Starting phenix.real_space_refine on Thu Feb 15 08:01:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zye_11560/02_2024/6zye_11560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zye_11560/02_2024/6zye_11560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zye_11560/02_2024/6zye_11560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zye_11560/02_2024/6zye_11560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zye_11560/02_2024/6zye_11560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zye_11560/02_2024/6zye_11560.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 7392 2.51 5 N 1995 2.21 5 O 2156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 186": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "G PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11592 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 6.56, per 1000 atoms: 0.57 Number of scatterers: 11592 At special positions: 0 Unit cell: (97.842, 98.9055, 108.477, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 2156 8.00 N 1995 7.00 C 7392 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: 5.05 Conformation dependent library (CDL) restraints added in 2.0 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 22 sheets defined 54.4% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'E' and resid -35 through -16 Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 160 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE E 224 " --> pdb=" O PHE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 298 through 320 Processing helix chain 'C' and resid -34 through -16 Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE C 224 " --> pdb=" O PHE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'A' and resid -34 through -16 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.661A pdb=" N ILE A 224 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.525A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'B' and resid -34 through -16 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE B 224 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'D' and resid -34 through -16 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.661A pdb=" N ILE D 224 " --> pdb=" O PHE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.525A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'F' and resid -34 through -16 Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 160 " --> pdb=" O VAL F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 219 through 224 removed outlier: 3.663A pdb=" N ILE F 224 " --> pdb=" O PHE F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'G' and resid -34 through -16 Processing helix chain 'G' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY G 157 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET G 158 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY G 160 " --> pdb=" O VAL G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE G 224 " --> pdb=" O PHE G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.525A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 Processing helix chain 'G' and resid 298 through 320 Processing sheet with id=AA1, first strand: chain 'E' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 226 through 227 removed outlier: 6.613A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 239 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 239 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER E 285 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 328 through 332 removed outlier: 8.444A pdb=" N GLN D 329 " --> pdb=" O SER E 328 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR E 330 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU D 331 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR E 332 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLN G 329 " --> pdb=" O SER C 328 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 330 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU G 331 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR C 332 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.612A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 6.613A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 239 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 239 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 285 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 239 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 239 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 239 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 239 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 285 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 239 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 239 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 285 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 239 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 239 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 285 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 280 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET F 289 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE F 278 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR G 239 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR G 239 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER G 285 " --> pdb=" O ALA G 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3843 1.34 - 1.46: 3054 1.46 - 1.58: 4835 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11823 Sorted by residual: bond pdb=" CG LEU D 214 " pdb=" CD2 LEU D 214 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.61e+00 bond pdb=" CG LEU F 214 " pdb=" CD2 LEU F 214 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.54e+00 bond pdb=" CG LEU C 214 " pdb=" CD2 LEU C 214 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.51e+00 bond pdb=" CG LEU B 214 " pdb=" CD2 LEU B 214 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.50e+00 bond pdb=" CB VAL D 196 " pdb=" CG2 VAL D 196 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 ... (remaining 11818 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.78: 189 104.78 - 112.08: 5809 112.08 - 119.38: 3926 119.38 - 126.69: 6015 126.69 - 133.99: 154 Bond angle restraints: 16093 Sorted by residual: angle pdb=" N LYS G 161 " pdb=" CA LYS G 161 " pdb=" C LYS G 161 " ideal model delta sigma weight residual 111.28 118.59 -7.31 1.09e+00 8.42e-01 4.50e+01 angle pdb=" N LYS C 161 " pdb=" CA LYS C 161 " pdb=" C LYS C 161 " ideal model delta sigma weight residual 111.28 118.56 -7.28 1.09e+00 8.42e-01 4.47e+01 angle pdb=" N LYS F 161 " pdb=" CA LYS F 161 " pdb=" C LYS F 161 " ideal model delta sigma weight residual 111.28 118.56 -7.28 1.09e+00 8.42e-01 4.46e+01 angle pdb=" N LYS E 161 " pdb=" CA LYS E 161 " pdb=" C LYS E 161 " ideal model delta sigma weight residual 111.28 118.55 -7.27 1.09e+00 8.42e-01 4.45e+01 angle pdb=" N LYS A 161 " pdb=" CA LYS A 161 " pdb=" C LYS A 161 " ideal model delta sigma weight residual 111.28 118.54 -7.26 1.09e+00 8.42e-01 4.44e+01 ... (remaining 16088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 6405 17.39 - 34.78: 476 34.78 - 52.16: 56 52.16 - 69.55: 14 69.55 - 86.94: 7 Dihedral angle restraints: 6958 sinusoidal: 2457 harmonic: 4501 Sorted by residual: dihedral pdb=" CA PHE D 326 " pdb=" C PHE D 326 " pdb=" N PRO D 327 " pdb=" CA PRO D 327 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE B 326 " pdb=" C PHE B 326 " pdb=" N PRO B 327 " pdb=" CA PRO B 327 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE G 326 " pdb=" C PHE G 326 " pdb=" N PRO G 327 " pdb=" CA PRO G 327 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1071 0.049 - 0.097: 541 0.097 - 0.146: 181 0.146 - 0.194: 55 0.194 - 0.243: 7 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CA LYS G 161 " pdb=" N LYS G 161 " pdb=" C LYS G 161 " pdb=" CB LYS G 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LYS A 161 " pdb=" N LYS A 161 " pdb=" C LYS A 161 " pdb=" CB LYS A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS F 161 " pdb=" N LYS F 161 " pdb=" C LYS F 161 " pdb=" CB LYS F 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1852 not shown) Planarity restraints: 2079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 160 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C GLY A 160 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY A 160 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 161 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 160 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C GLY B 160 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY B 160 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 161 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 160 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C GLY D 160 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY D 160 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS D 161 " -0.015 2.00e-02 2.50e+03 ... (remaining 2076 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2766 2.77 - 3.30: 12298 3.30 - 3.84: 18947 3.84 - 4.37: 22630 4.37 - 4.90: 38197 Nonbonded interactions: 94838 Sorted by model distance: nonbonded pdb=" OD2 ASP A 162 " pdb=" O SER B 222 " model vdw 2.241 3.040 nonbonded pdb=" O ILE B 268 " pdb=" NZ LYS B 295 " model vdw 2.290 2.520 nonbonded pdb=" O ILE C 268 " pdb=" NZ LYS C 295 " model vdw 2.290 2.520 nonbonded pdb=" O ARG C 202 " pdb=" ND2 ASN C 218 " model vdw 2.290 2.520 nonbonded pdb=" O ARG F 202 " pdb=" ND2 ASN F 218 " model vdw 2.290 2.520 ... (remaining 94833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.420 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: 2.520 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 33.430 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.016 0.082 11823 Z= 1.015 Angle : 1.047 8.425 16093 Z= 0.605 Chirality : 0.064 0.243 1855 Planarity : 0.006 0.040 2079 Dihedral : 13.053 86.940 4046 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -3.23 (0.22), residues: 1288 helix: -1.24 (0.21), residues: 490 sheet: -4.36 (0.29), residues: 161 loop : -2.20 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 184 HIS 0.006 0.002 HIS D 265 PHE 0.022 0.003 PHE G 281 TYR 0.020 0.003 TYR C 277 ARG 0.007 0.001 ARG G 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 189 ASP cc_start: 0.7123 (m-30) cc_final: 0.6844 (m-30) REVERT: E 215 TYR cc_start: 0.8494 (m-80) cc_final: 0.8175 (m-80) REVERT: E 312 LYS cc_start: 0.8415 (mttt) cc_final: 0.7859 (mttm) REVERT: C 164 LEU cc_start: 0.7669 (mt) cc_final: 0.7399 (mm) REVERT: C 165 SER cc_start: 0.8766 (m) cc_final: 0.8432 (p) REVERT: C 215 TYR cc_start: 0.8449 (m-80) cc_final: 0.8157 (m-10) REVERT: C 312 LYS cc_start: 0.8310 (mttt) cc_final: 0.7793 (mttp) REVERT: A 312 LYS cc_start: 0.8316 (mttt) cc_final: 0.7635 (mttm) REVERT: B 158 MET cc_start: 0.5287 (mtm) cc_final: 0.4790 (ttm) REVERT: B 185 ILE cc_start: 0.8606 (mt) cc_final: 0.8023 (mt) REVERT: B 312 LYS cc_start: 0.8431 (mttt) cc_final: 0.8009 (mttp) REVERT: D 179 PHE cc_start: 0.8182 (p90) cc_final: 0.7701 (p90) REVERT: D 312 LYS cc_start: 0.8357 (mttt) cc_final: 0.7712 (mttm) REVERT: F 260 GLU cc_start: 0.6706 (tp30) cc_final: 0.6463 (tp30) REVERT: F 291 TYR cc_start: 0.8027 (t80) cc_final: 0.7798 (t80) REVERT: F 312 LYS cc_start: 0.8257 (mttt) cc_final: 0.7637 (mttm) REVERT: G 312 LYS cc_start: 0.8322 (mttt) cc_final: 0.7589 (mttm) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.3033 time to fit residues: 145.7771 Evaluate side-chains 206 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 40.0000 chunk 73 optimal weight: 7.9990 chunk 89 optimal weight: 40.0000 chunk 139 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS B 211 ASN B 320 HIS ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 320 HIS ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11823 Z= 0.298 Angle : 0.690 7.655 16093 Z= 0.358 Chirality : 0.048 0.152 1855 Planarity : 0.004 0.034 2079 Dihedral : 5.398 18.709 1666 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: -1.27 (0.23), residues: 1288 helix: 1.16 (0.23), residues: 504 sheet: -3.21 (0.33), residues: 189 loop : -1.80 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 201 HIS 0.001 0.001 HIS E 265 PHE 0.014 0.002 PHE A 168 TYR 0.016 0.002 TYR B 291 ARG 0.006 0.001 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 MET cc_start: 0.6415 (tpt) cc_final: 0.5941 (tpt) REVERT: E 198 GLU cc_start: 0.7510 (pp20) cc_final: 0.7133 (pp20) REVERT: E 215 TYR cc_start: 0.8353 (m-80) cc_final: 0.8069 (m-80) REVERT: E 312 LYS cc_start: 0.8605 (mttt) cc_final: 0.8084 (mttm) REVERT: C 179 PHE cc_start: 0.8350 (p90) cc_final: 0.8060 (p90) REVERT: C 312 LYS cc_start: 0.8311 (mttt) cc_final: 0.7976 (mttp) REVERT: A 172 MET cc_start: 0.6739 (tpt) cc_final: 0.6070 (tpt) REVERT: B 172 MET cc_start: 0.6738 (tpt) cc_final: 0.5997 (tpt) REVERT: B 174 TYR cc_start: 0.4969 (t80) cc_final: 0.4700 (t80) REVERT: B 215 TYR cc_start: 0.8524 (m-80) cc_final: 0.8001 (m-80) REVERT: B 312 LYS cc_start: 0.8556 (mttt) cc_final: 0.8183 (mttm) REVERT: D 179 PHE cc_start: 0.8340 (p90) cc_final: 0.7987 (p90) REVERT: D 306 GLN cc_start: 0.7355 (tt0) cc_final: 0.6915 (tt0) REVERT: D 312 LYS cc_start: 0.8479 (mttt) cc_final: 0.8119 (mttm) REVERT: F 308 ASP cc_start: 0.7862 (p0) cc_final: 0.7533 (p0) REVERT: F 312 LYS cc_start: 0.8513 (mttt) cc_final: 0.7733 (mttm) REVERT: G 172 MET cc_start: 0.6732 (tpt) cc_final: 0.6051 (tpt) REVERT: G 179 PHE cc_start: 0.8360 (p90) cc_final: 0.8092 (p90) REVERT: G 279 ASN cc_start: 0.8352 (p0) cc_final: 0.8130 (p0) REVERT: G 312 LYS cc_start: 0.8626 (mttt) cc_final: 0.8065 (mptp) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2854 time to fit residues: 120.5927 Evaluate side-chains 195 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 112 optimal weight: 40.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11823 Z= 0.197 Angle : 0.582 7.431 16093 Z= 0.299 Chirality : 0.044 0.147 1855 Planarity : 0.003 0.024 2079 Dihedral : 4.866 18.334 1666 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.18 % Allowed : 2.88 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1288 helix: 2.49 (0.24), residues: 455 sheet: -2.07 (0.30), residues: 273 loop : -1.18 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.001 0.001 HIS C 320 PHE 0.009 0.001 PHE G 168 TYR 0.013 0.001 TYR G 291 ARG 0.006 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 278 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 312 LYS cc_start: 0.8495 (mttt) cc_final: 0.7926 (mttm) REVERT: C 312 LYS cc_start: 0.8182 (mttt) cc_final: 0.7925 (mmtt) REVERT: B 312 LYS cc_start: 0.8540 (mttt) cc_final: 0.8145 (mmtt) REVERT: D 210 ASP cc_start: 0.7716 (m-30) cc_final: 0.7370 (m-30) REVERT: D 261 MET cc_start: 0.8164 (tmm) cc_final: 0.7840 (tmm) REVERT: D 306 GLN cc_start: 0.7659 (tt0) cc_final: 0.7250 (tt0) REVERT: D 312 LYS cc_start: 0.8579 (mttt) cc_final: 0.8113 (mttm) REVERT: F 312 LYS cc_start: 0.8535 (mttt) cc_final: 0.7982 (mmtt) REVERT: G 179 PHE cc_start: 0.8267 (p90) cc_final: 0.8042 (p90) REVERT: G 312 LYS cc_start: 0.8633 (mttt) cc_final: 0.8064 (mttm) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.2766 time to fit residues: 105.3715 Evaluate side-chains 202 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 40.0000 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 133 optimal weight: 40.0000 chunk 40 optimal weight: 0.4980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 306 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN D 280 GLN D 329 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 HIS F 329 GLN ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11823 Z= 0.226 Angle : 0.594 6.100 16093 Z= 0.307 Chirality : 0.044 0.152 1855 Planarity : 0.003 0.034 2079 Dihedral : 4.780 18.555 1666 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % 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: 0.09 (0.24), residues: 1288 helix: 2.53 (0.24), residues: 455 sheet: -1.64 (0.27), residues: 343 loop : -0.97 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 201 HIS 0.002 0.001 HIS D 320 PHE 0.020 0.002 PHE G 209 TYR 0.020 0.002 TYR B 277 ARG 0.007 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 260 GLU cc_start: 0.7151 (tp30) cc_final: 0.6814 (tp30) REVERT: E 312 LYS cc_start: 0.8532 (mttt) cc_final: 0.7976 (mttm) REVERT: C 312 LYS cc_start: 0.8351 (mttt) cc_final: 0.8121 (mmtt) REVERT: B 312 LYS cc_start: 0.8514 (mttt) cc_final: 0.8250 (mmtt) REVERT: D 306 GLN cc_start: 0.7641 (tt0) cc_final: 0.7266 (tt0) REVERT: D 312 LYS cc_start: 0.8534 (mttt) cc_final: 0.8165 (mttm) REVERT: F 312 LYS cc_start: 0.8580 (mttt) cc_final: 0.7946 (mmtt) REVERT: G 179 PHE cc_start: 0.8251 (p90) cc_final: 0.7959 (p90) REVERT: G 312 LYS cc_start: 0.8615 (mttt) cc_final: 0.8211 (mttm) outliers start: 3 outliers final: 0 residues processed: 263 average time/residue: 0.2865 time to fit residues: 102.2177 Evaluate side-chains 195 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11823 Z= 0.239 Angle : 0.591 6.278 16093 Z= 0.308 Chirality : 0.044 0.147 1855 Planarity : 0.003 0.029 2079 Dihedral : 4.822 18.953 1666 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.18 % Allowed : 1.98 % Favored : 97.84 % 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: 0.02 (0.24), residues: 1288 helix: 2.35 (0.25), residues: 462 sheet: -1.68 (0.27), residues: 343 loop : -0.93 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 201 HIS 0.002 0.001 HIS A 265 PHE 0.011 0.001 PHE C 179 TYR 0.018 0.002 TYR G 277 ARG 0.005 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 257 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 219 SER cc_start: 0.8929 (p) cc_final: 0.8658 (m) REVERT: E 312 LYS cc_start: 0.8513 (mttt) cc_final: 0.8038 (mttm) REVERT: B 158 MET cc_start: 0.5718 (mpp) cc_final: 0.4517 (ttp) REVERT: B 312 LYS cc_start: 0.8582 (mttt) cc_final: 0.8297 (mmtt) REVERT: D 306 GLN cc_start: 0.7815 (tt0) cc_final: 0.7494 (tt0) REVERT: D 312 LYS cc_start: 0.8628 (mttt) cc_final: 0.8257 (mttm) REVERT: F 312 LYS cc_start: 0.8549 (mttt) cc_final: 0.8082 (mttt) REVERT: G 312 LYS cc_start: 0.8615 (mttt) cc_final: 0.8220 (mttm) outliers start: 2 outliers final: 0 residues processed: 257 average time/residue: 0.2550 time to fit residues: 90.6915 Evaluate side-chains 204 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 40.0000 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN A 270 GLN B 280 GLN D 280 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11823 Z= 0.230 Angle : 0.584 6.476 16093 Z= 0.304 Chirality : 0.044 0.179 1855 Planarity : 0.003 0.028 2079 Dihedral : 4.741 18.833 1666 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.05 (0.23), residues: 1288 helix: 2.39 (0.25), residues: 462 sheet: -1.55 (0.27), residues: 343 loop : -1.04 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 201 HIS 0.004 0.001 HIS G 265 PHE 0.011 0.001 PHE C 179 TYR 0.023 0.002 TYR D 245 ARG 0.004 0.001 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 219 SER cc_start: 0.8933 (p) cc_final: 0.8641 (m) REVERT: E 312 LYS cc_start: 0.8559 (mttt) cc_final: 0.8098 (mttm) REVERT: C 158 MET cc_start: 0.5343 (mpp) cc_final: 0.4480 (ptp) REVERT: B 158 MET cc_start: 0.5436 (mpp) cc_final: 0.4455 (ttp) REVERT: B 312 LYS cc_start: 0.8575 (mttt) cc_final: 0.8330 (mmtt) REVERT: B 333 MET cc_start: 0.7201 (mmm) cc_final: 0.6931 (mmm) REVERT: D 306 GLN cc_start: 0.7943 (tt0) cc_final: 0.7694 (tt0) REVERT: D 312 LYS cc_start: 0.8575 (mttt) cc_final: 0.8264 (mttm) REVERT: F 312 LYS cc_start: 0.8603 (mttt) cc_final: 0.8179 (mmtt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2432 time to fit residues: 86.0809 Evaluate side-chains 210 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 92 optimal weight: 30.0000 chunk 90 optimal weight: 40.0000 chunk 68 optimal weight: 40.0000 chunk 91 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 320 HIS ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 11823 Z= 0.452 Angle : 0.741 7.598 16093 Z= 0.388 Chirality : 0.048 0.158 1855 Planarity : 0.004 0.049 2079 Dihedral : 5.310 20.098 1666 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -0.76 (0.23), residues: 1288 helix: 1.26 (0.23), residues: 518 sheet: -1.92 (0.29), residues: 315 loop : -1.40 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 299 HIS 0.003 0.001 HIS D 320 PHE 0.018 0.002 PHE A 281 TYR 0.027 0.003 TYR B 277 ARG 0.005 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 312 LYS cc_start: 0.8526 (mttt) cc_final: 0.8241 (mttm) REVERT: C 158 MET cc_start: 0.5456 (mpp) cc_final: 0.4607 (ptp) REVERT: A 199 ILE cc_start: 0.8742 (mm) cc_final: 0.8301 (mm) REVERT: B 219 SER cc_start: 0.9079 (p) cc_final: 0.8842 (m) REVERT: B 312 LYS cc_start: 0.8599 (mttt) cc_final: 0.8196 (mttm) REVERT: D 312 LYS cc_start: 0.8581 (mttt) cc_final: 0.8344 (mttm) REVERT: F 158 MET cc_start: 0.6030 (mtp) cc_final: 0.5173 (ttm) REVERT: F 179 PHE cc_start: 0.8685 (p90) cc_final: 0.8465 (p90) REVERT: F 228 ASN cc_start: 0.8431 (m-40) cc_final: 0.7962 (m-40) REVERT: F 312 LYS cc_start: 0.8634 (mttt) cc_final: 0.8308 (mmtt) REVERT: G 260 GLU cc_start: 0.8099 (pp20) cc_final: 0.7661 (pp20) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2498 time to fit residues: 85.0323 Evaluate side-chains 197 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 29 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 40.0000 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 228 ASN D 280 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN G 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11823 Z= 0.180 Angle : 0.563 6.472 16093 Z= 0.295 Chirality : 0.043 0.162 1855 Planarity : 0.003 0.034 2079 Dihedral : 4.802 19.563 1666 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1288 helix: 2.27 (0.24), residues: 462 sheet: -1.76 (0.26), residues: 357 loop : -0.99 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 302 HIS 0.001 0.000 HIS B 320 PHE 0.016 0.001 PHE D 168 TYR 0.038 0.002 TYR B 245 ARG 0.009 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 312 LYS cc_start: 0.8491 (mttt) cc_final: 0.8065 (mttm) REVERT: C 158 MET cc_start: 0.5206 (mpp) cc_final: 0.4809 (ptp) REVERT: B 158 MET cc_start: 0.5520 (mpp) cc_final: 0.4664 (ptp) REVERT: B 219 SER cc_start: 0.9090 (p) cc_final: 0.8752 (m) REVERT: B 312 LYS cc_start: 0.8626 (mttt) cc_final: 0.8147 (mmtt) REVERT: D 306 GLN cc_start: 0.7966 (tt0) cc_final: 0.7683 (tt0) REVERT: D 312 LYS cc_start: 0.8578 (mttt) cc_final: 0.8269 (mttm) REVERT: F 158 MET cc_start: 0.5923 (mtp) cc_final: 0.5295 (ttm) REVERT: F 312 LYS cc_start: 0.8656 (mttt) cc_final: 0.8198 (mmtt) REVERT: G 158 MET cc_start: 0.5830 (mpp) cc_final: 0.4360 (ttt) REVERT: G 260 GLU cc_start: 0.7972 (pp20) cc_final: 0.7553 (pp20) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2564 time to fit residues: 91.9703 Evaluate side-chains 199 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 ASN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN F 280 GLN G 280 GLN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11823 Z= 0.196 Angle : 0.568 6.098 16093 Z= 0.298 Chirality : 0.043 0.162 1855 Planarity : 0.003 0.032 2079 Dihedral : 4.701 19.042 1666 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -0.00 (0.23), residues: 1288 helix: 2.41 (0.25), residues: 462 sheet: -1.57 (0.30), residues: 273 loop : -1.26 (0.22), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.001 0.001 HIS A 265 PHE 0.013 0.002 PHE E 179 TYR 0.028 0.002 TYR B 245 ARG 0.004 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 312 LYS cc_start: 0.8442 (mttt) cc_final: 0.8081 (mttm) REVERT: C 158 MET cc_start: 0.5080 (mpp) cc_final: 0.4836 (ptp) REVERT: A 158 MET cc_start: 0.5714 (mtm) cc_final: 0.5247 (ttm) REVERT: B 158 MET cc_start: 0.5512 (mpp) cc_final: 0.5061 (ptp) REVERT: B 219 SER cc_start: 0.9095 (p) cc_final: 0.8738 (m) REVERT: B 312 LYS cc_start: 0.8618 (mttt) cc_final: 0.8142 (mmtt) REVERT: D 312 LYS cc_start: 0.8528 (mttt) cc_final: 0.8226 (mttm) REVERT: F 158 MET cc_start: 0.5887 (mtp) cc_final: 0.5273 (ttm) REVERT: F 312 LYS cc_start: 0.8671 (mttt) cc_final: 0.8269 (mmtt) REVERT: G 158 MET cc_start: 0.5604 (mpp) cc_final: 0.4729 (ptp) REVERT: G 198 GLU cc_start: 0.7534 (pp20) cc_final: 0.7292 (pp20) REVERT: G 260 GLU cc_start: 0.8035 (pp20) cc_final: 0.7546 (pp20) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2362 time to fit residues: 81.9500 Evaluate side-chains 209 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9980 chunk 89 optimal weight: 40.0000 chunk 69 optimal weight: 40.0000 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN F 280 GLN G 280 GLN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11823 Z= 0.274 Angle : 0.624 7.217 16093 Z= 0.326 Chirality : 0.045 0.162 1855 Planarity : 0.003 0.034 2079 Dihedral : 4.882 19.323 1666 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.09 (0.23), residues: 1288 helix: 2.37 (0.24), residues: 462 sheet: -1.60 (0.26), residues: 357 loop : -1.22 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 302 HIS 0.002 0.001 HIS B 320 PHE 0.015 0.002 PHE B 168 TYR 0.029 0.002 TYR B 245 ARG 0.003 0.001 ARG C 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 312 LYS cc_start: 0.8499 (mttt) cc_final: 0.8155 (mmtt) REVERT: C 158 MET cc_start: 0.4958 (mpp) cc_final: 0.4719 (ptp) REVERT: A 158 MET cc_start: 0.5503 (mtm) cc_final: 0.5085 (ttm) REVERT: B 158 MET cc_start: 0.5540 (mpp) cc_final: 0.5078 (ptp) REVERT: B 219 SER cc_start: 0.9124 (p) cc_final: 0.8764 (m) REVERT: B 312 LYS cc_start: 0.8585 (mttt) cc_final: 0.8182 (mmtt) REVERT: D 312 LYS cc_start: 0.8584 (mttt) cc_final: 0.8310 (mttm) REVERT: F 158 MET cc_start: 0.6016 (mtp) cc_final: 0.5330 (ttm) REVERT: F 312 LYS cc_start: 0.8618 (mttt) cc_final: 0.8324 (mmtt) REVERT: G 158 MET cc_start: 0.5509 (mpp) cc_final: 0.4723 (ptp) REVERT: G 198 GLU cc_start: 0.7804 (pp20) cc_final: 0.7418 (pp20) REVERT: G 260 GLU cc_start: 0.8083 (pp20) cc_final: 0.7585 (pp20) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2332 time to fit residues: 77.7857 Evaluate side-chains 205 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 112 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN F 280 GLN G 280 GLN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076687 restraints weight = 33131.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078267 restraints weight = 19912.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079307 restraints weight = 14301.943| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11823 Z= 0.312 Angle : 0.657 7.030 16093 Z= 0.345 Chirality : 0.046 0.168 1855 Planarity : 0.003 0.034 2079 Dihedral : 5.035 19.533 1666 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -0.18 (0.23), residues: 1288 helix: 2.27 (0.24), residues: 462 sheet: -1.40 (0.27), residues: 343 loop : -1.49 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 302 HIS 0.002 0.001 HIS G 265 PHE 0.016 0.002 PHE E 168 TYR 0.029 0.002 TYR B 245 ARG 0.003 0.001 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.58 seconds wall clock time: 44 minutes 14.49 seconds (2654.49 seconds total)