Starting phenix.real_space_refine (version: dev) on Sun Dec 11 21:58:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/12_2022/6vwx_21425_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/12_2022/6vwx_21425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/12_2022/6vwx_21425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/12_2022/6vwx_21425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/12_2022/6vwx_21425_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwx_21425/12_2022/6vwx_21425_neut_updated.pdb" } resolution = 3.1 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 7782 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "D" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "E" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "F" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' NA': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.03, per 1000 atoms: 0.65 Number of scatterers: 7782 At special positions: 0 Unit cell: (121.426, 121.426, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 8 15.00 Na 2 11.00 O 1224 8.00 N 1188 7.00 C 5336 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: 3.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 0 sheets defined 70.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 23 through 44 removed outlier: 3.928A pdb=" N PHE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 56 through 76 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 109 through 124 removed outlier: 4.103A pdb=" N ILE A 114 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.513A pdb=" N ARG A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 removed outlier: 4.623A pdb=" N ASN A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 148 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 158 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 162 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.558A pdb=" N VAL A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.724A pdb=" N GLU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 236 removed outlier: 4.019A pdb=" N TRP A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 212 " --> pdb=" O TRP A 209 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 216 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 217 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 219 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 222 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 224 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 227 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A 228 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 232 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 234 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 44 removed outlier: 3.929A pdb=" N PHE D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 56 through 76 Processing helix chain 'D' and resid 88 through 102 Processing helix chain 'D' and resid 109 through 124 removed outlier: 4.103A pdb=" N ILE D 114 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.512A pdb=" N ARG D 132 " --> pdb=" O PRO D 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 133 " --> pdb=" O SER D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 removed outlier: 4.623A pdb=" N ASN D 146 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE D 147 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 148 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 153 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 158 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 161 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 162 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 188 removed outlier: 3.558A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.724A pdb=" N GLU D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 236 removed outlier: 4.019A pdb=" N TRP D 209 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 212 " --> pdb=" O TRP D 209 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 213 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 214 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 216 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 217 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY D 219 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE D 222 " --> pdb=" O GLY D 219 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE D 224 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 227 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 228 " --> pdb=" O ASN D 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 232 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN D 234 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 235 " --> pdb=" O VAL D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 44 removed outlier: 3.928A pdb=" N PHE E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 56 through 76 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 109 through 124 removed outlier: 4.103A pdb=" N ILE E 114 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.513A pdb=" N ARG E 132 " --> pdb=" O PRO E 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 163 removed outlier: 4.622A pdb=" N ASN E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE E 147 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU E 148 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 158 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 161 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY E 162 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 188 removed outlier: 3.558A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.725A pdb=" N GLU E 204 " --> pdb=" O PRO E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 236 removed outlier: 4.020A pdb=" N TRP E 209 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE E 212 " --> pdb=" O TRP E 209 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 213 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 214 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 216 " --> pdb=" O VAL E 213 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 217 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY E 219 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE E 222 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE E 224 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 227 " --> pdb=" O PHE E 224 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE E 228 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 232 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN E 234 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 235 " --> pdb=" O VAL E 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 44 removed outlier: 3.928A pdb=" N PHE F 27 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F 43 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR F 44 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 56 through 76 Processing helix chain 'F' and resid 88 through 102 Processing helix chain 'F' and resid 109 through 124 removed outlier: 4.103A pdb=" N ILE F 114 " --> pdb=" O VAL F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 138 removed outlier: 3.513A pdb=" N ARG F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 163 removed outlier: 4.623A pdb=" N ASN F 146 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE F 147 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU F 148 " --> pdb=" O GLY F 145 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE F 158 " --> pdb=" O PHE F 155 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 161 " --> pdb=" O PHE F 158 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY F 162 " --> pdb=" O ALA F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.559A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 removed outlier: 3.725A pdb=" N GLU F 204 " --> pdb=" O PRO F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 236 removed outlier: 4.019A pdb=" N TRP F 209 " --> pdb=" O PRO F 206 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE F 212 " --> pdb=" O TRP F 209 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL F 213 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 214 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL F 216 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 217 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY F 219 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE F 222 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE F 224 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE F 227 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE F 228 " --> pdb=" O ASN F 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL F 232 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN F 234 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 235 " --> pdb=" O VAL F 232 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 648 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: 1.93 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1052 1.30 - 1.43: 2291 1.43 - 1.55: 4540 1.55 - 1.68: 57 1.68 - 1.81: 48 Bond restraints: 7988 Sorted by residual: bond pdb=" C31 POV F 302 " pdb=" O31 POV F 302 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV D 301 " pdb=" O31 POV D 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV E 302 " pdb=" O31 POV E 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 POV E 302 " pdb=" O21 POV E 302 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7983 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.23: 219 107.23 - 113.94: 4824 113.94 - 120.65: 3358 120.65 - 127.35: 2310 127.35 - 134.06: 93 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C ASN E 79 " pdb=" N PRO E 80 " pdb=" CA PRO E 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.18e+01 angle pdb=" C ASN F 79 " pdb=" N PRO F 80 " pdb=" CA PRO F 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.17e+01 angle pdb=" C ASN A 79 " pdb=" N PRO A 80 " pdb=" CA PRO A 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.13e+01 angle pdb=" C ASN D 79 " pdb=" N PRO D 80 " pdb=" CA PRO D 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.12e+01 angle pdb=" N VAL E 197 " pdb=" CA VAL E 197 " pdb=" C VAL E 197 " ideal model delta sigma weight residual 110.72 118.38 -7.66 1.01e+00 9.80e-01 5.75e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 3928 23.68 - 47.37: 528 47.37 - 71.05: 128 71.05 - 94.73: 32 94.73 - 118.41: 4 Dihedral angle restraints: 4620 sinusoidal: 1972 harmonic: 2648 Sorted by residual: dihedral pdb=" C29 POV E 302 " pdb="C210 POV E 302 " pdb="C211 POV E 302 " pdb="C212 POV E 302 " ideal model delta sinusoidal sigma weight residual 112.25 -129.34 -118.41 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV A 301 " pdb="C210 POV A 301 " pdb="C211 POV A 301 " pdb="C212 POV A 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.35 -118.40 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV D 301 " pdb="C210 POV D 301 " pdb="C211 POV D 301 " pdb="C212 POV D 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.36 -118.39 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 4617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 935 0.052 - 0.104: 261 0.104 - 0.156: 32 0.156 - 0.209: 0 0.209 - 0.261: 4 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA MET E 198 " pdb=" N MET E 198 " pdb=" C MET E 198 " pdb=" CB MET E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET F 198 " pdb=" N MET F 198 " pdb=" C MET F 198 " pdb=" CB MET F 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET A 198 " pdb=" N MET A 198 " pdb=" C MET A 198 " pdb=" CB MET A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1229 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 199 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO F 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 199 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 199 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.52e+00 pdb=" N PRO E 200 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 200 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 200 " 0.037 5.00e-02 4.00e+02 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1130 2.74 - 3.28: 7905 3.28 - 3.82: 12251 3.82 - 4.36: 14901 4.36 - 4.90: 24900 Nonbonded interactions: 61087 Sorted by model distance: nonbonded pdb=" O SER D 78 " pdb=" OG SER D 78 " model vdw 2.200 2.440 nonbonded pdb=" O SER F 78 " pdb=" OG SER F 78 " model vdw 2.200 2.440 nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.200 2.440 nonbonded pdb=" O SER E 78 " pdb=" OG SER E 78 " model vdw 2.201 2.440 nonbonded pdb=" O PHE A 158 " pdb=" OH TYR A 211 " model vdw 2.277 2.440 ... (remaining 61082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 237 or resid 301 through 302)) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 24 5.16 5 Na 2 4.78 5 C 5336 2.51 5 N 1188 2.21 5 O 1224 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 3.670 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.080 Process input model: 24.740 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 32.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.011 0.098 7988 Z= 0.679 Angle : 1.291 11.973 10804 Z= 0.639 Chirality : 0.047 0.261 1232 Planarity : 0.006 0.064 1256 Dihedral : 22.594 118.414 2892 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.48 % Rotamer Outliers : 15.83 % 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: -4.41 (0.22), residues: 892 helix: -2.52 (0.15), residues: 644 sheet: None (None), residues: 0 loop : -3.55 (0.32), residues: 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 175 time to evaluate : 0.941 Fit side-chains outliers start: 126 outliers final: 83 residues processed: 263 average time/residue: 0.1670 time to fit residues: 60.6670 Evaluate side-chains 237 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 154 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.0945 time to fit residues: 13.7951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 186 GLN A 234 ASN D 167 GLN D 186 GLN D 234 ASN E 146 ASN E 167 GLN E 186 GLN E 234 ASN F 146 ASN F 167 GLN F 186 GLN F 234 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 7988 Z= 0.239 Angle : 0.603 10.819 10804 Z= 0.313 Chirality : 0.040 0.190 1232 Planarity : 0.006 0.057 1256 Dihedral : 19.164 107.421 1264 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.62 % Favored : 91.93 % Rotamer Outliers : 2.76 % 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: -2.47 (0.26), residues: 892 helix: -1.28 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -2.21 (0.42), residues: 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 197 average time/residue: 0.1488 time to fit residues: 42.6329 Evaluate side-chains 158 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0735 time to fit residues: 2.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS D 22 HIS E 22 HIS F 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 7988 Z= 0.218 Angle : 0.584 11.863 10804 Z= 0.297 Chirality : 0.040 0.192 1232 Planarity : 0.005 0.053 1256 Dihedral : 17.844 99.498 1264 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.06 % Favored : 92.49 % Rotamer Outliers : 5.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.27), residues: 892 helix: -0.88 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 0.957 Fit side-chains outliers start: 42 outliers final: 15 residues processed: 194 average time/residue: 0.1576 time to fit residues: 43.1828 Evaluate side-chains 168 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0739 time to fit residues: 3.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7988 Z= 0.181 Angle : 0.615 14.292 10804 Z= 0.292 Chirality : 0.040 0.232 1232 Planarity : 0.008 0.117 1256 Dihedral : 17.029 92.739 1264 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.50 % Favored : 93.05 % Rotamer Outliers : 3.77 % 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: -1.46 (0.27), residues: 892 helix: -0.58 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -1.71 (0.40), residues: 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 0.986 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 190 average time/residue: 0.1605 time to fit residues: 43.4559 Evaluate side-chains 160 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0733 time to fit residues: 2.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 146 ASN E 22 HIS F 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 7988 Z= 0.196 Angle : 0.589 13.443 10804 Z= 0.294 Chirality : 0.043 0.218 1232 Planarity : 0.004 0.041 1256 Dihedral : 16.591 90.243 1264 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.29 % 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: -1.31 (0.27), residues: 892 helix: -0.43 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 0.944 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 175 average time/residue: 0.1462 time to fit residues: 37.0928 Evaluate side-chains 154 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0694 time to fit residues: 2.0957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.0970 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 7988 Z= 0.142 Angle : 0.576 13.923 10804 Z= 0.287 Chirality : 0.041 0.191 1232 Planarity : 0.004 0.039 1256 Dihedral : 15.869 86.045 1264 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.28), residues: 892 helix: -0.21 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.965 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 163 average time/residue: 0.1511 time to fit residues: 35.9322 Evaluate side-chains 151 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0804 time to fit residues: 1.7766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 7988 Z= 0.169 Angle : 0.611 14.111 10804 Z= 0.294 Chirality : 0.041 0.206 1232 Planarity : 0.005 0.038 1256 Dihedral : 15.727 84.621 1264 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 2.26 % 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: -1.08 (0.28), residues: 892 helix: -0.21 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.84 (0.38), residues: 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.963 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 162 average time/residue: 0.1600 time to fit residues: 36.6498 Evaluate side-chains 154 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0665 time to fit residues: 1.9935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 HIS F 22 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 7988 Z= 0.179 Angle : 0.596 12.275 10804 Z= 0.291 Chirality : 0.042 0.179 1232 Planarity : 0.004 0.038 1256 Dihedral : 15.635 84.863 1264 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.28), residues: 892 helix: -0.14 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.82 (0.38), residues: 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.829 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 152 average time/residue: 0.1442 time to fit residues: 32.2902 Evaluate side-chains 145 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0802 time to fit residues: 1.4301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7988 Z= 0.171 Angle : 0.637 12.822 10804 Z= 0.301 Chirality : 0.042 0.174 1232 Planarity : 0.005 0.037 1256 Dihedral : 15.498 84.751 1264 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.38 % 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: -1.02 (0.28), residues: 892 helix: -0.13 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 0.985 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 150 average time/residue: 0.1414 time to fit residues: 31.6547 Evaluate side-chains 147 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0720 time to fit residues: 1.3922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7988 Z= 0.185 Angle : 0.687 17.939 10804 Z= 0.316 Chirality : 0.042 0.162 1232 Planarity : 0.005 0.037 1256 Dihedral : 15.444 84.916 1264 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.38 % 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: -1.10 (0.28), residues: 892 helix: -0.19 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.88 (0.38), residues: 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 0.924 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.1398 time to fit residues: 30.7844 Evaluate side-chains 145 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0708 time to fit residues: 1.4625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.137871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104053 restraints weight = 11651.369| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.97 r_work: 0.3202 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 7988 Z= 0.178 Angle : 0.609 12.068 10804 Z= 0.294 Chirality : 0.042 0.159 1232 Planarity : 0.005 0.037 1256 Dihedral : 15.383 84.867 1264 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.38 % 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: -1.01 (0.28), residues: 892 helix: -0.13 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 256 =============================================================================== Job complete usr+sys time: 1755.31 seconds wall clock time: 32 minutes 31.78 seconds (1951.78 seconds total)