Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:46:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwp_20510/02_2023/6pwp_20510.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwp_20510/02_2023/6pwp_20510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwp_20510/02_2023/6pwp_20510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwp_20510/02_2023/6pwp_20510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwp_20510/02_2023/6pwp_20510.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwp_20510/02_2023/6pwp_20510.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14903 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Time building chain proxies: 8.37, per 1000 atoms: 0.56 Number of scatterers: 14903 At special positions: 0 Unit cell: (98.952, 97.888, 151.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 2716 8.00 N 2590 7.00 C 9548 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: 7.03 Conformation dependent library (CDL) restraints added in 2.5 seconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 57.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 20 through 58 removed outlier: 3.855A pdb=" N TYR A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL B 6 " --> pdb=" O GLU B 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 7' Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.863A pdb=" N VAL C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 7' Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 7' Processing helix chain 'D' and resid 10 through 14 Processing helix chain 'D' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.691A pdb=" N ALA D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 243 through 265 removed outlier: 4.617A pdb=" N GLN D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 7' Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 20 through 58 removed outlier: 3.855A pdb=" N TYR E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.863A pdb=" N VAL F 6 " --> pdb=" O GLU F 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 7' Processing helix chain 'F' and resid 10 through 14 Processing helix chain 'F' and resid 20 through 58 removed outlier: 3.855A pdb=" N TYR F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU F 254 " --> pdb=" O TYR F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.863A pdb=" N VAL G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 7' Processing helix chain 'G' and resid 10 through 14 Processing helix chain 'G' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.689A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN G 247 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU G 254 " --> pdb=" O TYR G 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 3.580A pdb=" N VAL A 136 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 145 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 136 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL B 145 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG B 156 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 136 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL C 145 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG C 156 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 136 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL D 145 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG D 156 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 136 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL E 145 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG E 156 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 162 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 136 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL F 145 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ARG F 156 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 136 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL G 145 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG G 156 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE G 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 276 removed outlier: 3.914A pdb=" N ASN B 276 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 275 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN C 276 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 275 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN D 276 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN E 276 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 275 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN F 276 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 275 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN G 276 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N MET G 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP A 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL G 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN A 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 7.389A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 7.389A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2901 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: 4.38 Time building geometry restraints manager: 7.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4991 1.35 - 1.47: 3246 1.47 - 1.59: 6757 1.59 - 1.71: 0 1.71 - 1.83: 98 Bond restraints: 15092 Sorted by residual: bond pdb=" N GLY E 229 " pdb=" CA GLY E 229 " ideal model delta sigma weight residual 1.445 1.476 -0.031 9.20e-03 1.18e+04 1.15e+01 bond pdb=" N GLU E 227 " pdb=" CA GLU E 227 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.16e-02 7.43e+03 8.03e+00 bond pdb=" N GLU B 227 " pdb=" CA GLU B 227 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.16e-02 7.43e+03 7.45e+00 bond pdb=" N GLU C 227 " pdb=" CA GLU C 227 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.16e-02 7.43e+03 7.28e+00 bond pdb=" N GLU D 227 " pdb=" CA GLU D 227 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.16e-02 7.43e+03 7.18e+00 ... (remaining 15087 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 202 106.81 - 113.62: 9061 113.62 - 120.42: 5022 120.42 - 127.23: 6110 127.23 - 134.04: 87 Bond angle restraints: 20482 Sorted by residual: angle pdb=" CA GLY D 229 " pdb=" C GLY D 229 " pdb=" O GLY D 229 " ideal model delta sigma weight residual 121.90 118.06 3.84 1.02e+00 9.61e-01 1.42e+01 angle pdb=" CA GLY E 229 " pdb=" C GLY E 229 " pdb=" O GLY E 229 " ideal model delta sigma weight residual 122.33 118.19 4.14 1.11e+00 8.12e-01 1.39e+01 angle pdb=" CA GLY B 229 " pdb=" C GLY B 229 " pdb=" O GLY B 229 " ideal model delta sigma weight residual 121.90 118.12 3.78 1.02e+00 9.61e-01 1.37e+01 angle pdb=" CA GLY A 229 " pdb=" C GLY A 229 " pdb=" O GLY A 229 " ideal model delta sigma weight residual 121.90 118.14 3.76 1.02e+00 9.61e-01 1.36e+01 angle pdb=" CA GLY C 229 " pdb=" C GLY C 229 " pdb=" O GLY C 229 " ideal model delta sigma weight residual 121.90 118.16 3.74 1.02e+00 9.61e-01 1.34e+01 ... (remaining 20477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 8133 16.14 - 32.28: 728 32.28 - 48.42: 133 48.42 - 64.56: 36 64.56 - 80.70: 21 Dihedral angle restraints: 9051 sinusoidal: 3444 harmonic: 5607 Sorted by residual: dihedral pdb=" CA GLN D 149 " pdb=" C GLN D 149 " pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta harmonic sigma weight residual -180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN C 149 " pdb=" C GLN C 149 " pdb=" N ILE C 150 " pdb=" CA ILE C 150 " ideal model delta harmonic sigma weight residual 180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN G 149 " pdb=" C GLN G 149 " pdb=" N ILE G 150 " pdb=" CA ILE G 150 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 9048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2241 0.077 - 0.154: 253 0.154 - 0.232: 12 0.232 - 0.309: 0 0.309 - 0.386: 7 Chirality restraints: 2513 Sorted by residual: chirality pdb=" CG LEU B 225 " pdb=" CB LEU B 225 " pdb=" CD1 LEU B 225 " pdb=" CD2 LEU B 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CG LEU A 225 " pdb=" CB LEU A 225 " pdb=" CD1 LEU A 225 " pdb=" CD2 LEU A 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CG LEU F 225 " pdb=" CB LEU F 225 " pdb=" CD1 LEU F 225 " pdb=" CD2 LEU F 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 2510 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 226 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ASN E 226 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN E 226 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU E 227 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 226 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C ASN B 226 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN B 226 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU B 227 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 226 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C ASN D 226 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN D 226 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 227 " 0.017 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 403 2.66 - 3.22: 18114 3.22 - 3.78: 24893 3.78 - 4.34: 32109 4.34 - 4.90: 48902 Nonbonded interactions: 124421 Sorted by model distance: nonbonded pdb=" OD1 ASP B 262 " pdb=" N ALA B 263 " model vdw 2.096 2.520 nonbonded pdb=" OD1 ASP C 262 " pdb=" N ALA C 263 " model vdw 2.096 2.520 nonbonded pdb=" OD1 ASP D 262 " pdb=" N ALA D 263 " model vdw 2.096 2.520 nonbonded pdb=" OD1 ASP F 262 " pdb=" N ALA F 263 " model vdw 2.097 2.520 nonbonded pdb=" OD1 ASP G 262 " pdb=" N ALA G 263 " model vdw 2.097 2.520 ... (remaining 124416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 9548 2.51 5 N 2590 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.990 Check model and map are aligned: 0.210 Process input model: 40.980 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.010 0.061 15092 Z= 0.630 Angle : 0.856 6.289 20482 Z= 0.535 Chirality : 0.051 0.386 2513 Planarity : 0.004 0.035 2604 Dihedral : 13.542 80.704 5439 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.14), residues: 1946 helix: -1.62 (0.13), residues: 973 sheet: -2.80 (0.24), residues: 273 loop : -3.43 (0.16), residues: 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 96 average time/residue: 0.2728 time to fit residues: 39.9603 Evaluate side-chains 64 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 226 ASN C 226 ASN D 226 ASN F 226 ASN F 234 ASN G 234 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 15092 Z= 0.246 Angle : 0.605 8.737 20482 Z= 0.331 Chirality : 0.043 0.144 2513 Planarity : 0.004 0.029 2604 Dihedral : 4.990 22.723 2121 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.00 % 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: -1.09 (0.17), residues: 1946 helix: 0.74 (0.15), residues: 1029 sheet: -1.10 (0.30), residues: 210 loop : -2.88 (0.19), residues: 707 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.901 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2367 time to fit residues: 37.7525 Evaluate side-chains 68 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 30.0000 chunk 192 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN C 234 ASN D 234 ASN E 226 ASN E 234 ASN F 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 15092 Z= 0.393 Angle : 0.682 7.842 20482 Z= 0.379 Chirality : 0.043 0.151 2513 Planarity : 0.004 0.033 2604 Dihedral : 5.197 17.180 2121 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.00 % 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: -0.79 (0.18), residues: 1946 helix: 0.98 (0.15), residues: 1022 sheet: -1.19 (0.30), residues: 224 loop : -2.62 (0.22), residues: 700 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2337 time to fit residues: 34.7281 Evaluate side-chains 60 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 chunk 189 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 210 GLN E 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 15092 Z= 0.262 Angle : 0.580 8.233 20482 Z= 0.321 Chirality : 0.041 0.137 2513 Planarity : 0.004 0.029 2604 Dihedral : 4.948 16.702 2121 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.25 % 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: -0.33 (0.19), residues: 1946 helix: 1.27 (0.16), residues: 1029 sheet: -0.65 (0.31), residues: 224 loop : -2.42 (0.22), residues: 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 86 average time/residue: 0.2347 time to fit residues: 33.2118 Evaluate side-chains 66 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 161 optimal weight: 0.1980 chunk 130 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 226 ASN B 117 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 117 ASN D 226 ASN F 210 GLN G 210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 15092 Z= 0.291 Angle : 0.574 5.890 20482 Z= 0.318 Chirality : 0.040 0.130 2513 Planarity : 0.004 0.029 2604 Dihedral : 4.946 17.022 2121 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1946 helix: 1.38 (0.15), residues: 1022 sheet: -0.47 (0.31), residues: 224 loop : -2.40 (0.22), residues: 700 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2377 time to fit residues: 34.1174 Evaluate side-chains 61 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 37 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 226 ASN E 117 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN F 117 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 15092 Z= 0.279 Angle : 0.565 6.328 20482 Z= 0.311 Chirality : 0.040 0.128 2513 Planarity : 0.003 0.027 2604 Dihedral : 4.926 17.075 2121 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 1946 helix: 1.47 (0.15), residues: 1022 sheet: -0.83 (0.30), residues: 259 loop : -2.32 (0.22), residues: 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2252 time to fit residues: 31.2502 Evaluate side-chains 67 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 0.0170 chunk 107 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN C 117 ASN C 226 ASN D 226 ASN G 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 15092 Z= 0.200 Angle : 0.530 5.499 20482 Z= 0.287 Chirality : 0.040 0.128 2513 Planarity : 0.003 0.025 2604 Dihedral : 4.724 20.381 2121 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1946 helix: 1.77 (0.15), residues: 1022 sheet: -0.09 (0.32), residues: 224 loop : -2.41 (0.21), residues: 700 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.687 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2168 time to fit residues: 36.5901 Evaluate side-chains 75 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 30.0000 chunk 56 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN C 226 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 15092 Z= 0.413 Angle : 0.680 7.782 20482 Z= 0.374 Chirality : 0.042 0.132 2513 Planarity : 0.004 0.028 2604 Dihedral : 5.171 18.286 2121 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.00 % 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: -0.52 (0.18), residues: 1946 helix: 1.16 (0.15), residues: 1022 sheet: -1.08 (0.28), residues: 273 loop : -2.51 (0.23), residues: 651 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.845 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2230 time to fit residues: 32.8269 Evaluate side-chains 71 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 54 optimal weight: 0.0270 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 15092 Z= 0.164 Angle : 0.541 6.089 20482 Z= 0.288 Chirality : 0.040 0.159 2513 Planarity : 0.003 0.023 2604 Dihedral : 4.629 22.452 2121 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1946 helix: 1.65 (0.15), residues: 1022 sheet: 0.21 (0.34), residues: 210 loop : -2.40 (0.21), residues: 714 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.692 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2269 time to fit residues: 35.2401 Evaluate side-chains 76 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 195 optimal weight: 0.0870 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15092 Z= 0.170 Angle : 0.537 6.543 20482 Z= 0.285 Chirality : 0.040 0.178 2513 Planarity : 0.003 0.024 2604 Dihedral : 4.565 24.507 2121 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1946 helix: 1.73 (0.16), residues: 1022 sheet: 0.37 (0.34), residues: 210 loop : -2.36 (0.21), residues: 714 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.023 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2309 time to fit residues: 35.4185 Evaluate side-chains 80 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN C 226 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.023979 restraints weight = 143667.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.024636 restraints weight = 88059.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025118 restraints weight = 65047.882| |-----------------------------------------------------------------------------| r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 15092 Z= 0.253 Angle : 0.562 6.442 20482 Z= 0.305 Chirality : 0.040 0.158 2513 Planarity : 0.003 0.025 2604 Dihedral : 4.750 26.204 2121 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.00 % 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: 0.14 (0.19), residues: 1946 helix: 1.63 (0.15), residues: 1022 sheet: 0.11 (0.33), residues: 210 loop : -2.32 (0.21), residues: 714 =============================================================================== Job complete usr+sys time: 1904.51 seconds wall clock time: 36 minutes 26.54 seconds (2186.54 seconds total)