Starting phenix.real_space_refine on Fri Dec 15 20:07:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb0_24391/12_2023/7rb0_24391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb0_24391/12_2023/7rb0_24391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb0_24391/12_2023/7rb0_24391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb0_24391/12_2023/7rb0_24391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb0_24391/12_2023/7rb0_24391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb0_24391/12_2023/7rb0_24391.pdb" } resolution = 2.98 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16320 atoms to isotropic. 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 66 5.16 5 C 10512 2.51 5 N 2652 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 16": "OD1" <-> "OD2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 296": "OD1" <-> "OD2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F ASP 128": "OD1" <-> "OD2" Residue "F PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 301": "OD1" <-> "OD2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "E" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "F" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "A" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "B" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "C" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Time building chain proxies: 16.14, per 1000 atoms: 0.99 Number of scatterers: 16350 At special positions: 0 Unit cell: (108.861, 106.368, 125.481, 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 66 16.00 O 3120 8.00 N 2652 7.00 C 10512 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: 5.89 Conformation dependent library (CDL) restraints added in 5.7 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 36 sheets defined 26.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.862A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'E' and resid 1 through 12 Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.854A pdb=" N ILE E 235 " --> pdb=" O ALA E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 1 through 12 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.603A pdb=" N ILE F 235 " --> pdb=" O ALA F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.805A pdb=" N ILE A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'B' and resid 1 through 12 Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.525A pdb=" N PHE B 203 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.647A pdb=" N ILE B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.984A pdb=" N THR C 105 " --> pdb=" O CYS C 102 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP C 106 " --> pdb=" O SER C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 106' Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.507A pdb=" N ILE C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 298 through 309 Processing sheet with id=AA1, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.566A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 79 through 80 removed outlier: 6.967A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'D' and resid 264 through 266 removed outlier: 5.198A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.599A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.550A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.029A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AB1, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AB2, first strand: chain 'E' and resid 264 through 266 removed outlier: 3.886A pdb=" N GLU E 264 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 281 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 315 through 322 removed outlier: 6.126A pdb=" N LYS E 334 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 25 through 26 removed outlier: 6.541A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.063A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AB7, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AB8, first strand: chain 'F' and resid 264 through 266 removed outlier: 3.920A pdb=" N GLU F 264 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR F 281 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 322 removed outlier: 6.224A pdb=" N LYS F 334 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.551A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AC3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AC4, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AC5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.761A pdb=" N GLU A 264 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 281 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 315 through 322 removed outlier: 6.545A pdb=" N LYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 24 through 26 removed outlier: 6.543A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.067A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD1, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD2, first strand: chain 'B' and resid 264 through 266 removed outlier: 3.784A pdb=" N GLU B 264 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 281 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.645A pdb=" N LYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.542A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AD6, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AD7, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AD8, first strand: chain 'C' and resid 264 through 266 removed outlier: 3.927A pdb=" N GLU C 264 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 281 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 315 through 322 removed outlier: 6.234A pdb=" N LYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 6.38 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: 5054 1.33 - 1.45: 2602 1.45 - 1.57: 8940 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 16698 Sorted by residual: bond pdb=" CA LEU B 75 " pdb=" C LEU B 75 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.41e-02 5.03e+03 1.10e+01 bond pdb=" CA LEU C 75 " pdb=" C LEU C 75 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.80e-02 3.09e+03 6.54e+00 bond pdb=" CA LEU F 75 " pdb=" C LEU F 75 " ideal model delta sigma weight residual 1.523 1.478 0.046 1.80e-02 3.09e+03 6.47e+00 bond pdb=" CB VAL D 24 " pdb=" CG2 VAL D 24 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB VAL E 24 " pdb=" CG2 VAL E 24 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 16693 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.69: 309 105.69 - 112.76: 9111 112.76 - 119.84: 5212 119.84 - 126.91: 7895 126.91 - 133.99: 165 Bond angle restraints: 22692 Sorted by residual: angle pdb=" N TYR D 342 " pdb=" CA TYR D 342 " pdb=" C TYR D 342 " ideal model delta sigma weight residual 108.22 112.42 -4.20 9.00e-01 1.23e+00 2.18e+01 angle pdb=" CA LEU C 248 " pdb=" CB LEU C 248 " pdb=" CG LEU C 248 " ideal model delta sigma weight residual 116.30 127.73 -11.43 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA LEU F 248 " pdb=" CB LEU F 248 " pdb=" CG LEU F 248 " ideal model delta sigma weight residual 116.30 127.70 -11.40 3.50e+00 8.16e-02 1.06e+01 angle pdb=" N VAL C 101 " pdb=" CA VAL C 101 " pdb=" C VAL C 101 " ideal model delta sigma weight residual 111.48 108.58 2.90 9.40e-01 1.13e+00 9.50e+00 angle pdb=" CA TYR D 342 " pdb=" CB TYR D 342 " pdb=" CG TYR D 342 " ideal model delta sigma weight residual 113.90 119.41 -5.51 1.80e+00 3.09e-01 9.36e+00 ... (remaining 22687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 9073 17.05 - 34.09: 748 34.09 - 51.14: 98 51.14 - 68.18: 29 68.18 - 85.23: 18 Dihedral angle restraints: 9966 sinusoidal: 3900 harmonic: 6066 Sorted by residual: dihedral pdb=" CA LEU A 297 " pdb=" C LEU A 297 " pdb=" N LEU A 298 " pdb=" CA LEU A 298 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU C 297 " pdb=" C LEU C 297 " pdb=" N LEU C 298 " pdb=" CA LEU C 298 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU B 297 " pdb=" C LEU B 297 " pdb=" N LEU B 298 " pdb=" CA LEU B 298 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 9963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1566 0.044 - 0.088: 794 0.088 - 0.132: 230 0.132 - 0.176: 29 0.176 - 0.220: 3 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CG LEU F 248 " pdb=" CB LEU F 248 " pdb=" CD1 LEU F 248 " pdb=" CD2 LEU F 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEU C 248 " pdb=" CB LEU C 248 " pdb=" CD1 LEU C 248 " pdb=" CD2 LEU C 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE D 252 " pdb=" CA ILE D 252 " pdb=" CG1 ILE D 252 " pdb=" CG2 ILE D 252 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 2619 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 134 " 0.009 2.00e-02 2.50e+03 1.50e-02 3.91e+00 pdb=" CG PHE E 134 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE E 134 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 134 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE E 134 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 134 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 134 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 179 " 0.015 2.00e-02 2.50e+03 1.29e-02 3.31e+00 pdb=" CG TYR A 179 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 179 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 179 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 179 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 179 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 179 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 134 " -0.012 2.00e-02 2.50e+03 1.36e-02 3.23e+00 pdb=" CG PHE A 134 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 134 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 134 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 134 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 134 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 134 " 0.000 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 408 2.67 - 3.23: 16567 3.23 - 3.79: 25738 3.79 - 4.34: 36575 4.34 - 4.90: 59373 Nonbonded interactions: 138661 Sorted by model distance: nonbonded pdb=" OD2 ASP C 212 " pdb=" OH TYR C 225 " model vdw 2.115 2.440 nonbonded pdb=" OG1 THR F 98 " pdb=" OG1 THR F 105 " model vdw 2.140 2.440 nonbonded pdb=" OD2 ASP F 212 " pdb=" OH TYR F 225 " model vdw 2.142 2.440 nonbonded pdb=" OD2 ASP E 212 " pdb=" OH TYR E 225 " model vdw 2.149 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" OH TYR B 225 " model vdw 2.152 2.440 ... (remaining 138656 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 -1 through 35 or resid 37 through 345)) selection = (chain 'B' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'C' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'D' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'E' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'F' and (resid -1 through 35 or resid 37 through 345)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.010 Extract box with map and model: 4.630 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 53.780 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.009 0.055 16698 Z= 0.619 Angle : 0.762 11.430 22692 Z= 0.422 Chirality : 0.052 0.220 2622 Planarity : 0.004 0.040 2922 Dihedral : 13.468 85.227 6054 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.42 (0.18), residues: 2076 helix: -1.13 (0.20), residues: 516 sheet: -0.81 (0.28), residues: 354 loop : -0.83 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 332 HIS 0.006 0.001 HIS D 249 PHE 0.033 0.003 PHE E 134 TYR 0.031 0.003 TYR A 179 ARG 0.009 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.826 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 1.0545 time to fit residues: 368.3639 Evaluate side-chains 238 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 185 optimal weight: 20.0000 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 ASN E 82 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 242 HIS ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 242 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16698 Z= 0.167 Angle : 0.578 10.103 22692 Z= 0.305 Chirality : 0.046 0.183 2622 Planarity : 0.004 0.047 2922 Dihedral : 4.944 20.321 2208 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.64 % Allowed : 11.40 % Favored : 86.95 % 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: -0.88 (0.18), residues: 2076 helix: -0.14 (0.23), residues: 528 sheet: -0.36 (0.29), residues: 354 loop : -0.81 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 332 HIS 0.004 0.001 HIS E 337 PHE 0.015 0.002 PHE E 134 TYR 0.018 0.001 TYR C 342 ARG 0.007 0.001 ARG F 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 311 time to evaluate : 2.141 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 6 residues processed: 323 average time/residue: 1.0841 time to fit residues: 395.8811 Evaluate side-chains 256 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 1.937 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.2435 time to fit residues: 4.3626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 chunk 185 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 GLN D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 163 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 163 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16698 Z= 0.241 Angle : 0.582 8.433 22692 Z= 0.309 Chirality : 0.047 0.242 2622 Planarity : 0.004 0.051 2922 Dihedral : 4.813 19.744 2208 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.03 % Allowed : 14.80 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2076 helix: 0.03 (0.23), residues: 528 sheet: -0.17 (0.29), residues: 354 loop : -0.78 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 332 HIS 0.004 0.001 HIS E 337 PHE 0.018 0.002 PHE E 134 TYR 0.017 0.001 TYR C 342 ARG 0.007 0.001 ARG F 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 278 time to evaluate : 2.004 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 293 average time/residue: 1.0276 time to fit residues: 342.7807 Evaluate side-chains 266 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 1.855 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 4 residues processed: 10 average time/residue: 0.2289 time to fit residues: 6.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN D 152 GLN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16698 Z= 0.292 Angle : 0.598 9.561 22692 Z= 0.317 Chirality : 0.047 0.230 2622 Planarity : 0.004 0.053 2922 Dihedral : 4.817 19.932 2208 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.96 % Allowed : 15.41 % Favored : 81.63 % 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: -0.71 (0.18), residues: 2076 helix: 0.05 (0.23), residues: 528 sheet: -0.07 (0.29), residues: 354 loop : -0.80 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 332 HIS 0.003 0.001 HIS E 337 PHE 0.018 0.002 PHE E 134 TYR 0.013 0.002 TYR D 342 ARG 0.009 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 258 time to evaluate : 1.970 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 22 residues processed: 286 average time/residue: 1.0255 time to fit residues: 333.2884 Evaluate side-chains 275 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 8 residues processed: 14 average time/residue: 0.3034 time to fit residues: 8.6232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN D 163 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16698 Z= 0.152 Angle : 0.578 12.105 22692 Z= 0.301 Chirality : 0.046 0.205 2622 Planarity : 0.004 0.059 2922 Dihedral : 4.568 18.249 2208 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.41 % Allowed : 17.54 % Favored : 80.04 % 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: -0.54 (0.18), residues: 2076 helix: 0.21 (0.24), residues: 528 sheet: 0.16 (0.29), residues: 354 loop : -0.76 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 332 HIS 0.003 0.001 HIS E 337 PHE 0.018 0.002 PHE E 134 TYR 0.009 0.001 TYR B 32 ARG 0.007 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 296 time to evaluate : 1.821 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 17 residues processed: 321 average time/residue: 1.0425 time to fit residues: 381.0831 Evaluate side-chains 284 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 267 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 8 average time/residue: 0.2087 time to fit residues: 5.3140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 197 optimal weight: 0.0970 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN E 163 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN C 136 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16698 Z= 0.179 Angle : 0.580 10.385 22692 Z= 0.301 Chirality : 0.045 0.163 2622 Planarity : 0.004 0.052 2922 Dihedral : 4.470 17.485 2208 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.81 % Allowed : 19.68 % Favored : 78.51 % 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: -0.43 (0.18), residues: 2076 helix: 0.29 (0.24), residues: 528 sheet: 0.34 (0.29), residues: 354 loop : -0.71 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 332 HIS 0.003 0.001 HIS E 337 PHE 0.030 0.002 PHE C 134 TYR 0.011 0.001 TYR D 342 ARG 0.005 0.000 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 2.285 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 305 average time/residue: 1.0712 time to fit residues: 372.6832 Evaluate side-chains 277 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 264 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.1948 time to fit residues: 4.5880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 0.2980 chunk 144 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN D 208 GLN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16698 Z= 0.303 Angle : 0.620 10.155 22692 Z= 0.326 Chirality : 0.047 0.203 2622 Planarity : 0.004 0.052 2922 Dihedral : 4.672 18.704 2208 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.08 % Allowed : 20.29 % Favored : 77.63 % 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: -0.50 (0.18), residues: 2076 helix: 0.15 (0.24), residues: 528 sheet: 0.32 (0.29), residues: 354 loop : -0.73 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 332 HIS 0.005 0.001 HIS A 249 PHE 0.028 0.002 PHE B 134 TYR 0.013 0.002 TYR D 342 ARG 0.006 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 266 time to evaluate : 1.714 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 287 average time/residue: 1.0206 time to fit residues: 334.8659 Evaluate side-chains 272 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 7 average time/residue: 0.2439 time to fit residues: 5.3493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16698 Z= 0.194 Angle : 0.597 10.925 22692 Z= 0.311 Chirality : 0.046 0.167 2622 Planarity : 0.004 0.054 2922 Dihedral : 4.498 17.244 2208 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.54 % Allowed : 21.60 % Favored : 76.86 % 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: -0.45 (0.19), residues: 2076 helix: 0.25 (0.24), residues: 528 sheet: 0.43 (0.29), residues: 354 loop : -0.75 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 332 HIS 0.003 0.001 HIS E 337 PHE 0.022 0.002 PHE E 134 TYR 0.013 0.001 TYR E 342 ARG 0.006 0.001 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 1.696 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 299 average time/residue: 1.0543 time to fit residues: 357.5401 Evaluate side-chains 273 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 256 time to evaluate : 1.993 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.4803 time to fit residues: 6.4868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 0.0010 chunk 120 optimal weight: 8.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16698 Z= 0.169 Angle : 0.592 11.409 22692 Z= 0.308 Chirality : 0.045 0.169 2622 Planarity : 0.004 0.053 2922 Dihedral : 4.391 16.954 2208 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.43 % Allowed : 22.48 % Favored : 76.10 % 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: -0.36 (0.19), residues: 2076 helix: 0.25 (0.24), residues: 534 sheet: 0.54 (0.30), residues: 354 loop : -0.68 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 332 HIS 0.008 0.001 HIS A 249 PHE 0.021 0.002 PHE B 221 TYR 0.014 0.001 TYR A 342 ARG 0.008 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 2.014 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 294 average time/residue: 0.9923 time to fit residues: 333.2339 Evaluate side-chains 273 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 256 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.4132 time to fit residues: 5.9823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 10.0000 chunk 118 optimal weight: 0.0040 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16698 Z= 0.198 Angle : 0.612 11.921 22692 Z= 0.318 Chirality : 0.046 0.167 2622 Planarity : 0.004 0.053 2922 Dihedral : 4.426 16.931 2208 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.10 % Allowed : 23.30 % Favored : 75.60 % 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: -0.34 (0.19), residues: 2076 helix: 0.22 (0.24), residues: 534 sheet: 0.55 (0.30), residues: 354 loop : -0.64 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 332 HIS 0.006 0.001 HIS A 249 PHE 0.028 0.002 PHE E 194 TYR 0.015 0.001 TYR B 342 ARG 0.008 0.001 ARG A 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 265 time to evaluate : 1.804 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 284 average time/residue: 1.0468 time to fit residues: 339.5379 Evaluate side-chains 269 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 256 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 2.4937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 0.0070 chunk 162 optimal weight: 0.3980 chunk 67 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 18 GLN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN B 28 ASN B 163 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.173934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111962 restraints weight = 40644.946| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.95 r_work: 0.3209 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16698 Z= 0.180 Angle : 0.611 11.700 22692 Z= 0.316 Chirality : 0.046 0.166 2622 Planarity : 0.005 0.072 2922 Dihedral : 4.403 16.727 2208 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.10 % Allowed : 23.36 % Favored : 75.55 % 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: -0.31 (0.19), residues: 2076 helix: 0.22 (0.24), residues: 534 sheet: 0.61 (0.30), residues: 354 loop : -0.63 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 332 HIS 0.005 0.001 HIS C 249 PHE 0.021 0.002 PHE A 134 TYR 0.016 0.001 TYR B 342 ARG 0.014 0.001 ARG A 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6219.52 seconds wall clock time: 112 minutes 0.01 seconds (6720.01 seconds total)