.9129 (ptp) cc_final: 0.8761 (ptt) REVERT: D 287 TYR cc_start: 0.9180 (t80) cc_final: 0.8760 (t80) REVERT: D 425 PHE cc_start: 0.8368 (t80) cc_final: 0.7677 (t80) REVERT: D 435 ILE cc_start: 0.8971 (pt) cc_final: 0.8709 (tp) REVERT: E 62 THR cc_start: 0.8838 (p) cc_final: 0.8615 (p) REVERT: E 74 GLN cc_start: 0.8462 (mp10) cc_final: 0.8249 (mp10) REVERT: E 102 LEU cc_start: 0.9159 (tp) cc_final: 0.8550 (tp) REVERT: E 225 PHE cc_start: 0.8512 (m-80) cc_final: 0.8054 (m-80) REVERT: E 235 LEU cc_start: 0.9434 (mt) cc_final: 0.8797 (tp) REVERT: E 238 LEU cc_start: 0.9094 (mp) cc_final: 0.8762 (mp) REVERT: E 291 MET cc_start: 0.9072 (tpp) cc_final: 0.8482 (mmt) REVERT: E 428 PHE cc_start: 0.9458 (m-10) cc_final: 0.9146 (m-10) outliers start: 8 outliers final: 0 residues processed: 464 average time/residue: 0.1890 time to fit residues: 133.5284 Evaluate side-chains 378 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 304 ASN B 196 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12848 Z= 0.230 Angle : 0.668 12.565 17633 Z= 0.328 Chirality : 0.046 0.326 2167 Planarity : 0.004 0.050 2122 Dihedral : 6.758 51.600 1855 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 0.08 % Allowed : 7.38 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.59 (0.21), residues: 1610 helix: 1.36 (0.23), residues: 525 sheet: -0.98 (0.26), residues: 395 loop : -1.37 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 159 HIS 0.004 0.001 HIS D 131 PHE 0.028 0.002 PHE C 428 TYR 0.023 0.001 TYR D 252 ARG 0.004 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8083 (tttm) REVERT: A 173 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8075 (tp-100) REVERT: A 234 PHE cc_start: 0.8744 (t80) cc_final: 0.8419 (t80) REVERT: A 287 TYR cc_start: 0.9024 (t80) cc_final: 0.8496 (t80) REVERT: A 296 LEU cc_start: 0.9085 (mt) cc_final: 0.8786 (mt) REVERT: A 305 MET cc_start: 0.7609 (ppp) cc_final: 0.6740 (mmt) REVERT: A 429 LEU cc_start: 0.9043 (pp) cc_final: 0.8795 (pp) REVERT: B 187 VAL cc_start: 0.9521 (t) cc_final: 0.9179 (t) REVERT: B 256 LEU cc_start: 0.9520 (mm) cc_final: 0.9236 (mm) REVERT: B 266 MET cc_start: 0.9121 (ppp) cc_final: 0.8723 (ppp) REVERT: B 269 ASP cc_start: 0.7906 (m-30) cc_final: 0.7624 (m-30) REVERT: B 287 TYR cc_start: 0.8865 (t80) cc_final: 0.8424 (t80) REVERT: B 301 MET cc_start: 0.8997 (mmp) cc_final: 0.8423 (ptm) REVERT: C 231 LEU cc_start: 0.9006 (mt) cc_final: 0.8709 (mt) REVERT: C 238 LEU cc_start: 0.9032 (mp) cc_final: 0.8819 (mp) REVERT: C 252 TYR cc_start: 0.9111 (t80) cc_final: 0.8884 (t80) REVERT: C 266 MET cc_start: 0.9224 (ptp) cc_final: 0.8901 (ptm) REVERT: C 269 ASP cc_start: 0.8413 (m-30) cc_final: 0.8133 (m-30) REVERT: C 287 TYR cc_start: 0.8987 (t80) cc_final: 0.8447 (t80) REVERT: C 435 ILE cc_start: 0.8952 (pt) cc_final: 0.8674 (tp) REVERT: D 103 PHE cc_start: 0.8324 (m-80) cc_final: 0.7709 (m-80) REVERT: D 184 GLU cc_start: 0.8915 (pm20) cc_final: 0.8622 (pm20) REVERT: D 266 MET cc_start: 0.9248 (ptp) cc_final: 0.8905 (ptt) REVERT: D 287 TYR cc_start: 0.9243 (t80) cc_final: 0.8691 (t80) REVERT: D 295 ASN cc_start: 0.9121 (p0) cc_final: 0.8868 (p0) REVERT: D 425 PHE cc_start: 0.8332 (t80) cc_final: 0.7996 (t80) REVERT: E 62 THR cc_start: 0.8830 (p) cc_final: 0.8540 (p) REVERT: E 74 GLN cc_start: 0.8457 (mp10) cc_final: 0.8199 (mp10) REVERT: E 100 ILE cc_start: 0.9430 (mt) cc_final: 0.9213 (tp) REVERT: E 225 PHE cc_start: 0.8572 (m-80) cc_final: 0.8129 (m-80) REVERT: E 234 PHE cc_start: 0.8563 (t80) cc_final: 0.8300 (t80) REVERT: E 235 LEU cc_start: 0.9324 (mt) cc_final: 0.9092 (mt) REVERT: E 238 LEU cc_start: 0.8910 (mp) cc_final: 0.8552 (mp) REVERT: E 268 SER cc_start: 0.9149 (p) cc_final: 0.8890 (p) REVERT: E 287 TYR cc_start: 0.8921 (t80) cc_final: 0.8632 (t80) REVERT: E 301 MET cc_start: 0.7957 (mmm) cc_final: 0.7418 (mmm) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.1845 time to fit residues: 118.1257 Evaluate side-chains 380 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2756 > 50: distance: 5 - 10: 27.905 distance: 10 - 11: 22.131 distance: 11 - 12: 36.491 distance: 11 - 14: 45.529 distance: 12 - 13: 26.257 distance: 12 - 15: 37.296 distance: 15 - 16: 7.656 distance: 16 - 17: 33.412 distance: 16 - 19: 25.731 distance: 17 - 18: 35.234 distance: 17 - 23: 12.079 distance: 18 - 40: 42.652 distance: 19 - 20: 16.384 distance: 20 - 21: 31.499 distance: 20 - 22: 43.714 distance: 23 - 24: 33.055 distance: 24 - 25: 48.109 distance: 24 - 27: 37.837 distance: 25 - 26: 27.269 distance: 25 - 29: 50.486 distance: 27 - 28: 23.644 distance: 30 - 31: 26.364 distance: 30 - 33: 7.257 distance: 31 - 32: 17.679 distance: 31 - 40: 17.048 distance: 33 - 34: 22.451 distance: 34 - 35: 40.931 distance: 35 - 36: 18.176 distance: 36 - 37: 11.840 distance: 37 - 38: 13.223 distance: 37 - 39: 12.820 distance: 40 - 41: 36.094 distance: 41 - 42: 21.232 distance: 41 - 44: 19.562 distance: 42 - 43: 17.495 distance: 42 - 51: 35.137 distance: 44 - 45: 15.256 distance: 45 - 46: 12.173 distance: 45 - 47: 9.246 distance: 46 - 48: 21.774 distance: 47 - 49: 25.475 distance: 48 - 50: 15.058 distance: 49 - 50: 18.379 distance: 51 - 52: 10.896 distance: 51 - 57: 50.525 distance: 52 - 53: 29.900 distance: 52 - 55: 36.944 distance: 53 - 54: 14.011 distance: 53 - 58: 41.094 distance: 55 - 56: 23.787 distance: 56 - 57: 39.603 distance: 58 - 59: 18.565 distance: 59 - 60: 13.728 distance: 59 - 62: 43.109 distance: 60 - 61: 34.921 distance: 60 - 69: 48.763 distance: 62 - 63: 27.916 distance: 63 - 64: 8.411 distance: 63 - 65: 11.010 distance: 64 - 66: 15.217 distance: 65 - 67: 11.678 distance: 66 - 68: 14.967 distance: 67 - 68: 17.075 distance: 69 - 70: 10.844 distance: 70 - 71: 55.903 distance: 70 - 73: 26.717 distance: 71 - 72: 39.703 distance: 71 - 77: 47.313 distance: 73 - 74: 15.980 distance: 74 - 75: 45.140 distance: 74 - 76: 25.846 distance: 77 - 78: 26.523 distance: 78 - 79: 27.962 distance: 78 - 81: 35.076 distance: 79 - 80: 28.027 distance: 79 - 83: 47.688 distance: 81 - 82: 11.832 distance: 83 - 84: 42.872 distance: 84 - 85: 25.999 distance: 84 - 87: 12.878 distance: 85 - 86: 34.183 distance: 85 - 88: 7.856 distance: 94 - 100: 3.002