Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 10:20:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/10_2023/8f6h_28883.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/10_2023/8f6h_28883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/10_2023/8f6h_28883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/10_2023/8f6h_28883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/10_2023/8f6h_28883.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/10_2023/8f6h_28883.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 S 28 5.16 5 C 6652 2.51 5 N 1746 2.21 5 O 1989 1.98 5 H 10347 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 2": "OD1" <-> "OD2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4451 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 6, 'TRANS': 278} Chain: "B" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4213 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain breaks: 1 Chain: "C" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3134 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3134 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.03, per 1000 atoms: 0.43 Number of scatterers: 20768 At special positions: 0 Unit cell: (78.767, 158.613, 145.665, 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) Zn 6 29.99 S 28 16.00 O 1989 8.00 N 1746 7.00 C 6652 6.00 H 10347 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 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: 15.92 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 285 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 234 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 250 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 155 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 155 " 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 23 sheets defined 32.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 10 through 34 removed outlier: 3.566A pdb=" N ALA A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 Processing helix chain 'A' and resid 82 through 109 removed outlier: 4.004A pdb=" N ILE A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 4.389A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 176 removed outlier: 4.117A pdb=" N GLU A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 208 removed outlier: 3.612A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.502A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 34 removed outlier: 3.942A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 4.061A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 3.581A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 141 removed outlier: 3.618A pdb=" N GLY B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 175 removed outlier: 3.938A pdb=" N LEU B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 206 removed outlier: 3.585A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 257 through 277 removed outlier: 4.125A pdb=" N GLU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.277A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 184 through 190 removed outlier: 4.001A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 64 through 68 removed outlier: 4.012A pdb=" N LYS F 68 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.239A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.239A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 8 removed outlier: 4.399A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 76 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.803A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 35 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 99 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.634A pdb=" N ASN C 139 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 132 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.522A pdb=" N VAL D 15 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.522A pdb=" N VAL D 15 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS D 99 " --> pdb=" O TRP D 121 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TRP D 121 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG D 101 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.755A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 197 " --> pdb=" O CYS D 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 198 " --> pdb=" O HIS D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.755A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 194 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.585A pdb=" N ALA E 14 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 50 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.572A pdb=" N ASN E 139 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AC1, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.113A pdb=" N GLN F 6 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 21 " --> pdb=" O MET F 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 15 removed outlier: 6.776A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.575A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.575A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.571A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1515 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: 7.20 Time building geometry restraints manager: 16.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10345 1.03 - 1.23: 12 1.23 - 1.42: 4504 1.42 - 1.62: 6091 1.62 - 1.81: 38 Bond restraints: 20990 Sorted by residual: bond pdb=" N GLU D 4 " pdb=" CA GLU D 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N TYR A 7 " pdb=" CA TYR A 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLU F 4 " pdb=" CA GLU F 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU F 4 " pdb=" H GLU F 4 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N GLU D 4 " pdb=" H GLU D 4 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 20985 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 282 106.60 - 113.45: 24863 113.45 - 120.29: 6432 120.29 - 127.14: 6162 127.14 - 133.99: 127 Bond angle restraints: 37866 Sorted by residual: angle pdb=" C SER D 220 " pdb=" N ASN D 221 " pdb=" CA ASN D 221 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.88e+00 angle pdb=" N PHE A 249 " pdb=" CA PHE A 249 " pdb=" C PHE A 249 " ideal model delta sigma weight residual 108.60 111.40 -2.80 1.46e+00 4.69e-01 3.67e+00 angle pdb=" CA LYS E 147 " pdb=" CB LYS E 147 " pdb=" CG LYS E 147 " ideal model delta sigma weight residual 114.10 117.91 -3.81 2.00e+00 2.50e-01 3.63e+00 angle pdb=" C GLN A 248 " pdb=" N PHE A 249 " pdb=" CA PHE A 249 " ideal model delta sigma weight residual 121.80 118.58 3.22 1.71e+00 3.42e-01 3.56e+00 angle pdb=" N VAL A 122 " pdb=" CA VAL A 122 " pdb=" C VAL A 122 " ideal model delta sigma weight residual 111.89 109.18 2.71 1.44e+00 4.82e-01 3.53e+00 ... (remaining 37861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7872 17.99 - 35.98: 509 35.98 - 53.98: 79 53.98 - 71.97: 14 71.97 - 89.96: 12 Dihedral angle restraints: 8486 sinusoidal: 3819 harmonic: 4667 Sorted by residual: dihedral pdb=" CB CYS F 25 " pdb=" SG CYS F 25 " pdb=" SG CYS F 99 " pdb=" CB CYS F 99 " ideal model delta sinusoidal sigma weight residual 93.00 167.06 -74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS F 157 " pdb=" SG CYS F 157 " pdb=" SG CYS F 213 " pdb=" CB CYS F 213 " ideal model delta sinusoidal sigma weight residual 93.00 165.83 -72.83 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CA ILE B 283 " pdb=" C ILE B 283 " pdb=" N ILE B 284 " pdb=" CA ILE B 284 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 8483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1066 0.028 - 0.057: 417 0.057 - 0.085: 96 0.085 - 0.113: 82 0.113 - 0.141: 23 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA ILE E 22 " pdb=" N ILE E 22 " pdb=" C ILE E 22 " pdb=" CB ILE E 22 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE E 98 " pdb=" N ILE E 98 " pdb=" C ILE E 98 " pdb=" CB ILE E 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA LYS F 223 " pdb=" N LYS F 223 " pdb=" C LYS F 223 " pdb=" CB LYS F 223 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1681 not shown) Planarity restraints: 3110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 67 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 68 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 139 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO D 140 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 140 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 140 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 95 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO C 96 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 96 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 96 " 0.017 5.00e-02 4.00e+02 ... (remaining 3107 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 905 2.18 - 2.78: 41306 2.78 - 3.39: 54962 3.39 - 3.99: 69373 3.99 - 4.60: 107862 Nonbonded interactions: 274408 Sorted by model distance: nonbonded pdb=" OD1 ASP D 119 " pdb=" H TYR D 120 " model vdw 1.570 1.850 nonbonded pdb=" OE1 GLN B 290 " pdb=" H GLN B 290 " model vdw 1.618 1.850 nonbonded pdb=" OD1 ASP F 119 " pdb=" H TYR F 120 " model vdw 1.618 1.850 nonbonded pdb=" OD1 ASP B 51 " pdb=" HE2 HIS B 155 " model vdw 1.653 1.850 nonbonded pdb=" O GLY A 37 " pdb="HH12 ARG A 106 " model vdw 1.654 1.850 ... (remaining 274403 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 11 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA )) or resid 12 through 64 or resid 75 through \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2 or name H or name HA )) or resid 82 through \ 291 or resid 301 through 303)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.340 Extract box with map and model: 8.470 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 68.150 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.002 0.035 10643 Z= 0.162 Angle : 0.468 4.313 14486 Z= 0.250 Chirality : 0.038 0.141 1684 Planarity : 0.003 0.052 1820 Dihedral : 13.598 89.961 3747 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1332 helix: 1.88 (0.27), residues: 386 sheet: 0.18 (0.29), residues: 360 loop : -1.52 (0.26), residues: 586 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.563 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 outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4990 time to fit residues: 123.5129 Evaluate side-chains 144 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10643 Z= 0.226 Angle : 0.520 5.131 14486 Z= 0.277 Chirality : 0.040 0.146 1684 Planarity : 0.003 0.052 1820 Dihedral : 3.595 22.823 1457 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.08 % Favored : 93.77 % Rotamer: Outliers : 0.70 % Allowed : 7.81 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.15 (0.24), residues: 1332 helix: 2.37 (0.26), residues: 390 sheet: 0.21 (0.29), residues: 362 loop : -1.63 (0.25), residues: 580 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 0.4756 time to fit residues: 102.8843 Evaluate side-chains 142 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2492 time to fit residues: 3.5469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 0.0980 chunk 130 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10643 Z= 0.180 Angle : 0.492 6.357 14486 Z= 0.259 Chirality : 0.039 0.144 1684 Planarity : 0.003 0.053 1820 Dihedral : 3.548 22.669 1457 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 0.26 % Allowed : 10.01 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.24 (0.24), residues: 1332 helix: 2.59 (0.26), residues: 390 sheet: 0.16 (0.29), residues: 362 loop : -1.61 (0.25), residues: 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.671 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 outliers start: 3 outliers final: 2 residues processed: 156 average time/residue: 0.5121 time to fit residues: 111.3628 Evaluate side-chains 143 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2123 time to fit residues: 2.6397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10643 Z= 0.167 Angle : 0.486 6.280 14486 Z= 0.254 Chirality : 0.039 0.152 1684 Planarity : 0.003 0.054 1820 Dihedral : 3.507 22.226 1457 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 0.53 % Allowed : 10.36 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.24 (0.24), residues: 1332 helix: 2.65 (0.25), residues: 390 sheet: 0.12 (0.29), residues: 352 loop : -1.62 (0.25), residues: 590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.677 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 outliers start: 6 outliers final: 3 residues processed: 154 average time/residue: 0.4753 time to fit residues: 105.2987 Evaluate side-chains 147 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2178 time to fit residues: 3.1624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10643 Z= 0.254 Angle : 0.516 5.245 14486 Z= 0.274 Chirality : 0.040 0.153 1684 Planarity : 0.003 0.052 1820 Dihedral : 3.715 23.203 1457 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.83 % Favored : 93.02 % Rotamer: Outliers : 0.53 % Allowed : 11.15 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.16 (0.24), residues: 1332 helix: 2.61 (0.25), residues: 389 sheet: 0.10 (0.29), residues: 350 loop : -1.69 (0.25), residues: 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 156 average time/residue: 0.4637 time to fit residues: 102.6254 Evaluate side-chains 147 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2092 time to fit residues: 3.3761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.7998 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10643 Z= 0.196 Angle : 0.506 5.675 14486 Z= 0.265 Chirality : 0.039 0.141 1684 Planarity : 0.003 0.054 1820 Dihedral : 3.657 22.862 1457 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.07 % Rotamer: Outliers : 0.35 % Allowed : 12.82 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.19 (0.24), residues: 1332 helix: 2.63 (0.25), residues: 389 sheet: 0.09 (0.29), residues: 350 loop : -1.65 (0.25), residues: 593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 147 average time/residue: 0.4749 time to fit residues: 100.0861 Evaluate side-chains 141 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2751 time to fit residues: 3.4198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10643 Z= 0.231 Angle : 0.510 5.575 14486 Z= 0.270 Chirality : 0.040 0.139 1684 Planarity : 0.003 0.053 1820 Dihedral : 3.702 23.282 1457 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.61 % Favored : 93.17 % Rotamer: Outliers : 0.61 % Allowed : 12.99 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.17 (0.24), residues: 1332 helix: 2.62 (0.25), residues: 389 sheet: 0.04 (0.29), residues: 348 loop : -1.64 (0.25), residues: 595 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 148 average time/residue: 0.4815 time to fit residues: 103.2048 Evaluate side-chains 143 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4131 time to fit residues: 3.8094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10643 Z= 0.213 Angle : 0.509 5.213 14486 Z= 0.268 Chirality : 0.040 0.139 1684 Planarity : 0.003 0.054 1820 Dihedral : 3.704 23.113 1457 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.23 % Favored : 93.54 % Rotamer: Outliers : 0.44 % Allowed : 13.70 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.15 (0.24), residues: 1332 helix: 2.63 (0.26), residues: 389 sheet: -0.16 (0.28), residues: 370 loop : -1.57 (0.26), residues: 573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 144 average time/residue: 0.4875 time to fit residues: 100.1813 Evaluate side-chains 141 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2990 time to fit residues: 2.7405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 93 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7970 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10643 Z= 0.149 Angle : 0.500 7.783 14486 Z= 0.257 Chirality : 0.040 0.136 1684 Planarity : 0.003 0.054 1820 Dihedral : 3.532 22.470 1457 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.03 % Favored : 94.74 % Rotamer: Outliers : 0.35 % Allowed : 13.96 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1332 helix: 2.76 (0.26), residues: 389 sheet: -0.08 (0.28), residues: 370 loop : -1.46 (0.26), residues: 573 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 155 average time/residue: 0.5052 time to fit residues: 109.8584 Evaluate side-chains 148 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.654 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2262 time to fit residues: 3.6796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10643 Z= 0.170 Angle : 0.503 8.554 14486 Z= 0.260 Chirality : 0.040 0.136 1684 Planarity : 0.003 0.054 1820 Dihedral : 3.519 22.058 1457 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.63 % Favored : 94.14 % Rotamer: Outliers : 0.26 % Allowed : 14.31 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.30 (0.24), residues: 1332 helix: 2.65 (0.26), residues: 401 sheet: -0.10 (0.28), residues: 370 loop : -1.47 (0.26), residues: 561 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 150 average time/residue: 0.4819 time to fit residues: 103.8824 Evaluate side-chains 147 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2883 time to fit residues: 2.9430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.156127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118394 restraints weight = 51518.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119408 restraints weight = 50285.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120369 restraints weight = 46173.024| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10643 Z= 0.202 Angle : 0.517 9.346 14486 Z= 0.268 Chirality : 0.040 0.137 1684 Planarity : 0.003 0.053 1820 Dihedral : 3.594 22.393 1457 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.53 % Favored : 93.24 % Rotamer: Outliers : 0.18 % Allowed : 14.75 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1332 helix: 2.62 (0.26), residues: 401 sheet: -0.12 (0.28), residues: 370 loop : -1.50 (0.26), residues: 561 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.54 seconds wall clock time: 73 minutes 36.12 seconds (4416.12 seconds total)