Starting phenix.real_space_refine (version: dev) on Tue Feb 21 02:57:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/02_2023/8ew0_28639.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/02_2023/8ew0_28639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/02_2023/8ew0_28639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/02_2023/8ew0_28639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/02_2023/8ew0_28639.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/02_2023/8ew0_28639.pdb" } resolution = 2.7 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 68": "OD1" <-> "OD2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "D ASP 69": "OD1" <-> "OD2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 404": "OD1" <-> "OD2" Residue "D TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D ASP 476": "OD1" <-> "OD2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E ASP 119": "OD1" <-> "OD2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 458": "OE1" <-> "OE2" Residue "E TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 476": "OD1" <-> "OD2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 119": "OD1" <-> "OD2" Residue "F ASP 138": "OD1" <-> "OD2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F ASP 168": "OD1" <-> "OD2" Residue "F TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "F TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F ASP 438": "OD1" <-> "OD2" Residue "F ASP 447": "OD1" <-> "OD2" Residue "F GLU 458": "OE1" <-> "OE2" Residue "F ASP 476": "OD1" <-> "OD2" Residue "F GLU 487": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13636 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2276 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 2 Chain: "B" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2268 Classifications: {'peptide': 290} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 278} Chain breaks: 2 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2272 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Chain: "D" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2272 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2276 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 2 Chain: "F" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2272 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Time building chain proxies: 7.66, per 1000 atoms: 0.56 Number of scatterers: 13636 At special positions: 0 Unit cell: (91.84, 95.94, 155.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2557 8.00 N 2419 7.00 C 8588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 2.1 seconds 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 3 sheets defined 59.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.548A pdb=" N TYR A 136 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.527A pdb=" N CYS A 197 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.603A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.804A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.550A pdb=" N ALA A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 118 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.584A pdb=" N TYR B 136 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.557A pdb=" N CYS B 197 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 421 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.806A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 Processing helix chain 'C' and resid 100 through 118 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.218A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.546A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 421 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.867A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.515A pdb=" N ALA C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.674A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.522A pdb=" N MET D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.511A pdb=" N CYS D 197 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 226 Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 421 Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.830A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 489 removed outlier: 3.590A pdb=" N ALA D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 118 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.023A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 226 Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 421 Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.836A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 489 removed outlier: 3.771A pdb=" N ALA E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.280A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 226 Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 398 through 421 removed outlier: 3.574A pdb=" N PHE F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.873A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 489 removed outlier: 3.550A pdb=" N ALA F 480 " --> pdb=" O ASP F 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.510A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS A 90 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA A 127 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY A 92 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL A 129 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 94 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS E 90 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA E 127 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY E 92 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL E 129 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG E 94 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.535A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS B 90 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA B 127 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY B 92 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 129 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 94 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS D 90 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA D 127 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY D 92 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL D 129 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG D 94 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.569A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS C 90 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA C 127 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 92 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL C 129 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG C 94 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2469 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4512 1.34 - 1.46: 2958 1.46 - 1.58: 6334 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 13924 Sorted by residual: bond pdb=" C ARG C 86 " pdb=" N THR C 87 " ideal model delta sigma weight residual 1.331 1.276 0.055 1.36e-02 5.41e+03 1.64e+01 bond pdb=" C LYS C 53 " pdb=" N PRO C 54 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.20e-02 6.94e+03 4.03e+00 bond pdb=" C LYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.20e-02 6.94e+03 4.00e+00 bond pdb=" C LYS B 53 " pdb=" N PRO B 54 " ideal model delta sigma weight residual 1.329 1.352 -0.023 1.20e-02 6.94e+03 3.80e+00 bond pdb=" C LYS F 53 " pdb=" N PRO F 54 " ideal model delta sigma weight residual 1.329 1.351 -0.023 1.20e-02 6.94e+03 3.59e+00 ... (remaining 13919 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.84: 373 106.84 - 113.62: 7625 113.62 - 120.40: 5111 120.40 - 127.18: 5540 127.18 - 133.97: 148 Bond angle restraints: 18797 Sorted by residual: angle pdb=" N ILE F 430 " pdb=" CA ILE F 430 " pdb=" C ILE F 430 " ideal model delta sigma weight residual 113.47 108.65 4.82 1.01e+00 9.80e-01 2.27e+01 angle pdb=" C ARG C 86 " pdb=" N THR C 87 " pdb=" CA THR C 87 " ideal model delta sigma weight residual 122.70 130.94 -8.24 1.98e+00 2.55e-01 1.73e+01 angle pdb=" CB MET C 411 " pdb=" CG MET C 411 " pdb=" SD MET C 411 " ideal model delta sigma weight residual 112.70 122.95 -10.25 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C SER C 213 " pdb=" N ALA C 214 " pdb=" CA ALA C 214 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.68e+00 angle pdb=" C LYS C 90 " pdb=" N GLY C 91 " pdb=" CA GLY C 91 " ideal model delta sigma weight residual 120.92 117.65 3.27 1.30e+00 5.92e-01 6.34e+00 ... (remaining 18792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 6973 18.07 - 36.15: 951 36.15 - 54.22: 281 54.22 - 72.29: 56 72.29 - 90.37: 20 Dihedral angle restraints: 8281 sinusoidal: 3300 harmonic: 4981 Sorted by residual: dihedral pdb=" CG ARG A 66 " pdb=" CD ARG A 66 " pdb=" NE ARG A 66 " pdb=" CZ ARG A 66 " ideal model delta sinusoidal sigma weight residual 90.00 41.03 48.97 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA ASP D 138 " pdb=" CB ASP D 138 " pdb=" CG ASP D 138 " pdb=" OD1 ASP D 138 " ideal model delta sinusoidal sigma weight residual -30.00 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CB GLU F 103 " pdb=" CG GLU F 103 " pdb=" CD GLU F 103 " pdb=" OE1 GLU F 103 " ideal model delta sinusoidal sigma weight residual 0.00 90.37 -90.37 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 8278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1066 0.026 - 0.053: 561 0.053 - 0.079: 283 0.079 - 0.105: 102 0.105 - 0.132: 28 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " 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 ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA ILE F 75 " pdb=" N ILE F 75 " pdb=" C ILE F 75 " pdb=" CB ILE F 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 2037 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 428 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.67e+00 pdb=" N PRO C 429 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 429 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 429 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 164 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 165 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 431 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO C 432 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 432 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 432 " -0.028 5.00e-02 4.00e+02 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2178 2.76 - 3.29: 12520 3.29 - 3.83: 24373 3.83 - 4.36: 28413 4.36 - 4.90: 48543 Nonbonded interactions: 116027 Sorted by model distance: nonbonded pdb=" OE2 GLU E 458 " pdb=" NH1 ARG E 462 " model vdw 2.224 2.520 nonbonded pdb=" NH2 ARG C 79 " pdb=" OD1 ASP C 163 " model vdw 2.226 2.520 nonbonded pdb=" OD2 ASP E 69 " pdb=" OG SER E 71 " model vdw 2.239 2.440 nonbonded pdb=" NZ LYS E 90 " pdb=" OG1 THR E 199 " model vdw 2.239 2.520 nonbonded pdb=" O ASP B 181 " pdb=" OG SER B 185 " model vdw 2.254 2.440 ... (remaining 116022 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 53 through 422 or resid 427 through 489)) selection = chain 'B' selection = (chain 'C' and (resid 53 through 422 or resid 427 through 489)) selection = (chain 'D' and (resid 53 through 422 or resid 427 through 489)) selection = (chain 'E' and (resid 53 through 422 or resid 427 through 489)) selection = (chain 'F' and (resid 53 through 422 or resid 427 through 489)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8588 2.51 5 N 2419 2.21 5 O 2557 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: 0.770 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: 5.060 Check model and map are aligned: 0.220 Process input model: 36.570 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 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 : 0.003 0.055 13924 Z= 0.191 Angle : 0.572 10.248 18797 Z= 0.353 Chirality : 0.041 0.132 2040 Planarity : 0.005 0.069 2425 Dihedral : 18.435 90.369 5113 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.87 % Favored : 98.01 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.98 (0.21), residues: 1711 helix: 2.65 (0.16), residues: 936 sheet: -0.31 (0.31), residues: 279 loop : -0.29 (0.28), residues: 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 207 time to evaluate : 1.685 Fit side-chains outliers start: 41 outliers final: 29 residues processed: 238 average time/residue: 1.6715 time to fit residues: 425.3921 Evaluate side-chains 227 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 0.1668 time to fit residues: 2.4448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 135 ASN C 414 GLN D 56 ASN D 84 GLN D 135 ASN E 414 GLN E 472 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 13924 Z= 0.409 Angle : 0.610 7.881 18797 Z= 0.333 Chirality : 0.049 0.149 2040 Planarity : 0.005 0.060 2425 Dihedral : 4.502 19.321 1921 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.90 % Rotamer Outliers : 7.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.21), residues: 1711 helix: 2.49 (0.16), residues: 950 sheet: -0.34 (0.31), residues: 283 loop : -0.01 (0.29), residues: 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 200 time to evaluate : 1.723 Fit side-chains outliers start: 109 outliers final: 64 residues processed: 266 average time/residue: 1.5939 time to fit residues: 454.9176 Evaluate side-chains 261 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 197 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 43 residues processed: 21 average time/residue: 0.4238 time to fit residues: 13.0308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 189 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN D 472 ASN E 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 13924 Z= 0.254 Angle : 0.511 8.534 18797 Z= 0.278 Chirality : 0.043 0.135 2040 Planarity : 0.005 0.059 2425 Dihedral : 4.205 17.802 1921 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.52 % Favored : 98.36 % Rotamer Outliers : 6.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.25 (0.21), residues: 1711 helix: 2.78 (0.16), residues: 950 sheet: -0.29 (0.32), residues: 282 loop : 0.01 (0.29), residues: 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 203 time to evaluate : 1.720 Fit side-chains outliers start: 96 outliers final: 58 residues processed: 262 average time/residue: 1.6456 time to fit residues: 461.9378 Evaluate side-chains 259 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 201 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 41 residues processed: 17 average time/residue: 0.4804 time to fit residues: 12.1664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 84 GLN E 84 GLN F 82 HIS F 437 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 13924 Z= 0.470 Angle : 0.635 9.613 18797 Z= 0.347 Chirality : 0.050 0.156 2040 Planarity : 0.005 0.058 2425 Dihedral : 4.643 20.123 1921 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.63 % Favored : 97.25 % Rotamer Outliers : 7.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.86 (0.20), residues: 1711 helix: 2.40 (0.16), residues: 947 sheet: -0.33 (0.32), residues: 282 loop : -0.09 (0.29), residues: 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 202 time to evaluate : 1.674 Fit side-chains outliers start: 112 outliers final: 68 residues processed: 267 average time/residue: 1.5721 time to fit residues: 450.9108 Evaluate side-chains 266 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 198 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 46 residues processed: 22 average time/residue: 0.3758 time to fit residues: 12.8261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN E 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13924 Z= 0.228 Angle : 0.499 9.609 18797 Z= 0.271 Chirality : 0.042 0.133 2040 Planarity : 0.004 0.060 2425 Dihedral : 4.198 17.904 1921 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.64 % Favored : 98.25 % Rotamer Outliers : 5.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.30 (0.21), residues: 1711 helix: 2.81 (0.16), residues: 950 sheet: -0.25 (0.32), residues: 282 loop : 0.02 (0.29), residues: 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 205 time to evaluate : 1.820 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 56 residues processed: 265 average time/residue: 1.6066 time to fit residues: 457.3699 Evaluate side-chains 258 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 202 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 46 residues processed: 10 average time/residue: 0.1332 time to fit residues: 4.4374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 168 optimal weight: 0.0020 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 84 GLN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13924 Z= 0.228 Angle : 0.499 10.633 18797 Z= 0.268 Chirality : 0.042 0.132 2040 Planarity : 0.004 0.059 2425 Dihedral : 4.118 17.498 1921 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.10 % Favored : 97.78 % Rotamer Outliers : 5.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.44 (0.21), residues: 1711 helix: 2.95 (0.16), residues: 950 sheet: -0.25 (0.32), residues: 282 loop : 0.05 (0.29), residues: 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 207 time to evaluate : 1.670 Fit side-chains outliers start: 85 outliers final: 61 residues processed: 263 average time/residue: 1.4497 time to fit residues: 410.6839 Evaluate side-chains 268 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 207 time to evaluate : 1.660 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 48 residues processed: 13 average time/residue: 0.5031 time to fit residues: 10.2770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 84 GLN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13924 Z= 0.159 Angle : 0.457 11.152 18797 Z= 0.243 Chirality : 0.040 0.125 2040 Planarity : 0.004 0.059 2425 Dihedral : 3.854 16.220 1921 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.69 % Favored : 98.19 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.69 (0.21), residues: 1711 helix: 3.23 (0.16), residues: 950 sheet: -0.23 (0.32), residues: 282 loop : 0.07 (0.29), residues: 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 210 time to evaluate : 1.603 Fit side-chains outliers start: 71 outliers final: 57 residues processed: 261 average time/residue: 1.4371 time to fit residues: 403.2463 Evaluate side-chains 263 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 206 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 47 residues processed: 10 average time/residue: 0.2738 time to fit residues: 6.0470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 84 GLN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13924 Z= 0.333 Angle : 0.563 12.958 18797 Z= 0.302 Chirality : 0.046 0.144 2040 Planarity : 0.005 0.057 2425 Dihedral : 4.299 18.917 1921 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.16 % Favored : 97.72 % Rotamer Outliers : 5.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.37 (0.21), residues: 1711 helix: 2.88 (0.16), residues: 947 sheet: -0.20 (0.32), residues: 282 loop : 0.03 (0.29), residues: 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 201 time to evaluate : 1.618 Fit side-chains outliers start: 84 outliers final: 60 residues processed: 256 average time/residue: 1.5613 time to fit residues: 429.6491 Evaluate side-chains 261 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 201 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 48 residues processed: 12 average time/residue: 0.7078 time to fit residues: 11.9175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 84 GLN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13924 Z= 0.190 Angle : 0.487 12.624 18797 Z= 0.258 Chirality : 0.041 0.126 2040 Planarity : 0.004 0.058 2425 Dihedral : 3.997 17.079 1921 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.58 % Favored : 98.31 % Rotamer Outliers : 4.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.59 (0.21), residues: 1711 helix: 3.14 (0.16), residues: 947 sheet: -0.23 (0.32), residues: 282 loop : 0.03 (0.29), residues: 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 200 time to evaluate : 1.655 Fit side-chains outliers start: 63 outliers final: 53 residues processed: 251 average time/residue: 1.5765 time to fit residues: 425.4858 Evaluate side-chains 252 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 48 residues processed: 5 average time/residue: 0.3581 time to fit residues: 4.6226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 84 GLN E 84 GLN E 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 13924 Z= 0.396 Angle : 0.608 13.695 18797 Z= 0.327 Chirality : 0.048 0.180 2040 Planarity : 0.005 0.055 2425 Dihedral : 4.461 19.702 1921 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.57 % Favored : 97.31 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.17 (0.20), residues: 1711 helix: 2.69 (0.16), residues: 947 sheet: -0.24 (0.32), residues: 282 loop : -0.00 (0.29), residues: 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 198 time to evaluate : 1.658 Fit side-chains outliers start: 70 outliers final: 57 residues processed: 247 average time/residue: 1.5858 time to fit residues: 422.2154 Evaluate side-chains 253 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 47 residues processed: 10 average time/residue: 0.8116 time to fit residues: 11.4280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 84 GLN E 84 GLN E 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.120975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097200 restraints weight = 14471.784| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.18 r_work: 0.2858 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13924 Z= 0.267 Angle : 0.542 13.489 18797 Z= 0.289 Chirality : 0.043 0.178 2040 Planarity : 0.005 0.057 2425 Dihedral : 4.243 18.297 1921 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.90 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.32 (0.21), residues: 1711 helix: 2.85 (0.16), residues: 947 sheet: -0.26 (0.32), residues: 282 loop : 0.00 (0.29), residues: 482 =============================================================================== Job complete usr+sys time: 6178.21 seconds wall clock time: 110 minutes 2.73 seconds (6602.73 seconds total)