Starting phenix.real_space_refine on Sun Mar 17 06:49:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/03_2024/5bkj_9406_updated.pdb" } resolution = 3.5 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= 0.004 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 K 2 8.98 5 P 4 5.49 5 S 68 5.16 5 C 10692 2.51 5 N 2897 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ASP 309": "OD1" <-> "OD2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F ASP 309": "OD1" <-> "OD2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 184": "OD1" <-> "OD2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H ASP 226": "OD1" <-> "OD2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "H GLU 266": "OE1" <-> "OE2" Residue "H ASP 309": "OD1" <-> "OD2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ASP 284": "OD1" <-> "OD2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E ASP 284": "OD1" <-> "OD2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 145": "OD1" <-> "OD2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ASP 226": "OD1" <-> "OD2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G ASP 284": "OD1" <-> "OD2" Residue "G PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16939 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "C" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' K': 2, 'PGW': 1, 'YQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.08, per 1000 atoms: 0.54 Number of scatterers: 16939 At special positions: 0 Unit cell: (150.7, 150.7, 117.7, 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) K 2 19.00 S 68 16.00 P 4 15.00 O 3276 8.00 N 2897 7.00 C 10692 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: 6.33 Conformation dependent library (CDL) restraints added in 3.0 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 16 sheets defined 40.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 22 through 42 removed outlier: 3.600A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 70 through 104 removed outlier: 3.758A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 128 No H-bonds generated for 'chain 'A' and resid 125 through 128' Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 167 through 170 No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.662A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.633A pdb=" N ILE A 217 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU A 218 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 223 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.505A pdb=" N TYR A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 4.081A pdb=" N ARG B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.736A pdb=" N LYS B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 223 removed outlier: 4.554A pdb=" N GLU B 218 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 219 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 223 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 285 through 288 No H-bonds generated for 'chain 'B' and resid 285 through 288' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.771A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 removed outlier: 4.081A pdb=" N ARG D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.737A pdb=" N LYS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 223 removed outlier: 4.554A pdb=" N GLU D 218 " --> pdb=" O GLU D 215 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D 219 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 220 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 223 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 285 through 288 No H-bonds generated for 'chain 'D' and resid 285 through 288' Processing helix chain 'D' and resid 324 through 333 removed outlier: 3.771A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 4.080A pdb=" N ARG F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 167 through 170 No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 188 through 201 removed outlier: 3.737A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 223 removed outlier: 4.554A pdb=" N GLU F 218 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN F 219 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 220 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 223 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 248 through 255 Processing helix chain 'F' and resid 285 through 288 No H-bonds generated for 'chain 'F' and resid 285 through 288' Processing helix chain 'F' and resid 324 through 333 removed outlier: 3.770A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 133 removed outlier: 4.080A pdb=" N ARG H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 155 Processing helix chain 'H' and resid 167 through 170 No H-bonds generated for 'chain 'H' and resid 167 through 170' Processing helix chain 'H' and resid 188 through 201 removed outlier: 3.737A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 223 removed outlier: 4.554A pdb=" N GLU H 218 " --> pdb=" O GLU H 215 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN H 219 " --> pdb=" O ASN H 216 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU H 220 " --> pdb=" O ILE H 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 223 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 239 Processing helix chain 'H' and resid 248 through 255 Processing helix chain 'H' and resid 285 through 288 No H-bonds generated for 'chain 'H' and resid 285 through 288' Processing helix chain 'H' and resid 324 through 333 removed outlier: 3.771A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 42 removed outlier: 3.600A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 70 through 104 removed outlier: 3.759A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 128 No H-bonds generated for 'chain 'C' and resid 125 through 128' Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 167 through 170 No H-bonds generated for 'chain 'C' and resid 167 through 170' Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.662A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 removed outlier: 3.633A pdb=" N ILE C 217 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU C 218 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 223 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 285 through 288 No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.505A pdb=" N TYR C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 42 removed outlier: 3.600A pdb=" N PHE E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 70 through 104 removed outlier: 3.759A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 128 No H-bonds generated for 'chain 'E' and resid 125 through 128' Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 167 through 170 No H-bonds generated for 'chain 'E' and resid 167 through 170' Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.662A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 223 removed outlier: 3.633A pdb=" N ILE E 217 " --> pdb=" O TYR E 214 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU E 218 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 223 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 239 Processing helix chain 'E' and resid 248 through 256 Processing helix chain 'E' and resid 280 through 283 No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 285 through 288 No H-bonds generated for 'chain 'E' and resid 285 through 288' Processing helix chain 'E' and resid 326 through 333 removed outlier: 3.506A pdb=" N TYR E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 42 removed outlier: 3.600A pdb=" N PHE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 70 through 104 removed outlier: 3.758A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 128 No H-bonds generated for 'chain 'G' and resid 125 through 128' Processing helix chain 'G' and resid 147 through 155 Processing helix chain 'G' and resid 167 through 170 No H-bonds generated for 'chain 'G' and resid 167 through 170' Processing helix chain 'G' and resid 189 through 201 removed outlier: 3.663A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 223 removed outlier: 3.633A pdb=" N ILE G 217 " --> pdb=" O TYR G 214 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU G 218 " --> pdb=" O GLU G 215 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 223 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 239 Processing helix chain 'G' and resid 248 through 256 Processing helix chain 'G' and resid 280 through 283 No H-bonds generated for 'chain 'G' and resid 280 through 283' Processing helix chain 'G' and resid 285 through 288 No H-bonds generated for 'chain 'G' and resid 285 through 288' Processing helix chain 'G' and resid 326 through 333 removed outlier: 3.506A pdb=" N TYR G 333 " --> pdb=" O ARG G 329 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 227 through 230 removed outlier: 6.452A pdb=" N ASN A 158 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA A 143 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL A 160 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.966A pdb=" N VAL B 119 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN B 158 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA B 143 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL B 160 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 206 through 208 removed outlier: 6.967A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN D 158 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA D 143 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL D 160 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 206 through 208 removed outlier: 6.967A pdb=" N VAL F 119 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN F 158 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA F 143 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL F 160 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.511A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 206 through 208 removed outlier: 6.967A pdb=" N VAL H 119 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN H 158 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA H 143 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL H 160 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 227 through 230 removed outlier: 6.453A pdb=" N ASN C 158 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA C 143 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL C 160 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 227 through 230 removed outlier: 6.454A pdb=" N ASN E 158 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA E 143 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL E 160 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.872A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 227 through 230 removed outlier: 6.452A pdb=" N ASN G 158 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA G 143 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL G 160 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.871A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1680 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: 6.90 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: 4581 1.33 - 1.45: 2559 1.45 - 1.57: 9908 1.57 - 1.69: 4 1.69 - 1.80: 116 Bond restraints: 17168 Sorted by residual: bond pdb=" O12 PGW C 401 " pdb=" P PGW C 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" O12 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O12 PGW A 401 " pdb=" P PGW A 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O12 PGW E 401 " pdb=" P PGW E 401 " ideal model delta sigma weight residual 1.636 1.690 -0.054 2.00e-02 2.50e+03 7.40e+00 bond pdb=" O14 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.00e-02 2.50e+03 6.81e+00 ... (remaining 17163 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 368 106.87 - 113.64: 9791 113.64 - 120.41: 6835 120.41 - 127.19: 6076 127.19 - 133.96: 116 Bond angle restraints: 23186 Sorted by residual: angle pdb=" CG1 ILE D 285 " pdb=" CB ILE D 285 " pdb=" CG2 ILE D 285 " ideal model delta sigma weight residual 110.70 120.04 -9.34 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CG1 ILE F 285 " pdb=" CB ILE F 285 " pdb=" CG2 ILE F 285 " ideal model delta sigma weight residual 110.70 120.00 -9.30 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CG1 ILE H 285 " pdb=" CB ILE H 285 " pdb=" CG2 ILE H 285 " ideal model delta sigma weight residual 110.70 119.99 -9.29 3.00e+00 1.11e-01 9.59e+00 angle pdb=" CG1 ILE B 285 " pdb=" CB ILE B 285 " pdb=" CG2 ILE B 285 " ideal model delta sigma weight residual 110.70 119.96 -9.26 3.00e+00 1.11e-01 9.54e+00 angle pdb=" N LYS H 274 " pdb=" CA LYS H 274 " pdb=" C LYS H 274 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.47e+00 ... (remaining 23181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 9880 24.59 - 49.18: 524 49.18 - 73.77: 44 73.77 - 98.35: 28 98.35 - 122.94: 4 Dihedral angle restraints: 10480 sinusoidal: 4328 harmonic: 6152 Sorted by residual: dihedral pdb=" C01 PGW C 401 " pdb=" C19 PGW C 401 " pdb=" O03 PGW C 401 " pdb=" O04 PGW C 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.94 -122.94 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C01 PGW E 401 " pdb=" C19 PGW E 401 " pdb=" O03 PGW E 401 " pdb=" O04 PGW E 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.93 -122.93 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C01 PGW A 401 " pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " pdb=" O04 PGW A 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.89 -122.89 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 10477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 2655 0.152 - 0.304: 29 0.304 - 0.455: 0 0.455 - 0.607: 0 0.607 - 0.759: 4 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CB ILE F 285 " pdb=" CA ILE F 285 " pdb=" CG1 ILE F 285 " pdb=" CG2 ILE F 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CB ILE H 285 " pdb=" CA ILE H 285 " pdb=" CG1 ILE H 285 " pdb=" CG2 ILE H 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CB ILE D 285 " pdb=" CA ILE D 285 " pdb=" CG1 ILE D 285 " pdb=" CG2 ILE D 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 2685 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 252 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C VAL F 252 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL F 252 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN F 253 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 252 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C VAL B 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL B 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN B 253 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 252 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C VAL H 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL H 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN H 253 " 0.011 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5170 2.83 - 3.41: 16443 3.41 - 3.98: 30504 3.98 - 4.56: 41665 4.56 - 5.14: 65341 Nonbonded interactions: 159123 Sorted by model distance: nonbonded pdb=" NH1 ARG A 154 " pdb=" O HIS C 161 " model vdw 2.251 2.520 nonbonded pdb=" O HIS A 161 " pdb=" NH1 ARG G 154 " model vdw 2.258 2.520 nonbonded pdb=" NH1 ARG C 154 " pdb=" O HIS E 161 " model vdw 2.273 2.520 nonbonded pdb=" NH1 ARG E 154 " pdb=" O HIS G 161 " model vdw 2.283 2.520 nonbonded pdb=" O PHE A 75 " pdb=" OG1 THR A 78 " model vdw 2.304 2.440 ... (remaining 159118 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 20 through 336 or resid 401)) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.590 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: 3.850 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 45.890 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.006 0.055 17168 Z= 0.386 Angle : 0.805 9.342 23186 Z= 0.451 Chirality : 0.061 0.759 2688 Planarity : 0.005 0.034 3000 Dihedral : 15.406 122.943 6528 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.09 % Allowed : 7.64 % Favored : 91.27 % 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: -3.93 (0.13), residues: 2140 helix: -2.86 (0.11), residues: 980 sheet: -0.60 (0.25), residues: 356 loop : -3.04 (0.16), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 123 HIS 0.004 0.001 HIS A 117 PHE 0.007 0.001 PHE C 40 TYR 0.015 0.002 TYR C 51 ARG 0.004 0.000 ARG G 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 519 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8109 (m-80) cc_final: 0.7308 (m-80) REVERT: A 82 LEU cc_start: 0.9295 (mt) cc_final: 0.8800 (mp) REVERT: A 105 LYS cc_start: 0.8850 (tttt) cc_final: 0.8597 (tttm) REVERT: A 174 ASN cc_start: 0.8910 (t0) cc_final: 0.8412 (t0) REVERT: A 319 LEU cc_start: 0.9182 (tp) cc_final: 0.8978 (tp) REVERT: B 174 ASN cc_start: 0.8532 (m110) cc_final: 0.8323 (m-40) REVERT: B 310 TYR cc_start: 0.7881 (t80) cc_final: 0.7500 (t80) REVERT: B 316 ASP cc_start: 0.8070 (m-30) cc_final: 0.7837 (m-30) REVERT: D 310 TYR cc_start: 0.7899 (t80) cc_final: 0.7507 (t80) REVERT: D 333 TYR cc_start: 0.8638 (t80) cc_final: 0.8090 (t80) REVERT: F 310 TYR cc_start: 0.7710 (t80) cc_final: 0.7415 (t80) REVERT: F 333 TYR cc_start: 0.8559 (t80) cc_final: 0.8074 (t80) REVERT: H 310 TYR cc_start: 0.7671 (t80) cc_final: 0.7455 (t80) REVERT: H 333 TYR cc_start: 0.8557 (t80) cc_final: 0.8075 (t80) REVERT: C 82 LEU cc_start: 0.9220 (mt) cc_final: 0.8755 (mp) REVERT: C 102 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 105 LYS cc_start: 0.8836 (tttt) cc_final: 0.8599 (tttm) REVERT: C 174 ASN cc_start: 0.8920 (t0) cc_final: 0.8428 (t0) REVERT: C 305 ASP cc_start: 0.7778 (t0) cc_final: 0.7567 (t70) REVERT: E 33 TYR cc_start: 0.8685 (t80) cc_final: 0.8278 (t80) REVERT: E 96 GLU cc_start: 0.7580 (tt0) cc_final: 0.7356 (tt0) REVERT: E 105 LYS cc_start: 0.8835 (tttt) cc_final: 0.8565 (tttm) REVERT: E 174 ASN cc_start: 0.8898 (t0) cc_final: 0.8418 (t0) REVERT: E 270 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7537 (Cg_exo) REVERT: E 305 ASP cc_start: 0.7785 (t0) cc_final: 0.7531 (t70) REVERT: E 319 LEU cc_start: 0.9035 (tp) cc_final: 0.8831 (tp) REVERT: G 105 LYS cc_start: 0.8835 (tttt) cc_final: 0.8571 (tttm) REVERT: G 174 ASN cc_start: 0.8924 (t0) cc_final: 0.8420 (t0) outliers start: 20 outliers final: 0 residues processed: 527 average time/residue: 0.3296 time to fit residues: 245.2821 Evaluate side-chains 373 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS B 332 ASN D 286 HIS H 286 HIS H 332 ASN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17168 Z= 0.173 Angle : 0.457 4.851 23186 Z= 0.246 Chirality : 0.046 0.181 2688 Planarity : 0.003 0.046 3000 Dihedral : 9.010 76.281 2532 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.64 % Allowed : 14.03 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2140 helix: -1.15 (0.15), residues: 976 sheet: -0.05 (0.26), residues: 356 loop : -2.67 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 123 HIS 0.008 0.001 HIS B 286 PHE 0.010 0.001 PHE F 251 TYR 0.018 0.001 TYR A 33 ARG 0.005 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 401 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8190 (m-80) cc_final: 0.7404 (m-80) REVERT: A 174 ASN cc_start: 0.8877 (t0) cc_final: 0.8539 (t0) REVERT: A 319 LEU cc_start: 0.9070 (tp) cc_final: 0.8835 (tp) REVERT: B 310 TYR cc_start: 0.8060 (t80) cc_final: 0.7845 (t80) REVERT: D 200 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8437 (tttt) REVERT: D 333 TYR cc_start: 0.8614 (t80) cc_final: 0.8180 (t80) REVERT: F 333 TYR cc_start: 0.8617 (t80) cc_final: 0.8357 (t80) REVERT: H 333 TYR cc_start: 0.8634 (t80) cc_final: 0.8184 (t80) REVERT: C 82 LEU cc_start: 0.9198 (mt) cc_final: 0.8773 (mp) REVERT: C 174 ASN cc_start: 0.8895 (t0) cc_final: 0.8394 (t0) REVERT: E 82 LEU cc_start: 0.9167 (mt) cc_final: 0.8783 (mp) REVERT: E 174 ASN cc_start: 0.8892 (t0) cc_final: 0.8403 (t0) REVERT: G 82 LEU cc_start: 0.9153 (mt) cc_final: 0.8779 (mp) REVERT: G 174 ASN cc_start: 0.8894 (t0) cc_final: 0.8395 (t0) outliers start: 30 outliers final: 25 residues processed: 418 average time/residue: 0.3195 time to fit residues: 192.9323 Evaluate side-chains 410 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 385 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain F residue 308 ARG Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.0970 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN D 332 ASN F 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17168 Z= 0.160 Angle : 0.425 4.429 23186 Z= 0.227 Chirality : 0.045 0.146 2688 Planarity : 0.003 0.033 3000 Dihedral : 7.899 73.688 2532 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.35 % Allowed : 16.05 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2140 helix: -0.35 (0.16), residues: 984 sheet: 0.22 (0.27), residues: 356 loop : -2.45 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 123 HIS 0.008 0.001 HIS F 286 PHE 0.005 0.001 PHE H 140 TYR 0.024 0.001 TYR E 33 ARG 0.007 0.000 ARG H 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 398 time to evaluate : 2.015 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8131 (m-80) cc_final: 0.7342 (m-80) REVERT: A 102 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 174 ASN cc_start: 0.8813 (t0) cc_final: 0.8484 (t0) REVERT: A 210 GLU cc_start: 0.7597 (tt0) cc_final: 0.7361 (tt0) REVERT: A 237 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7556 (mmt90) REVERT: D 200 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8415 (tttt) REVERT: D 333 TYR cc_start: 0.8631 (t80) cc_final: 0.8302 (t80) REVERT: F 132 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7556 (ttm170) REVERT: F 333 TYR cc_start: 0.8703 (t80) cc_final: 0.8452 (t80) REVERT: H 333 TYR cc_start: 0.8645 (t80) cc_final: 0.8328 (t80) REVERT: C 82 LEU cc_start: 0.9210 (mt) cc_final: 0.8780 (mp) REVERT: C 102 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 174 ASN cc_start: 0.8878 (t0) cc_final: 0.8552 (t0) REVERT: E 82 LEU cc_start: 0.9208 (mt) cc_final: 0.8812 (mp) REVERT: E 102 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8103 (mm-30) REVERT: E 174 ASN cc_start: 0.8864 (t0) cc_final: 0.8554 (t0) REVERT: G 82 LEU cc_start: 0.9202 (mt) cc_final: 0.8817 (mp) REVERT: G 102 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8086 (mm-30) REVERT: G 174 ASN cc_start: 0.8855 (t0) cc_final: 0.8513 (t0) REVERT: G 247 TYR cc_start: 0.8800 (m-80) cc_final: 0.8536 (m-80) outliers start: 43 outliers final: 31 residues processed: 421 average time/residue: 0.3158 time to fit residues: 192.4368 Evaluate side-chains 414 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 383 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 332 ASN C 39 HIS E 39 HIS G 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17168 Z= 0.229 Angle : 0.454 5.106 23186 Z= 0.241 Chirality : 0.046 0.143 2688 Planarity : 0.003 0.026 3000 Dihedral : 7.681 75.454 2532 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.89 % Allowed : 17.30 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2140 helix: 0.04 (0.17), residues: 988 sheet: 0.26 (0.28), residues: 356 loop : -2.30 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 123 HIS 0.003 0.001 HIS G 117 PHE 0.007 0.001 PHE H 140 TYR 0.024 0.001 TYR A 33 ARG 0.008 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 399 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8193 (m-80) cc_final: 0.7334 (m-80) REVERT: A 174 ASN cc_start: 0.8834 (t0) cc_final: 0.8490 (t0) REVERT: A 210 GLU cc_start: 0.7618 (tt0) cc_final: 0.7385 (tt0) REVERT: A 237 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7586 (mmt90) REVERT: D 200 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8389 (tttt) REVERT: D 333 TYR cc_start: 0.8657 (t80) cc_final: 0.8391 (t80) REVERT: F 282 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6486 (p0) REVERT: H 333 TYR cc_start: 0.8653 (t80) cc_final: 0.8378 (t80) REVERT: C 65 TYR cc_start: 0.8253 (m-80) cc_final: 0.7449 (m-80) REVERT: C 82 LEU cc_start: 0.9243 (mt) cc_final: 0.8787 (mp) REVERT: C 174 ASN cc_start: 0.8864 (t0) cc_final: 0.8530 (t0) REVERT: E 65 TYR cc_start: 0.8319 (m-80) cc_final: 0.7482 (m-80) REVERT: E 174 ASN cc_start: 0.8872 (t0) cc_final: 0.8549 (t0) REVERT: G 65 TYR cc_start: 0.8301 (m-80) cc_final: 0.7478 (m-80) REVERT: G 104 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7969 (ttp) REVERT: G 174 ASN cc_start: 0.8860 (t0) cc_final: 0.8520 (t0) outliers start: 53 outliers final: 43 residues processed: 425 average time/residue: 0.2970 time to fit residues: 185.0361 Evaluate side-chains 431 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 386 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17168 Z= 0.288 Angle : 0.482 6.821 23186 Z= 0.255 Chirality : 0.048 0.149 2688 Planarity : 0.003 0.024 3000 Dihedral : 7.599 77.440 2532 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.17 % Allowed : 19.92 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2140 helix: 0.38 (0.17), residues: 980 sheet: 0.24 (0.28), residues: 356 loop : -2.14 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 123 HIS 0.003 0.001 HIS A 117 PHE 0.009 0.001 PHE D 140 TYR 0.025 0.001 TYR G 33 ARG 0.005 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 385 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8262 (m-80) cc_final: 0.7441 (m-80) REVERT: A 174 ASN cc_start: 0.8827 (t0) cc_final: 0.8481 (t0) REVERT: A 210 GLU cc_start: 0.7662 (tt0) cc_final: 0.7438 (tt0) REVERT: A 237 ARG cc_start: 0.7854 (mtt90) cc_final: 0.7616 (mmt90) REVERT: D 332 ASN cc_start: 0.7700 (m110) cc_final: 0.7077 (m110) REVERT: D 333 TYR cc_start: 0.8663 (t80) cc_final: 0.8426 (t80) REVERT: F 282 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6559 (p0) REVERT: H 333 TYR cc_start: 0.8638 (t80) cc_final: 0.8385 (t80) REVERT: C 65 TYR cc_start: 0.8248 (m-80) cc_final: 0.7420 (m-80) REVERT: C 82 LEU cc_start: 0.9298 (mt) cc_final: 0.8818 (mp) REVERT: C 104 MET cc_start: 0.8308 (ttt) cc_final: 0.7932 (ttp) REVERT: C 174 ASN cc_start: 0.8859 (t0) cc_final: 0.8507 (t0) REVERT: E 65 TYR cc_start: 0.8259 (m-80) cc_final: 0.7423 (m-80) REVERT: E 82 LEU cc_start: 0.9276 (mt) cc_final: 0.8828 (mp) REVERT: E 104 MET cc_start: 0.8333 (ttt) cc_final: 0.7947 (ttp) REVERT: E 174 ASN cc_start: 0.8867 (t0) cc_final: 0.8520 (t0) REVERT: G 65 TYR cc_start: 0.8248 (m-80) cc_final: 0.7436 (m-80) REVERT: G 82 LEU cc_start: 0.9275 (mt) cc_final: 0.8832 (mp) REVERT: G 104 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7863 (ttp) REVERT: G 174 ASN cc_start: 0.8856 (t0) cc_final: 0.8487 (t0) outliers start: 58 outliers final: 47 residues processed: 416 average time/residue: 0.2909 time to fit residues: 178.1718 Evaluate side-chains 424 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 375 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE 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: 58.974 > 50: distance: 60 - 66: 23.741 distance: 66 - 67: 26.669 distance: 67 - 68: 38.144 distance: 67 - 70: 16.380 distance: 68 - 69: 58.974 distance: 68 - 74: 38.884 distance: 70 - 71: 28.771 distance: 70 - 72: 35.865 distance: 71 - 73: 11.670 distance: 74 - 75: 36.523 distance: 75 - 76: 12.578 distance: 75 - 78: 16.397 distance: 76 - 77: 31.591 distance: 76 - 82: 25.512 distance: 78 - 79: 34.994 distance: 79 - 80: 12.113 distance: 79 - 81: 16.217 distance: 82 - 83: 24.655 distance: 82 - 88: 28.574 distance: 83 - 84: 16.103 distance: 83 - 86: 12.327 distance: 84 - 85: 20.092 distance: 84 - 89: 15.759 distance: 86 - 87: 24.885 distance: 87 - 88: 18.897 distance: 89 - 90: 36.906 distance: 89 - 95: 19.703 distance: 90 - 91: 33.422 distance: 90 - 93: 23.768 distance: 91 - 92: 19.366 distance: 91 - 96: 27.093 distance: 93 - 94: 34.630 distance: 94 - 95: 37.918 distance: 96 - 97: 7.601 distance: 97 - 98: 10.326 distance: 97 - 100: 10.968 distance: 98 - 99: 23.433 distance: 98 - 107: 7.202 distance: 100 - 101: 15.826 distance: 101 - 102: 19.931 distance: 102 - 103: 11.050 distance: 103 - 104: 8.598 distance: 104 - 105: 11.433 distance: 104 - 106: 21.134 distance: 107 - 108: 10.548 distance: 108 - 109: 14.479 distance: 108 - 111: 12.181 distance: 109 - 110: 21.091 distance: 109 - 115: 8.451 distance: 111 - 112: 5.006 distance: 112 - 113: 15.567 distance: 112 - 114: 7.558 distance: 115 - 116: 16.128 distance: 116 - 117: 20.017 distance: 116 - 119: 4.467 distance: 117 - 118: 21.072 distance: 117 - 127: 15.564 distance: 119 - 120: 12.223 distance: 120 - 121: 21.657 distance: 120 - 122: 7.391 distance: 121 - 123: 7.285 distance: 122 - 124: 7.073 distance: 123 - 125: 12.939 distance: 124 - 125: 16.709 distance: 125 - 126: 13.633 distance: 127 - 128: 7.319 distance: 128 - 129: 11.069 distance: 128 - 131: 11.331 distance: 129 - 130: 17.774 distance: 129 - 133: 12.583 distance: 131 - 132: 18.088 distance: 133 - 134: 25.502 distance: 134 - 135: 14.619 distance: 134 - 137: 27.479 distance: 135 - 136: 16.102 distance: 135 - 144: 23.218 distance: 138 - 139: 21.427 distance: 138 - 140: 6.743 distance: 139 - 141: 10.517 distance: 140 - 142: 9.309 distance: 141 - 143: 14.108 distance: 142 - 143: 14.731 distance: 144 - 145: 9.919 distance: 145 - 146: 19.627 distance: 145 - 148: 6.638 distance: 146 - 147: 3.815 distance: 146 - 155: 31.864 distance: 148 - 149: 19.373 distance: 149 - 150: 6.450 distance: 150 - 151: 19.223 distance: 151 - 152: 8.348 distance: 152 - 153: 3.160 distance: 152 - 154: 12.113