Starting phenix.real_space_refine on Sat Mar 16 11:09:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbi_27285/03_2024/8dbi_27285_updated.pdb" } resolution = 2.0 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= 0.333 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8982 2.51 5 N 2520 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E GLU 298": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14496 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 318 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 306 not shown) Time building chain proxies: 7.06, per 1000 atoms: 0.49 Number of scatterers: 14496 At special positions: 0 Unit cell: (122.396, 128.185, 76.911, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 30 15.00 Mg 12 11.99 O 2850 8.00 N 2520 7.00 C 8982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.76 Conformation dependent library (CDL) restraints added in 2.9 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 24 sheets defined 36.6% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.552A pdb=" N ALA C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA D 175 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.690A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 310 through 313 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 172 through 185 removed outlier: 3.552A pdb=" N ALA F 175 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 310 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG A 243 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 218 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR A 245 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP A 220 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 247 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 268 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A 248 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 270 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 191 through 194 Processing sheet with id= E, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= G, first strand: chain 'B' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG B 243 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 218 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR B 245 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP B 220 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 247 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA B 268 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 248 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 270 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 191 through 194 Processing sheet with id= I, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.262A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= K, first strand: chain 'C' and resid 166 through 169 removed outlier: 6.354A pdb=" N ARG C 243 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU C 218 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 245 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP C 220 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 247 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 268 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU C 248 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 270 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 191 through 194 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.260A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'D' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG D 243 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU D 218 " --> pdb=" O ARG D 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR D 245 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP D 220 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 247 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA D 268 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU D 248 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 270 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 191 through 194 Processing sheet with id= Q, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= S, first strand: chain 'E' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG E 243 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU E 218 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR E 245 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP E 220 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE E 247 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA E 268 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU E 248 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL E 270 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 191 through 194 Processing sheet with id= U, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= W, first strand: chain 'F' and resid 166 through 169 removed outlier: 6.354A pdb=" N ARG F 243 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU F 218 " --> pdb=" O ARG F 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR F 245 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP F 220 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE F 247 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA F 268 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU F 248 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL F 270 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 191 through 194 504 hydrogen bonds defined for protein. 1242 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: 4.84 Time building geometry restraints manager: 7.19 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: 4818 1.34 - 1.46: 1911 1.46 - 1.57: 7773 1.57 - 1.69: 36 1.69 - 1.81: 150 Bond restraints: 14688 Sorted by residual: bond pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP B 401 " pdb=" C4' ATP B 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP E 401 " pdb=" C4' ATP E 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP D 401 " pdb=" C4' ATP D 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ATP A 401 " pdb=" C4' ATP A 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.26e+02 ... (remaining 14683 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.89: 336 105.89 - 112.92: 8417 112.92 - 119.96: 4761 119.96 - 126.99: 6228 126.99 - 134.02: 184 Bond angle restraints: 19926 Sorted by residual: angle pdb=" C1' ATP B 401 " pdb=" N9 ATP B 401 " pdb=" C8 ATP B 401 " ideal model delta sigma weight residual 92.72 126.87 -34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C1' ATP D 401 " pdb=" N9 ATP D 401 " pdb=" C8 ATP D 401 " ideal model delta sigma weight residual 92.72 126.86 -34.14 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C1' ATP A 401 " pdb=" N9 ATP A 401 " pdb=" C8 ATP A 401 " ideal model delta sigma weight residual 92.72 126.85 -34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP F 401 " pdb=" N9 ATP F 401 " pdb=" C8 ATP F 401 " ideal model delta sigma weight residual 92.72 126.85 -34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP E 401 " pdb=" N9 ATP E 401 " pdb=" C8 ATP E 401 " ideal model delta sigma weight residual 92.72 126.84 -34.12 3.00e+00 1.11e-01 1.29e+02 ... (remaining 19921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.89: 8412 26.89 - 53.79: 465 53.79 - 80.68: 81 80.68 - 107.57: 12 107.57 - 134.46: 18 Dihedral angle restraints: 8988 sinusoidal: 3612 harmonic: 5376 Sorted by residual: dihedral pdb=" CA ASP B 101 " pdb=" C ASP B 101 " pdb=" N LYS B 102 " pdb=" CA LYS B 102 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP A 101 " pdb=" C ASP A 101 " pdb=" N LYS A 102 " pdb=" CA LYS A 102 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP D 101 " pdb=" C ASP D 101 " pdb=" N LYS D 102 " pdb=" CA LYS D 102 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 8985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1433 0.048 - 0.096: 647 0.096 - 0.144: 195 0.144 - 0.192: 23 0.192 - 0.240: 12 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CG LEU C 248 " pdb=" CB LEU C 248 " pdb=" CD1 LEU C 248 " pdb=" CD2 LEU C 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU F 248 " pdb=" CB LEU F 248 " pdb=" CD1 LEU F 248 " pdb=" CD2 LEU F 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU E 248 " pdb=" CB LEU E 248 " pdb=" CD1 LEU E 248 " pdb=" CD2 LEU E 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2307 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX D 402 " -0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX D 402 " -0.852 2.00e-02 2.50e+03 pdb=" C3 HSX D 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4 HSX D 402 " 0.320 2.00e-02 2.50e+03 pdb=" C5 HSX D 402 " -0.562 2.00e-02 2.50e+03 pdb=" O1 HSX D 402 " 0.781 2.00e-02 2.50e+03 pdb=" O2 HSX D 402 " -0.858 2.00e-02 2.50e+03 pdb=" O3 HSX D 402 " 1.241 2.00e-02 2.50e+03 pdb=" O4 HSX D 402 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX A 402 " -0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX A 402 " -0.851 2.00e-02 2.50e+03 pdb=" C3 HSX A 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4 HSX A 402 " 0.320 2.00e-02 2.50e+03 pdb=" C5 HSX A 402 " -0.562 2.00e-02 2.50e+03 pdb=" O1 HSX A 402 " 0.780 2.00e-02 2.50e+03 pdb=" O2 HSX A 402 " -0.858 2.00e-02 2.50e+03 pdb=" O3 HSX A 402 " 1.242 2.00e-02 2.50e+03 pdb=" O4 HSX A 402 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX E 402 " 0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX E 402 " 0.852 2.00e-02 2.50e+03 pdb=" C3 HSX E 402 " -0.038 2.00e-02 2.50e+03 pdb=" C4 HSX E 402 " -0.320 2.00e-02 2.50e+03 pdb=" C5 HSX E 402 " 0.562 2.00e-02 2.50e+03 pdb=" O1 HSX E 402 " -0.781 2.00e-02 2.50e+03 pdb=" O2 HSX E 402 " 0.858 2.00e-02 2.50e+03 pdb=" O3 HSX E 402 " -1.241 2.00e-02 2.50e+03 pdb=" O4 HSX E 402 " -0.165 2.00e-02 2.50e+03 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 105 2.51 - 3.11: 10915 3.11 - 3.70: 23599 3.70 - 4.30: 34470 4.30 - 4.90: 55799 Nonbonded interactions: 124888 Sorted by model distance: nonbonded pdb=" CE MET A 68 " pdb=" CE MET F 68 " model vdw 1.910 3.880 nonbonded pdb=" CE MET B 68 " pdb=" CE MET C 68 " model vdw 1.911 3.880 nonbonded pdb=" CE MET D 68 " pdb=" CE MET E 68 " model vdw 1.912 3.880 nonbonded pdb="MG MG D 404 " pdb=" O HOH D 502 " model vdw 1.949 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 502 " model vdw 1.949 2.170 ... (remaining 124883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.01 max=1.00 mean=0.91 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: 2.890 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: 7.570 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.600 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.012 0.225 14688 Z= 0.824 Angle : 1.174 34.147 19926 Z= 0.524 Chirality : 0.057 0.240 2310 Planarity : 0.042 0.678 2514 Dihedral : 18.164 134.464 5484 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.15 % Allowed : 11.83 % Favored : 87.02 % 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: 0.57 (0.20), residues: 1830 helix: 1.71 (0.20), residues: 732 sheet: -0.63 (0.23), residues: 498 loop : -0.22 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP E 162 HIS 0.005 0.002 HIS C 231 PHE 0.018 0.002 PHE D 189 TYR 0.021 0.003 TYR E 146 ARG 0.010 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 1.527 Fit side-chains REVERT: A 294 MET cc_start: 0.8756 (pmm) cc_final: 0.8474 (pmm) REVERT: C 127 MET cc_start: 0.8873 (ttm) cc_final: 0.8361 (ttm) REVERT: D 127 MET cc_start: 0.8874 (ttm) cc_final: 0.8363 (ttm) REVERT: F 294 MET cc_start: 0.8757 (pmm) cc_final: 0.8481 (pmm) outliers start: 18 outliers final: 8 residues processed: 288 average time/residue: 1.5097 time to fit residues: 472.3129 Evaluate side-chains 255 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 13 GLN B 38 GLN B 288 GLN C 17 GLN C 38 GLN D 17 GLN D 38 GLN D 288 GLN E 13 GLN E 38 GLN E 288 GLN F 13 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14688 Z= 0.195 Angle : 1.631 46.306 19926 Z= 0.593 Chirality : 0.048 0.173 2310 Planarity : 0.004 0.023 2514 Dihedral : 16.233 114.321 2138 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.23 % Allowed : 11.07 % Favored : 86.70 % 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: 0.80 (0.21), residues: 1830 helix: 1.88 (0.21), residues: 732 sheet: -0.41 (0.24), residues: 498 loop : -0.18 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 162 HIS 0.003 0.001 HIS B 193 PHE 0.014 0.001 PHE C 189 TYR 0.010 0.002 TYR F 146 ARG 0.005 0.001 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 266 time to evaluate : 1.797 Fit side-chains REVERT: C 127 MET cc_start: 0.8780 (ttm) cc_final: 0.8347 (ttm) REVERT: D 127 MET cc_start: 0.8779 (ttm) cc_final: 0.8346 (ttm) outliers start: 35 outliers final: 11 residues processed: 289 average time/residue: 1.4724 time to fit residues: 462.1703 Evaluate side-chains 263 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 252 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN C 38 GLN D 38 GLN E 38 GLN F 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14688 Z= 0.236 Angle : 1.650 46.842 19926 Z= 0.604 Chirality : 0.050 0.176 2310 Planarity : 0.004 0.027 2514 Dihedral : 14.727 105.653 2130 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.16 % Allowed : 10.69 % Favored : 87.15 % 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: 0.67 (0.20), residues: 1830 helix: 1.69 (0.21), residues: 732 sheet: -0.38 (0.24), residues: 498 loop : -0.22 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.004 0.001 HIS A 193 PHE 0.013 0.002 PHE A 189 TYR 0.010 0.002 TYR A 146 ARG 0.007 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 262 time to evaluate : 1.731 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 284 average time/residue: 1.4233 time to fit residues: 439.3973 Evaluate side-chains 278 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 258 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN C 38 GLN D 38 GLN F 262 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.003 0.040 14688 Z= 0.198 Angle : 1.626 47.058 19926 Z= 0.588 Chirality : 0.049 0.173 2310 Planarity : 0.003 0.027 2514 Dihedral : 12.729 86.865 2130 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.42 % Allowed : 10.88 % Favored : 86.70 % 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: 0.73 (0.20), residues: 1830 helix: 1.75 (0.21), residues: 732 sheet: -0.33 (0.24), residues: 498 loop : -0.22 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 162 HIS 0.003 0.001 HIS E 193 PHE 0.013 0.001 PHE F 189 TYR 0.009 0.001 TYR A 146 ARG 0.007 0.001 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 253 time to evaluate : 1.796 Fit side-chains REVERT: A 191 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6641 (mt) REVERT: D 205 MET cc_start: 0.6343 (mmm) cc_final: 0.6018 (mmm) REVERT: F 191 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6629 (mt) outliers start: 38 outliers final: 26 residues processed: 275 average time/residue: 1.4554 time to fit residues: 434.9591 Evaluate side-chains 277 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 262 ASN B 38 GLN B 288 GLN C 38 GLN D 38 GLN E 38 GLN E 288 GLN F 262 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14688 Z= 0.250 Angle : 1.653 46.764 19926 Z= 0.604 Chirality : 0.051 0.186 2310 Planarity : 0.004 0.023 2514 Dihedral : 12.493 89.846 2130 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.67 % Allowed : 10.43 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1830 helix: 1.58 (0.21), residues: 738 sheet: -0.35 (0.24), residues: 498 loop : -0.17 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 162 HIS 0.004 0.001 HIS C 130 PHE 0.012 0.001 PHE C 189 TYR 0.014 0.002 TYR A 146 ARG 0.007 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 262 time to evaluate : 1.726 Fit side-chains REVERT: D 205 MET cc_start: 0.6339 (mmm) cc_final: 0.5992 (mmm) outliers start: 42 outliers final: 22 residues processed: 288 average time/residue: 1.3775 time to fit residues: 431.9981 Evaluate side-chains 280 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 258 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 54.6969 > 50: distance: 23 - 126: 16.604 distance: 26 - 135: 8.725 distance: 37 - 138: 19.259 distance: 53 - 72: 24.548 distance: 56 - 69: 15.563 distance: 63 - 69: 17.561 distance: 69 - 70: 16.269 distance: 70 - 71: 24.143 distance: 70 - 73: 10.255 distance: 71 - 72: 13.164 distance: 71 - 76: 18.800 distance: 73 - 74: 26.486 distance: 73 - 75: 32.010 distance: 76 - 77: 29.593 distance: 77 - 78: 13.025 distance: 78 - 79: 12.215 distance: 78 - 80: 16.744 distance: 80 - 81: 16.011 distance: 81 - 82: 19.432 distance: 81 - 84: 14.434 distance: 82 - 83: 18.915 distance: 82 - 88: 16.538 distance: 84 - 85: 28.196 distance: 85 - 86: 15.564 distance: 85 - 87: 8.470 distance: 88 - 89: 11.611 distance: 89 - 90: 36.713 distance: 89 - 92: 16.625 distance: 90 - 91: 27.357 distance: 90 - 95: 20.933 distance: 92 - 93: 24.581 distance: 92 - 94: 21.909 distance: 95 - 96: 25.162 distance: 96 - 97: 11.014 distance: 96 - 99: 19.419 distance: 97 - 98: 20.590 distance: 97 - 104: 5.328 distance: 99 - 100: 20.457 distance: 100 - 101: 11.640 distance: 101 - 102: 7.721 distance: 102 - 103: 20.473 distance: 104 - 105: 8.177 distance: 105 - 106: 9.142 distance: 105 - 108: 18.329 distance: 106 - 107: 16.391 distance: 106 - 112: 24.438 distance: 108 - 109: 25.168 distance: 109 - 110: 27.682 distance: 109 - 111: 18.911 distance: 112 - 113: 10.941 distance: 113 - 114: 15.201 distance: 113 - 116: 13.926 distance: 114 - 115: 22.619 distance: 114 - 123: 18.303 distance: 116 - 117: 18.522 distance: 117 - 118: 14.302 distance: 118 - 119: 9.926 distance: 120 - 121: 3.231 distance: 120 - 122: 3.251 distance: 123 - 124: 16.389 distance: 124 - 125: 4.892 distance: 124 - 127: 4.276 distance: 125 - 126: 16.582 distance: 125 - 130: 5.599 distance: 127 - 128: 23.661 distance: 127 - 129: 19.355 distance: 130 - 131: 14.173 distance: 131 - 132: 17.391 distance: 131 - 134: 6.980 distance: 132 - 133: 26.736 distance: 132 - 135: 10.203 distance: 135 - 136: 7.961 distance: 136 - 137: 13.025 distance: 136 - 139: 15.911 distance: 137 - 138: 20.508 distance: 137 - 143: 11.066 distance: 139 - 140: 19.631 distance: 139 - 141: 33.871 distance: 140 - 142: 16.409