Starting phenix.real_space_refine on Sat Mar 16 23:45:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/03_2024/7ssp_25412.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/03_2024/7ssp_25412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/03_2024/7ssp_25412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/03_2024/7ssp_25412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/03_2024/7ssp_25412.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/03_2024/7ssp_25412.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 5175 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 69 5.16 5 C 6909 2.51 5 N 1912 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ASP 268": "OD1" <-> "OD2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G ASP 160": "OD1" <-> "OD2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "G TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H ASP 160": "OD1" <-> "OD2" Residue "H GLU 166": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10930 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1298 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.18, per 1000 atoms: 0.57 Number of scatterers: 10930 At special positions: 0 Unit cell: (98.04, 108.3, 96.9, 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 69 16.00 O 2040 8.00 N 1912 7.00 C 6909 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: 4.33 Conformation dependent library (CDL) restraints added in 2.0 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.594A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 117 through 125 removed outlier: 4.037A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 199 through 207 removed outlier: 3.878A pdb=" N ALA A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 4.148A pdb=" N TYR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.684A pdb=" N THR A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 244 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 282 removed outlier: 4.668A pdb=" N ASP A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.994A pdb=" N ARG B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 4.381A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 144 through 169 removed outlier: 4.057A pdb=" N LEU B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 199 through 207 removed outlier: 3.871A pdb=" N ALA B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.694A pdb=" N THR B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 244 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 282 removed outlier: 4.908A pdb=" N ASP B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.893A pdb=" N ARG C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 142 through 166 removed outlier: 4.083A pdb=" N ILE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 199 through 207 removed outlier: 3.879A pdb=" N ALA C 203 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.636A pdb=" N THR C 242 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 244 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 282 removed outlier: 4.824A pdb=" N ASP C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.832A pdb=" N ARG D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.264A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 166 removed outlier: 4.326A pdb=" N ILE D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 199 through 207 removed outlier: 3.854A pdb=" N ALA D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 230 removed outlier: 4.131A pdb=" N TYR D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.678A pdb=" N THR D 242 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG D 244 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 282 removed outlier: 4.832A pdb=" N ASP D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 74 removed outlier: 3.728A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 105 removed outlier: 3.930A pdb=" N ILE E 83 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 130 through 155 removed outlier: 3.971A pdb=" N ALA E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 197 through 205 Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.643A pdb=" N SER E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 215 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 74 removed outlier: 4.456A pdb=" N ARG F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 104 removed outlier: 3.633A pdb=" N ILE F 83 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 85 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.520A pdb=" N ALA F 124 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 155 removed outlier: 3.825A pdb=" N VAL F 139 " --> pdb=" O MET F 135 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 195 through 217 removed outlier: 3.564A pdb=" N LEU F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY F 206 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 211 " --> pdb=" O CYS F 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 removed outlier: 3.688A pdb=" N ILE G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 104 removed outlier: 3.718A pdb=" N ILE G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 104 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 136 through 155 removed outlier: 3.626A pdb=" N THR G 155 " --> pdb=" O ASN G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 180 Processing helix chain 'G' and resid 195 through 217 removed outlier: 3.586A pdb=" N LEU G 199 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY G 206 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 211 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 74 removed outlier: 3.818A pdb=" N ILE H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 104 removed outlier: 3.756A pdb=" N ILE H 83 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 104 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 137 through 155 removed outlier: 3.614A pdb=" N THR H 155 " --> pdb=" O ASN H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 180 Processing helix chain 'H' and resid 195 through 217 removed outlier: 3.801A pdb=" N LEU H 199 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS H 200 " --> pdb=" O TYR H 196 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY H 206 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE H 211 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU H 215 " --> pdb=" O ILE H 211 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) 667 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: 2.60 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3676 1.34 - 1.46: 2044 1.46 - 1.58: 5292 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 11138 Sorted by residual: bond pdb=" CB VAL G 55 " pdb=" CG2 VAL G 55 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" C ILE C 194 " pdb=" N PRO C 195 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.30e-02 5.92e+03 1.39e+00 bond pdb=" CA LYS G 131 " pdb=" C LYS G 131 " ideal model delta sigma weight residual 1.523 1.504 0.020 1.80e-02 3.09e+03 1.18e+00 bond pdb=" CB VAL H 55 " pdb=" CG2 VAL H 55 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" N GLN B 172 " pdb=" CA GLN B 172 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.15e-02 7.56e+03 8.40e-01 ... (remaining 11133 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.76: 302 106.76 - 113.61: 6242 113.61 - 120.46: 4564 120.46 - 127.31: 3818 127.31 - 134.16: 152 Bond angle restraints: 15078 Sorted by residual: angle pdb=" N ALA E 124 " pdb=" CA ALA E 124 " pdb=" C ALA E 124 " ideal model delta sigma weight residual 114.56 108.60 5.96 1.27e+00 6.20e-01 2.20e+01 angle pdb=" N ALA G 124 " pdb=" CA ALA G 124 " pdb=" C ALA G 124 " ideal model delta sigma weight residual 114.56 108.66 5.90 1.27e+00 6.20e-01 2.16e+01 angle pdb=" N ALA F 124 " pdb=" CA ALA F 124 " pdb=" C ALA F 124 " ideal model delta sigma weight residual 114.56 108.73 5.83 1.27e+00 6.20e-01 2.11e+01 angle pdb=" N ALA H 124 " pdb=" CA ALA H 124 " pdb=" C ALA H 124 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.09e+01 angle pdb=" N VAL H 117 " pdb=" CA VAL H 117 " pdb=" C VAL H 117 " ideal model delta sigma weight residual 113.42 108.52 4.90 1.17e+00 7.31e-01 1.76e+01 ... (remaining 15073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5958 17.79 - 35.58: 622 35.58 - 53.38: 116 53.38 - 71.17: 11 71.17 - 88.96: 11 Dihedral angle restraints: 6718 sinusoidal: 2702 harmonic: 4016 Sorted by residual: dihedral pdb=" CA GLU G 165 " pdb=" C GLU G 165 " pdb=" N GLU G 166 " pdb=" CA GLU G 166 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU H 165 " pdb=" C GLU H 165 " pdb=" N GLU H 166 " pdb=" CA GLU H 166 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLU F 165 " pdb=" C GLU F 165 " pdb=" N GLU F 166 " pdb=" CA GLU F 166 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1011 0.029 - 0.058: 494 0.058 - 0.087: 145 0.087 - 0.117: 40 0.117 - 0.146: 6 Chirality restraints: 1696 Sorted by residual: chirality pdb=" CA MET C 281 " pdb=" N MET C 281 " pdb=" C MET C 281 " pdb=" CB MET C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO G 81 " pdb=" N PRO G 81 " pdb=" C PRO G 81 " pdb=" CB PRO G 81 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1693 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 144 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C GLU A 144 " -0.038 2.00e-02 2.50e+03 pdb=" O GLU A 144 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 145 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 112 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 111 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 112 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.026 5.00e-02 4.00e+02 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2038 2.77 - 3.30: 10425 3.30 - 3.83: 16849 3.83 - 4.37: 18638 4.37 - 4.90: 32859 Nonbonded interactions: 80809 Sorted by model distance: nonbonded pdb=" OD2 ASP D 233 " pdb=" NH1 ARG D 244 " model vdw 2.232 2.520 nonbonded pdb=" OD2 ASP B 233 " pdb=" NH1 ARG B 244 " model vdw 2.236 2.520 nonbonded pdb=" OD2 ASP A 233 " pdb=" NH1 ARG A 244 " model vdw 2.310 2.520 nonbonded pdb=" O SER B 143 " pdb=" OG SER B 143 " model vdw 2.311 2.440 nonbonded pdb=" OD1 ASP D 233 " pdb=" NH1 ARG D 243 " model vdw 2.333 2.520 ... (remaining 80804 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' and (resid 93 through 127 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB )) or resid 142 through 284)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 45 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 217)) selection = (chain 'F' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) selection = (chain 'G' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) selection = (chain 'H' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) } 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 2.210 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.000 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.004 0.044 11138 Z= 0.232 Angle : 0.626 8.298 15078 Z= 0.370 Chirality : 0.037 0.146 1696 Planarity : 0.005 0.053 1940 Dihedral : 14.584 88.962 4102 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: -3.24 (0.20), residues: 1344 helix: -1.28 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -4.52 (0.25), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 115 HIS 0.006 0.001 HIS E 147 PHE 0.010 0.001 PHE C 110 TYR 0.011 0.001 TYR G 212 ARG 0.004 0.000 ARG F 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.215 Fit side-chains REVERT: A 226 ASP cc_start: 0.7551 (m-30) cc_final: 0.7260 (m-30) REVERT: A 266 PHE cc_start: 0.7627 (m-80) cc_final: 0.7421 (m-80) REVERT: B 163 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6987 (tt0) REVERT: B 202 ARG cc_start: 0.7747 (tmt-80) cc_final: 0.7399 (tpt90) REVERT: C 159 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7075 (ttm-80) REVERT: C 167 LEU cc_start: 0.8274 (tp) cc_final: 0.8051 (tt) REVERT: C 202 ARG cc_start: 0.7749 (tmt-80) cc_final: 0.7450 (tpt90) REVERT: C 226 ASP cc_start: 0.7462 (m-30) cc_final: 0.7138 (m-30) REVERT: C 281 MET cc_start: 0.6922 (tpp) cc_final: 0.6527 (mmp) REVERT: D 119 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5621 (tm-30) REVERT: D 226 ASP cc_start: 0.7512 (m-30) cc_final: 0.7253 (m-30) REVERT: D 266 PHE cc_start: 0.7658 (m-80) cc_final: 0.7437 (m-80) REVERT: D 281 MET cc_start: 0.6674 (mmm) cc_final: 0.6317 (mmp) REVERT: E 67 TYR cc_start: 0.8693 (m-10) cc_final: 0.7824 (m-10) REVERT: E 101 MET cc_start: 0.8400 (ttm) cc_final: 0.8057 (ttp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2893 time to fit residues: 102.1734 Evaluate side-chains 209 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN E 70 GLN E 147 HIS F 70 GLN F 147 HIS G 70 GLN G 147 HIS H 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11138 Z= 0.270 Angle : 0.636 8.895 15078 Z= 0.323 Chirality : 0.038 0.134 1696 Planarity : 0.005 0.066 1940 Dihedral : 4.266 20.735 1488 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.39 % Allowed : 12.62 % Favored : 85.99 % 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: -0.97 (0.23), residues: 1344 helix: 0.39 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -4.00 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 228 HIS 0.006 0.001 HIS D 114 PHE 0.014 0.002 PHE B 266 TYR 0.016 0.002 TYR B 230 ARG 0.005 0.001 ARG F 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 1.179 Fit side-chains REVERT: A 164 GLU cc_start: 0.7724 (tm-30) cc_final: 0.6907 (tt0) REVERT: A 208 MET cc_start: 0.7977 (ttm) cc_final: 0.7715 (mtt) REVERT: A 226 ASP cc_start: 0.7555 (m-30) cc_final: 0.7276 (m-30) REVERT: B 164 GLU cc_start: 0.7742 (tm-30) cc_final: 0.6974 (tt0) REVERT: B 202 ARG cc_start: 0.7633 (tmt-80) cc_final: 0.7390 (tpt90) REVERT: B 208 MET cc_start: 0.8066 (ttm) cc_final: 0.7792 (mtt) REVERT: B 226 ASP cc_start: 0.7795 (m-30) cc_final: 0.7539 (m-30) REVERT: C 208 MET cc_start: 0.8137 (ttm) cc_final: 0.7816 (mtt) REVERT: C 226 ASP cc_start: 0.7491 (m-30) cc_final: 0.7198 (m-30) REVERT: C 281 MET cc_start: 0.6828 (tpp) cc_final: 0.6495 (tpp) REVERT: D 208 MET cc_start: 0.8013 (ttm) cc_final: 0.7765 (mtt) REVERT: D 226 ASP cc_start: 0.7543 (m-30) cc_final: 0.7226 (m-30) REVERT: D 281 MET cc_start: 0.6850 (mmm) cc_final: 0.6548 (mmp) REVERT: F 208 ARG cc_start: 0.6866 (tmt170) cc_final: 0.5883 (ttp80) REVERT: G 208 ARG cc_start: 0.7206 (tmt170) cc_final: 0.5867 (ttp80) REVERT: H 208 ARG cc_start: 0.7324 (tmt170) cc_final: 0.6183 (ttp80) outliers start: 16 outliers final: 12 residues processed: 211 average time/residue: 0.2861 time to fit residues: 80.3880 Evaluate side-chains 200 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 0.0060 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 169 GLN B 275 ASN C 275 ASN D 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11138 Z= 0.159 Angle : 0.533 7.238 15078 Z= 0.271 Chirality : 0.036 0.203 1696 Planarity : 0.005 0.063 1940 Dihedral : 3.844 19.858 1488 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.04 % Allowed : 14.53 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1344 helix: 1.28 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -3.61 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 115 HIS 0.005 0.001 HIS H 147 PHE 0.008 0.001 PHE B 266 TYR 0.007 0.001 TYR B 230 ARG 0.004 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 114 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7137 (t-90) REVERT: A 164 GLU cc_start: 0.7682 (tm-30) cc_final: 0.6902 (tt0) REVERT: A 208 MET cc_start: 0.8019 (ttm) cc_final: 0.7816 (mtt) REVERT: B 164 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7014 (tt0) REVERT: B 208 MET cc_start: 0.8027 (ttm) cc_final: 0.7764 (mtt) REVERT: C 208 MET cc_start: 0.8066 (ttm) cc_final: 0.7799 (mtt) REVERT: C 226 ASP cc_start: 0.7369 (m-30) cc_final: 0.7125 (m-30) REVERT: D 119 GLU cc_start: 0.6344 (tm-30) cc_final: 0.6005 (tm-30) REVERT: D 123 GLU cc_start: 0.7039 (tt0) cc_final: 0.6604 (tm-30) REVERT: D 208 MET cc_start: 0.8065 (ttm) cc_final: 0.7829 (mtt) REVERT: D 278 ASN cc_start: 0.7196 (m-40) cc_final: 0.6877 (m-40) REVERT: D 281 MET cc_start: 0.6865 (mmm) cc_final: 0.6557 (mmp) REVERT: E 67 TYR cc_start: 0.8666 (m-10) cc_final: 0.7958 (m-10) REVERT: E 135 MET cc_start: 0.7780 (mmp) cc_final: 0.7377 (mmt) REVERT: F 208 ARG cc_start: 0.7050 (tmt170) cc_final: 0.5937 (ttp80) REVERT: G 67 TYR cc_start: 0.8711 (m-10) cc_final: 0.8086 (m-10) REVERT: G 208 ARG cc_start: 0.7000 (tmt170) cc_final: 0.5679 (ttp80) REVERT: H 67 TYR cc_start: 0.8712 (m-10) cc_final: 0.8055 (m-10) REVERT: H 208 ARG cc_start: 0.7213 (tmt170) cc_final: 0.6096 (ttp80) outliers start: 12 outliers final: 7 residues processed: 213 average time/residue: 0.2539 time to fit residues: 73.4391 Evaluate side-chains 192 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 275 ASN C 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11138 Z= 0.155 Angle : 0.522 8.655 15078 Z= 0.262 Chirality : 0.035 0.193 1696 Planarity : 0.005 0.058 1940 Dihedral : 3.670 19.472 1488 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.04 % Allowed : 16.71 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1344 helix: 1.61 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -3.35 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 115 HIS 0.005 0.001 HIS H 147 PHE 0.007 0.001 PHE B 266 TYR 0.015 0.001 TYR H 212 ARG 0.004 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 114 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7092 (t-90) REVERT: A 164 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6868 (tt0) REVERT: A 208 MET cc_start: 0.7911 (ttm) cc_final: 0.7703 (mtt) REVERT: B 164 GLU cc_start: 0.7693 (tm-30) cc_final: 0.6962 (tt0) REVERT: B 208 MET cc_start: 0.7942 (ttm) cc_final: 0.7718 (mtt) REVERT: C 208 MET cc_start: 0.8025 (ttm) cc_final: 0.7802 (mtt) REVERT: D 114 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.6094 (t-90) REVERT: D 123 GLU cc_start: 0.6854 (tt0) cc_final: 0.6566 (tm-30) REVERT: D 281 MET cc_start: 0.6879 (mmm) cc_final: 0.6599 (mmp) REVERT: E 67 TYR cc_start: 0.8655 (m-10) cc_final: 0.7996 (m-10) REVERT: E 135 MET cc_start: 0.7749 (mmp) cc_final: 0.7393 (mmt) REVERT: F 208 ARG cc_start: 0.7008 (tmt170) cc_final: 0.5853 (ttp80) REVERT: G 67 TYR cc_start: 0.8710 (m-10) cc_final: 0.8125 (m-10) REVERT: G 208 ARG cc_start: 0.7013 (tmt170) cc_final: 0.5651 (ttp80) REVERT: H 67 TYR cc_start: 0.8703 (m-10) cc_final: 0.8076 (m-10) REVERT: H 208 ARG cc_start: 0.7185 (tmt170) cc_final: 0.6097 (ttp80) outliers start: 12 outliers final: 8 residues processed: 190 average time/residue: 0.2437 time to fit residues: 63.0556 Evaluate side-chains 182 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain D residue 114 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 169 GLN C 275 ASN D 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11138 Z= 0.203 Angle : 0.557 8.921 15078 Z= 0.279 Chirality : 0.036 0.206 1696 Planarity : 0.004 0.051 1940 Dihedral : 3.753 19.406 1488 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.18 % Allowed : 16.28 % Favored : 81.55 % 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: 0.99 (0.25), residues: 1344 helix: 1.74 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -3.24 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 200 HIS 0.005 0.001 HIS H 147 PHE 0.007 0.001 PHE C 181 TYR 0.010 0.001 TYR C 230 ARG 0.004 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7634 (tm-30) cc_final: 0.6825 (tt0) REVERT: B 164 GLU cc_start: 0.7639 (tm-30) cc_final: 0.6874 (tt0) REVERT: C 196 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: D 114 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.5787 (t-90) REVERT: D 123 GLU cc_start: 0.6859 (tt0) cc_final: 0.6567 (tm-30) REVERT: D 281 MET cc_start: 0.6994 (mmm) cc_final: 0.6735 (mmp) REVERT: E 67 TYR cc_start: 0.8709 (m-10) cc_final: 0.8012 (m-10) REVERT: E 135 MET cc_start: 0.7732 (mmp) cc_final: 0.7416 (mmt) REVERT: F 208 ARG cc_start: 0.7038 (tmt170) cc_final: 0.5807 (ttp80) REVERT: G 168 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7589 (tt) REVERT: G 208 ARG cc_start: 0.7041 (tmt170) cc_final: 0.5652 (ttp80) REVERT: H 168 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7534 (tt) REVERT: H 208 ARG cc_start: 0.7223 (tmt170) cc_final: 0.6003 (ttp80) outliers start: 25 outliers final: 14 residues processed: 193 average time/residue: 0.2499 time to fit residues: 66.2136 Evaluate side-chains 191 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 114 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 GLN B 275 ASN C 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11138 Z= 0.165 Angle : 0.530 8.426 15078 Z= 0.267 Chirality : 0.036 0.212 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.632 19.132 1488 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.91 % Allowed : 16.88 % Favored : 81.20 % 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: 1.38 (0.25), residues: 1344 helix: 2.03 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -3.18 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 115 HIS 0.004 0.001 HIS H 147 PHE 0.008 0.001 PHE C 110 TYR 0.008 0.001 TYR B 230 ARG 0.006 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6836 (tt0) REVERT: B 159 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.6893 (ttm-80) REVERT: B 164 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6888 (tt0) REVERT: C 196 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: C 281 MET cc_start: 0.6807 (tpp) cc_final: 0.6542 (tpp) REVERT: D 114 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5648 (t-90) REVERT: D 281 MET cc_start: 0.6941 (mmm) cc_final: 0.6693 (mmp) REVERT: E 67 TYR cc_start: 0.8685 (m-10) cc_final: 0.8025 (m-10) REVERT: E 135 MET cc_start: 0.7731 (mmp) cc_final: 0.7392 (mmt) REVERT: F 208 ARG cc_start: 0.6982 (tmt170) cc_final: 0.5821 (ttp80) REVERT: G 208 ARG cc_start: 0.7027 (tmt170) cc_final: 0.5661 (ttp80) REVERT: H 208 ARG cc_start: 0.7248 (tmt170) cc_final: 0.5974 (ttp80) outliers start: 22 outliers final: 14 residues processed: 190 average time/residue: 0.2590 time to fit residues: 67.0193 Evaluate side-chains 182 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 114 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11138 Z= 0.152 Angle : 0.522 8.093 15078 Z= 0.262 Chirality : 0.035 0.221 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.527 19.475 1488 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.65 % Allowed : 17.15 % Favored : 81.20 % 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: 1.67 (0.25), residues: 1344 helix: 2.23 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -3.06 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 115 HIS 0.004 0.001 HIS H 147 PHE 0.010 0.001 PHE C 110 TYR 0.007 0.001 TYR B 230 ARG 0.005 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.129 Fit side-chains REVERT: A 159 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.6866 (ttm-80) REVERT: A 164 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6868 (tt0) REVERT: B 159 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6864 (ttm-80) REVERT: B 164 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6908 (tt0) REVERT: C 159 ARG cc_start: 0.7317 (ttm-80) cc_final: 0.6833 (ttm-80) REVERT: C 196 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: C 281 MET cc_start: 0.6785 (tpp) cc_final: 0.6522 (tpp) REVERT: D 114 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.5608 (t-90) REVERT: D 159 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6829 (ttm-80) REVERT: D 281 MET cc_start: 0.6939 (mmm) cc_final: 0.6693 (mmp) REVERT: E 67 TYR cc_start: 0.8667 (m-10) cc_final: 0.8053 (m-10) REVERT: E 135 MET cc_start: 0.7676 (mmp) cc_final: 0.7365 (mmt) REVERT: F 208 ARG cc_start: 0.6970 (tmt170) cc_final: 0.5809 (ttp80) REVERT: G 95 LYS cc_start: 0.8733 (tptp) cc_final: 0.8526 (tptp) REVERT: G 208 ARG cc_start: 0.7013 (tmt170) cc_final: 0.5666 (ttp80) REVERT: H 67 TYR cc_start: 0.8768 (m-10) cc_final: 0.8128 (m-10) REVERT: H 71 MET cc_start: 0.8267 (tpp) cc_final: 0.8062 (tpt) REVERT: H 208 ARG cc_start: 0.7206 (tmt170) cc_final: 0.5964 (ttp80) outliers start: 19 outliers final: 14 residues processed: 187 average time/residue: 0.2467 time to fit residues: 63.9055 Evaluate side-chains 185 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 114 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 HIS B 275 ASN C 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11138 Z= 0.150 Angle : 0.531 8.229 15078 Z= 0.265 Chirality : 0.035 0.221 1696 Planarity : 0.004 0.048 1940 Dihedral : 3.467 19.245 1488 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.09 % Allowed : 17.06 % Favored : 80.85 % 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: 1.97 (0.25), residues: 1344 helix: 2.43 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.92 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 115 HIS 0.004 0.001 HIS H 147 PHE 0.010 0.001 PHE C 110 TYR 0.007 0.001 TYR B 230 ARG 0.005 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6867 (tt0) REVERT: B 164 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6912 (tt0) REVERT: C 159 ARG cc_start: 0.7318 (ttm-80) cc_final: 0.6843 (ttm-80) REVERT: C 164 GLU cc_start: 0.7395 (tp30) cc_final: 0.6585 (tt0) REVERT: C 196 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: C 281 MET cc_start: 0.6776 (tpp) cc_final: 0.6522 (tpp) REVERT: D 114 HIS cc_start: 0.6216 (OUTLIER) cc_final: 0.5562 (t-90) REVERT: D 159 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6833 (ttm-80) REVERT: D 281 MET cc_start: 0.6950 (mmm) cc_final: 0.6695 (mmp) REVERT: E 67 TYR cc_start: 0.8684 (m-10) cc_final: 0.8042 (m-10) REVERT: E 71 MET cc_start: 0.8228 (tpp) cc_final: 0.7932 (tpt) REVERT: E 135 MET cc_start: 0.7752 (mmp) cc_final: 0.7442 (mmt) REVERT: F 208 ARG cc_start: 0.6958 (tmt170) cc_final: 0.5815 (ttp80) REVERT: G 208 ARG cc_start: 0.7013 (tmt170) cc_final: 0.5520 (ttp80) REVERT: H 71 MET cc_start: 0.8291 (tpp) cc_final: 0.8076 (tpt) REVERT: H 208 ARG cc_start: 0.7192 (tmt170) cc_final: 0.5957 (ttp80) outliers start: 24 outliers final: 18 residues processed: 185 average time/residue: 0.2402 time to fit residues: 61.9152 Evaluate side-chains 188 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 114 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN C 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11138 Z= 0.215 Angle : 0.571 8.165 15078 Z= 0.285 Chirality : 0.037 0.213 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.640 21.785 1488 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.26 % Allowed : 17.32 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.25), residues: 1344 helix: 2.34 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.87 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 200 HIS 0.004 0.001 HIS H 147 PHE 0.013 0.001 PHE C 110 TYR 0.015 0.001 TYR G 212 ARG 0.005 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7544 (tm-30) cc_final: 0.6861 (tt0) REVERT: B 164 GLU cc_start: 0.7625 (tm-30) cc_final: 0.6913 (tt0) REVERT: C 144 GLU cc_start: 0.5897 (mt-10) cc_final: 0.5604 (mp0) REVERT: C 196 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: C 281 MET cc_start: 0.6778 (tpp) cc_final: 0.6539 (tpp) REVERT: D 114 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.5785 (t-90) REVERT: D 281 MET cc_start: 0.6868 (mmm) cc_final: 0.6621 (mmp) REVERT: E 67 TYR cc_start: 0.8731 (m-10) cc_final: 0.8181 (m-10) REVERT: E 135 MET cc_start: 0.7719 (mmp) cc_final: 0.7404 (mmt) REVERT: F 208 ARG cc_start: 0.7038 (tmt170) cc_final: 0.5743 (ttp80) REVERT: G 208 ARG cc_start: 0.6991 (tmt170) cc_final: 0.5599 (ttp80) REVERT: H 208 ARG cc_start: 0.7204 (tmt170) cc_final: 0.5978 (ttp80) outliers start: 26 outliers final: 18 residues processed: 191 average time/residue: 0.2656 time to fit residues: 69.8269 Evaluate side-chains 186 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 114 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 275 ASN C 275 ASN D 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11138 Z= 0.149 Angle : 0.545 8.921 15078 Z= 0.271 Chirality : 0.035 0.219 1696 Planarity : 0.004 0.050 1940 Dihedral : 3.489 19.702 1488 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.22 % Allowed : 17.84 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.25), residues: 1344 helix: 2.56 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.74 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 115 HIS 0.004 0.001 HIS H 147 PHE 0.017 0.001 PHE C 110 TYR 0.006 0.001 TYR B 230 ARG 0.007 0.000 ARG D 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7508 (tm-30) cc_final: 0.6855 (tt0) REVERT: B 164 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6804 (tt0) REVERT: C 159 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.6851 (ttm-80) REVERT: C 164 GLU cc_start: 0.7380 (tp30) cc_final: 0.6594 (tt0) REVERT: C 196 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: C 281 MET cc_start: 0.6791 (tpp) cc_final: 0.6582 (tpp) REVERT: D 114 HIS cc_start: 0.6308 (OUTLIER) cc_final: 0.5602 (t-90) REVERT: D 281 MET cc_start: 0.6954 (mmm) cc_final: 0.6695 (mmp) REVERT: D 283 MET cc_start: 0.4808 (mmt) cc_final: 0.4588 (mmt) REVERT: E 67 TYR cc_start: 0.8733 (m-10) cc_final: 0.8188 (m-10) REVERT: E 71 MET cc_start: 0.8256 (tpp) cc_final: 0.7965 (tpt) REVERT: E 135 MET cc_start: 0.7709 (mmp) cc_final: 0.7390 (mmt) REVERT: F 208 ARG cc_start: 0.6996 (tmt170) cc_final: 0.5769 (ttp80) REVERT: G 71 MET cc_start: 0.8187 (tpp) cc_final: 0.7935 (tpt) REVERT: G 208 ARG cc_start: 0.7031 (tmt170) cc_final: 0.5520 (ttp80) REVERT: H 71 MET cc_start: 0.8299 (tpp) cc_final: 0.8004 (tpt) REVERT: H 208 ARG cc_start: 0.7238 (tmt170) cc_final: 0.6000 (ttp80) outliers start: 14 outliers final: 10 residues processed: 179 average time/residue: 0.2552 time to fit residues: 62.7893 Evaluate side-chains 176 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 114 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 0.0070 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN C 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.118058 restraints weight = 13548.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120935 restraints weight = 9017.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122789 restraints weight = 7010.753| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11138 Z= 0.200 Angle : 0.562 8.331 15078 Z= 0.279 Chirality : 0.036 0.210 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.595 21.691 1488 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.65 % Allowed : 17.49 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.25), residues: 1344 helix: 2.49 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.55 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 200 HIS 0.004 0.001 HIS H 147 PHE 0.018 0.001 PHE C 110 TYR 0.015 0.001 TYR G 212 ARG 0.006 0.000 ARG A 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.45 seconds wall clock time: 38 minutes 51.35 seconds (2331.35 seconds total)