Starting phenix.real_space_refine (version: dev) on Wed Feb 22 08:29:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_9406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_9406.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_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_9406/02_2023/5bkj_9406_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_9406_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_9406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_9406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_9406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkj_9406/02_2023/5bkj_9406_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 9 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: 9 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: 9 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: 9 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: 10.14, per 1000 atoms: 0.60 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: 6.50 Conformation dependent library (CDL) restraints added in 2.6 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: 1.54 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: 5.11 Time building geometry restraints manager: 7.00 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: 9860 24.59 - 49.18: 520 49.18 - 73.77: 40 73.77 - 98.35: 20 98.35 - 122.94: 4 Dihedral angle restraints: 10444 sinusoidal: 4292 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 10441 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 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. 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: 1.200 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: 4.590 Check model and map are aligned: 0.270 Process input model: 45.920 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 14.994 122.943 6492 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.09 % 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 *********************** 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 : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 0 residues processed: 527 average time/residue: 0.3394 time to fit residues: 252.6872 Evaluate side-chains 371 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6869 ------------------------------------------------------------------------------- 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: 0.9990 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 E 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 17168 Z= 0.171 Angle : 0.457 4.820 23186 Z= 0.246 Chirality : 0.046 0.160 2688 Planarity : 0.003 0.045 3000 Dihedral : 8.318 98.087 2496 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.75 % 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: -2.32 (0.16), residues: 2140 helix: -1.13 (0.15), residues: 976 sheet: -0.03 (0.26), residues: 356 loop : -2.67 (0.17), residues: 808 *********************** 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 428 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 396 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 415 average time/residue: 0.3217 time to fit residues: 191.8165 Evaluate side-chains 408 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 384 time to evaluate : 2.138 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1974 time to fit residues: 11.0400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.0000 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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: 0.8413 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 17168 Z= 0.196 Angle : 0.447 6.811 23186 Z= 0.239 Chirality : 0.046 0.148 2688 Planarity : 0.003 0.033 3000 Dihedral : 7.456 92.622 2496 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.47 % 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: -1.58 (0.17), residues: 2140 helix: -0.36 (0.16), residues: 984 sheet: 0.17 (0.27), residues: 356 loop : -2.47 (0.18), residues: 800 *********************** 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 429 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 402 time to evaluate : 2.129 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 416 average time/residue: 0.3127 time to fit residues: 189.8642 Evaluate side-chains 400 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 384 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1465 time to fit residues: 7.1880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 332 ASN G 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 17168 Z= 0.231 Angle : 0.459 6.847 23186 Z= 0.243 Chirality : 0.047 0.148 2688 Planarity : 0.003 0.027 3000 Dihedral : 7.282 86.800 2496 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.42 % 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: -1.19 (0.17), residues: 2140 helix: 0.05 (0.17), residues: 988 sheet: 0.20 (0.27), residues: 356 loop : -2.33 (0.18), residues: 796 *********************** 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 418 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 392 time to evaluate : 1.970 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 406 average time/residue: 0.3223 time to fit residues: 190.2492 Evaluate side-chains 396 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 377 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1925 time to fit residues: 9.3886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 141 optimal weight: 0.0370 chunk 0 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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: 0.8389 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 17168 Z= 0.113 Angle : 0.411 6.808 23186 Z= 0.217 Chirality : 0.045 0.139 2688 Planarity : 0.003 0.037 3000 Dihedral : 6.709 73.334 2496 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.31 % 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: -0.66 (0.18), residues: 2140 helix: 0.56 (0.17), residues: 980 sheet: 0.36 (0.28), residues: 356 loop : -2.08 (0.19), residues: 804 *********************** 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 421 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 397 time to evaluate : 2.162 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 407 average time/residue: 0.3097 time to fit residues: 184.6566 Evaluate side-chains 388 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 371 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1685 time to fit residues: 7.8714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 chunk 205 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN F 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 17168 Z= 0.144 Angle : 0.422 5.805 23186 Z= 0.221 Chirality : 0.045 0.144 2688 Planarity : 0.002 0.024 3000 Dihedral : 6.510 67.240 2496 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.93 % 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: -0.40 (0.18), residues: 2140 helix: 0.81 (0.17), residues: 980 sheet: 0.44 (0.28), residues: 356 loop : -1.98 (0.19), residues: 804 *********************** REFINEMENT MACRO_CYCLE 6 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 400 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 383 time to evaluate : 1.866 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 393 average time/residue: 0.3195 time to fit residues: 182.9375 Evaluate side-chains 381 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 368 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1593 time to fit residues: 7.2410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- 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: 0.8421 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 17168 Z= 0.209 Angle : 0.454 6.172 23186 Z= 0.238 Chirality : 0.046 0.145 2688 Planarity : 0.003 0.034 3000 Dihedral : 6.569 64.181 2496 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 1.15 % 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: -0.20 (0.18), residues: 2140 helix: 1.06 (0.17), residues: 960 sheet: 0.40 (0.27), residues: 356 loop : -1.83 (0.19), residues: 824 *********************** REFINEMENT MACRO_CYCLE 7 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 398 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 377 time to evaluate : 1.974 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 384 average time/residue: 0.3163 time to fit residues: 177.0778 Evaluate side-chains 384 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 370 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1510 time to fit residues: 6.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 17168 Z= 0.158 Angle : 0.440 6.593 23186 Z= 0.230 Chirality : 0.046 0.195 2688 Planarity : 0.002 0.042 3000 Dihedral : 6.276 59.549 2496 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.71 % 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: -0.13 (0.18), residues: 2140 helix: 1.00 (0.17), residues: 992 sheet: 0.52 (0.28), residues: 356 loop : -1.80 (0.20), residues: 792 *********************** REFINEMENT MACRO_CYCLE 8 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 389 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 376 time to evaluate : 2.109 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 385 average time/residue: 0.3316 time to fit residues: 185.6101 Evaluate side-chains 369 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 363 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1520 time to fit residues: 4.5416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.0870 chunk 178 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 172 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8398 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 17168 Z= 0.142 Angle : 0.442 7.407 23186 Z= 0.229 Chirality : 0.046 0.255 2688 Planarity : 0.002 0.038 3000 Dihedral : 5.941 56.358 2496 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.71 % 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: 0.03 (0.18), residues: 2140 helix: 1.14 (0.17), residues: 988 sheet: 0.59 (0.28), residues: 356 loop : -1.72 (0.20), residues: 796 *********************** REFINEMENT MACRO_CYCLE 9 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 388 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 375 time to evaluate : 2.036 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 378 average time/residue: 0.3089 time to fit residues: 172.0163 Evaluate side-chains 369 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 361 time to evaluate : 2.027 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1531 time to fit residues: 5.2476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17168 Z= 0.170 Angle : 0.460 8.274 23186 Z= 0.237 Chirality : 0.046 0.211 2688 Planarity : 0.003 0.035 3000 Dihedral : 5.832 59.688 2496 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.33 % 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: 0.08 (0.18), residues: 2140 helix: 1.18 (0.17), residues: 988 sheet: 0.58 (0.28), residues: 356 loop : -1.65 (0.20), residues: 796 ********************** REFINEMENT MACRO_CYCLE 10 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 366 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 360 time to evaluate : 2.180 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 363 average time/residue: 0.3228 time to fit residues: 172.7560 Evaluate side-chains 364 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 362 time to evaluate : 2.469 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1432 time to fit residues: 3.3691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 0.0040 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 0.0070 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.112832 restraints weight = 21245.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115431 restraints weight = 13948.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117334 restraints weight = 10432.200| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 17168 Z= 0.117 Angle : 0.447 7.934 23186 Z= 0.228 Chirality : 0.046 0.232 2688 Planarity : 0.002 0.022 3000 Dihedral : 5.399 56.345 2496 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.33 % 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: 0.25 (0.18), residues: 2140 helix: 1.33 (0.17), residues: 984 sheet: 0.75 (0.28), residues: 352 loop : -1.62 (0.20), residues: 804 =============================================================================== Job complete usr+sys time: 3857.84 seconds wall clock time: 69 minutes 51.89 seconds (4191.89 seconds total)