Starting phenix.real_space_refine on Sat Mar 16 03:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/03_2024/8ew0_28639.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/03_2024/8ew0_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_28639/03_2024/8ew0_28639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/03_2024/8ew0_28639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/03_2024/8ew0_28639.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew0_28639/03_2024/8ew0_28639.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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 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. 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-5265/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: 6.69, per 1000 atoms: 0.49 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: 4.73 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: 1.19 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: 3.21 Time building geometry restraints manager: 5.15 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 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.370 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.970 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 % Allowed : 27.20 % Favored : 69.97 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 385 HIS 0.004 0.001 HIS D 82 PHE 0.010 0.001 PHE B 63 TYR 0.010 0.001 TYR C 190 ARG 0.010 0.000 ARG A 66 *********************** 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 : 1.581 Fit side-chains REVERT: A 66 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7939 (mtp180) REVERT: B 435 GLU cc_start: 0.7245 (pm20) cc_final: 0.6940 (pt0) REVERT: C 472 ASN cc_start: 0.7752 (t0) cc_final: 0.7529 (t0) REVERT: D 78 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.6918 (p90) outliers start: 41 outliers final: 29 residues processed: 238 average time/residue: 1.6154 time to fit residues: 411.4325 Evaluate side-chains 228 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 170 SER 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: 3.9990 chunk 136 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** B 472 ASN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13924 Z= 0.381 Angle : 0.592 7.591 18797 Z= 0.323 Chirality : 0.048 0.148 2040 Planarity : 0.005 0.061 2425 Dihedral : 7.016 62.797 1975 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 6.27 % Allowed : 22.66 % Favored : 71.07 % 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: 2.04 (0.21), residues: 1711 helix: 2.56 (0.16), residues: 950 sheet: -0.34 (0.31), residues: 283 loop : 0.00 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 385 HIS 0.008 0.002 HIS C 195 PHE 0.012 0.002 PHE E 226 TYR 0.014 0.002 TYR C 190 ARG 0.006 0.001 ARG A 66 *********************** 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 289 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 198 time to evaluate : 1.418 Fit side-chains REVERT: A 66 ARG cc_start: 0.8281 (ttt90) cc_final: 0.8081 (mtp180) REVERT: A 142 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: A 387 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8963 (tttp) REVERT: A 397 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8715 (mt) REVERT: A 438 ASP cc_start: 0.7616 (m-30) cc_final: 0.7389 (m-30) REVERT: A 459 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: B 78 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7034 (p90) REVERT: B 84 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: C 84 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: C 397 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8672 (mt) REVERT: C 459 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7706 (ttm170) REVERT: C 472 ASN cc_start: 0.7832 (t0) cc_final: 0.7477 (t0) REVERT: D 78 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7057 (p90) REVERT: E 195 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.7030 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8888 (mm110) REVERT: E 435 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7416 (mp0) outliers start: 91 outliers final: 47 residues processed: 249 average time/residue: 1.6250 time to fit residues: 433.6209 Evaluate side-chains 255 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 196 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN E 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0888 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= 0.200 Angle : 0.481 8.626 18797 Z= 0.262 Chirality : 0.041 0.131 2040 Planarity : 0.004 0.060 2425 Dihedral : 5.982 77.240 1949 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.46 % Favored : 98.42 % Rotamer: Outliers : 5.30 % Allowed : 22.93 % Favored : 71.76 % 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: 2.41 (0.21), residues: 1711 helix: 2.93 (0.16), residues: 950 sheet: -0.30 (0.32), residues: 282 loop : 0.07 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 385 HIS 0.004 0.001 HIS C 195 PHE 0.009 0.001 PHE B 63 TYR 0.011 0.001 TYR C 190 ARG 0.005 0.000 ARG A 66 *********************** 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 280 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 203 time to evaluate : 1.611 Fit side-chains REVERT: A 459 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7727 (ttm170) REVERT: B 78 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.6951 (p90) REVERT: B 84 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: B 465 MET cc_start: 0.8226 (mtt) cc_final: 0.7980 (mtt) REVERT: B 469 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6348 (mpp) REVERT: C 84 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: C 195 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.6222 (t70) REVERT: C 459 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7765 (ttm170) REVERT: C 472 ASN cc_start: 0.7842 (t0) cc_final: 0.7486 (t0) REVERT: D 78 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7038 (p90) REVERT: D 138 ASP cc_start: 0.8254 (m-30) cc_final: 0.8013 (m-30) REVERT: E 195 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6979 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8885 (mm110) REVERT: F 435 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7373 (mp0) outliers start: 77 outliers final: 40 residues processed: 247 average time/residue: 1.6631 time to fit residues: 439.6430 Evaluate side-chains 254 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 204 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 56 ASN D 82 HIS D 84 GLN E 84 GLN E 414 GLN F 82 HIS F 437 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.066 13924 Z= 0.623 Angle : 0.718 10.176 18797 Z= 0.393 Chirality : 0.056 0.178 2040 Planarity : 0.006 0.057 2425 Dihedral : 6.056 54.845 1941 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.57 % Favored : 97.31 % Rotamer: Outliers : 7.71 % Allowed : 21.07 % Favored : 71.21 % 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: 1.61 (0.20), residues: 1711 helix: 2.14 (0.16), residues: 950 sheet: -0.35 (0.31), residues: 283 loop : -0.12 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 385 HIS 0.014 0.002 HIS C 195 PHE 0.012 0.003 PHE F 220 TYR 0.025 0.003 TYR C 190 ARG 0.007 0.001 ARG E 86 *********************** 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 : 1.776 Fit side-chains REVERT: A 387 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9053 (tttp) REVERT: A 420 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7982 (tptt) REVERT: A 459 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7703 (ttm170) REVERT: B 78 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7151 (p90) REVERT: B 84 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: C 84 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: C 195 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6100 (t70) REVERT: C 459 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7705 (ttm170) REVERT: D 138 ASP cc_start: 0.8283 (m-30) cc_final: 0.8021 (m-30) REVERT: E 173 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: E 205 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8929 (mm110) REVERT: E 398 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8285 (p) outliers start: 112 outliers final: 61 residues processed: 268 average time/residue: 1.5844 time to fit residues: 455.2019 Evaluate side-chains 272 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 200 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 D 56 ASN D 84 GLN E 84 GLN F 437 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13924 Z= 0.139 Angle : 0.444 10.677 18797 Z= 0.241 Chirality : 0.039 0.121 2040 Planarity : 0.004 0.057 2425 Dihedral : 5.207 55.925 1939 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.46 % Favored : 98.42 % Rotamer: Outliers : 4.41 % Allowed : 23.97 % Favored : 71.63 % 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: 2.48 (0.21), residues: 1711 helix: 3.02 (0.16), residues: 950 sheet: -0.24 (0.31), residues: 282 loop : 0.02 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 385 HIS 0.005 0.001 HIS E 195 PHE 0.008 0.001 PHE B 63 TYR 0.007 0.001 TYR C 190 ARG 0.005 0.000 ARG E 86 *********************** 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 271 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 207 time to evaluate : 1.680 Fit side-chains REVERT: A 397 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8707 (mt) REVERT: A 420 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7929 (tptt) REVERT: A 459 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7778 (ttm170) REVERT: B 78 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.6935 (p90) REVERT: B 414 GLN cc_start: 0.8503 (tt0) cc_final: 0.8136 (tt0) REVERT: B 465 MET cc_start: 0.8319 (mtt) cc_final: 0.8025 (mtt) REVERT: B 469 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6304 (mpp) REVERT: C 195 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.5969 (t70) REVERT: C 397 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8709 (mt) REVERT: C 459 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7770 (ttm170) REVERT: D 138 ASP cc_start: 0.8207 (m-30) cc_final: 0.7958 (m-30) REVERT: E 205 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8954 (mm110) REVERT: F 397 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8466 (mm) outliers start: 64 outliers final: 29 residues processed: 243 average time/residue: 1.6640 time to fit residues: 432.1686 Evaluate side-chains 239 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 162 optimal weight: 0.0030 overall best weight: 2.3194 ------------------------------------------------------------------------------- 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 C 414 GLN D 84 GLN F 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13924 Z= 0.222 Angle : 0.495 12.606 18797 Z= 0.265 Chirality : 0.042 0.134 2040 Planarity : 0.004 0.059 2425 Dihedral : 5.138 55.484 1937 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 4.75 % Allowed : 23.69 % Favored : 71.56 % 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: 2.54 (0.21), residues: 1711 helix: 3.06 (0.16), residues: 950 sheet: -0.21 (0.31), residues: 282 loop : 0.04 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 385 HIS 0.005 0.001 HIS C 195 PHE 0.009 0.001 PHE B 63 TYR 0.010 0.001 TYR C 190 ARG 0.004 0.000 ARG E 86 *********************** 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 272 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 203 time to evaluate : 1.629 Fit side-chains REVERT: A 397 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8715 (mt) REVERT: A 420 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7913 (tptt) REVERT: A 459 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7797 (ttm170) REVERT: B 78 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7007 (p90) REVERT: B 84 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: B 414 GLN cc_start: 0.8533 (tt0) cc_final: 0.8217 (tt0) REVERT: B 465 MET cc_start: 0.8358 (mtt) cc_final: 0.8018 (mtt) REVERT: B 469 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6336 (mpp) REVERT: C 195 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6076 (t70) REVERT: C 397 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8753 (mt) REVERT: C 459 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7798 (ttm170) REVERT: E 205 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8957 (mm110) REVERT: F 397 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8524 (mm) outliers start: 69 outliers final: 33 residues processed: 238 average time/residue: 1.6407 time to fit residues: 417.9242 Evaluate side-chains 246 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 202 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN 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: 0.7980 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.8816 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13924 Z= 0.162 Angle : 0.454 10.983 18797 Z= 0.242 Chirality : 0.040 0.125 2040 Planarity : 0.004 0.060 2425 Dihedral : 4.950 54.873 1937 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.58 % Favored : 98.31 % Rotamer: Outliers : 4.41 % Allowed : 24.04 % Favored : 71.56 % 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: 2.73 (0.21), residues: 1711 helix: 3.27 (0.16), residues: 950 sheet: -0.19 (0.31), residues: 282 loop : 0.05 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 385 HIS 0.003 0.001 HIS C 195 PHE 0.008 0.001 PHE B 63 TYR 0.008 0.001 TYR C 190 ARG 0.004 0.000 ARG E 86 *********************** 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 268 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 1.638 Fit side-chains REVERT: A 397 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8710 (mt) REVERT: A 420 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7867 (tptt) REVERT: A 459 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7776 (ttm170) REVERT: B 78 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.6878 (p90) REVERT: B 84 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: B 414 GLN cc_start: 0.8474 (tt0) cc_final: 0.8043 (tt0) REVERT: B 465 MET cc_start: 0.8329 (mtt) cc_final: 0.7992 (mtt) REVERT: B 469 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6267 (mpp) REVERT: C 195 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.5970 (t70) REVERT: C 397 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8752 (mt) REVERT: C 459 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7766 (ttm170) REVERT: E 205 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8969 (mm110) outliers start: 64 outliers final: 34 residues processed: 240 average time/residue: 1.7124 time to fit residues: 438.8905 Evaluate side-chains 243 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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: 0.8843 moved from start: 0.1254 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= 0.232 Angle : 0.498 12.299 18797 Z= 0.265 Chirality : 0.042 0.135 2040 Planarity : 0.004 0.060 2425 Dihedral : 5.088 55.281 1937 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.84 % Rotamer: Outliers : 5.23 % Allowed : 23.00 % Favored : 71.76 % 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: 2.63 (0.21), residues: 1711 helix: 3.16 (0.16), residues: 947 sheet: -0.18 (0.32), residues: 282 loop : 0.04 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 385 HIS 0.005 0.001 HIS C 195 PHE 0.009 0.001 PHE A 63 TYR 0.011 0.001 TYR C 190 ARG 0.003 0.000 ARG E 86 *********************** 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 276 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 200 time to evaluate : 1.700 Fit side-chains REVERT: A 397 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 420 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7869 (tptt) REVERT: A 459 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7808 (ttm170) REVERT: B 78 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6923 (p90) REVERT: B 84 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: B 414 GLN cc_start: 0.8543 (tt0) cc_final: 0.8285 (tt0) REVERT: B 465 MET cc_start: 0.8364 (mtt) cc_final: 0.8023 (mtt) REVERT: B 469 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6325 (mpp) REVERT: C 84 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: C 195 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6065 (t70) REVERT: C 397 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8751 (mt) REVERT: C 458 GLU cc_start: 0.8310 (tt0) cc_final: 0.8034 (tt0) REVERT: C 459 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7780 (ttm170) REVERT: E 205 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8973 (mm110) REVERT: F 397 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8376 (mm) outliers start: 76 outliers final: 44 residues processed: 243 average time/residue: 1.6155 time to fit residues: 420.1225 Evaluate side-chains 253 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 102 optimal weight: 0.1980 chunk 165 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 56 ASN D 84 GLN E 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13924 Z= 0.142 Angle : 0.445 12.366 18797 Z= 0.235 Chirality : 0.039 0.125 2040 Planarity : 0.004 0.062 2425 Dihedral : 4.816 54.919 1937 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 3.58 % Allowed : 24.59 % Favored : 71.83 % 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: 2.85 (0.21), residues: 1711 helix: 3.41 (0.16), residues: 947 sheet: -0.18 (0.31), residues: 282 loop : 0.03 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 385 HIS 0.003 0.001 HIS D 195 PHE 0.007 0.001 PHE B 63 TYR 0.008 0.001 TYR C 190 ARG 0.004 0.000 ARG D 66 *********************** 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 253 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 201 time to evaluate : 1.571 Fit side-chains REVERT: A 397 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 420 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7930 (tptt) REVERT: A 459 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7749 (ttm170) REVERT: B 78 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.6941 (p90) REVERT: B 84 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7776 (mp10) REVERT: B 414 GLN cc_start: 0.8441 (tt0) cc_final: 0.8039 (tt0) REVERT: C 84 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: C 195 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.5989 (t70) REVERT: C 397 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8762 (mt) outliers start: 52 outliers final: 29 residues processed: 229 average time/residue: 1.6427 time to fit residues: 402.0724 Evaluate side-chains 236 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE 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: 9.9990 chunk 114 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 56 ASN D 84 GLN E 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13924 Z= 0.390 Angle : 0.592 13.257 18797 Z= 0.318 Chirality : 0.048 0.146 2040 Planarity : 0.005 0.060 2425 Dihedral : 5.107 56.966 1931 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.10 % Favored : 97.78 % Rotamer: Outliers : 4.27 % Allowed : 24.10 % Favored : 71.63 % 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: 2.34 (0.20), residues: 1711 helix: 2.83 (0.16), residues: 947 sheet: -0.16 (0.32), residues: 282 loop : 0.05 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 72 HIS 0.008 0.001 HIS C 195 PHE 0.012 0.002 PHE C 63 TYR 0.016 0.002 TYR C 190 ARG 0.006 0.001 ARG D 66 ********************** 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 264 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 1.689 Fit side-chains REVERT: A 397 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8732 (mt) REVERT: A 420 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7957 (tptt) REVERT: A 459 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7794 (ttm170) REVERT: B 78 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7043 (p90) REVERT: B 84 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: B 414 GLN cc_start: 0.8630 (tt0) cc_final: 0.8394 (tt0) REVERT: C 84 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: C 195 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6121 (t70) REVERT: C 397 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 414 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: C 458 GLU cc_start: 0.8339 (tt0) cc_final: 0.8055 (tt0) REVERT: E 94 ARG cc_start: 0.8519 (ttm170) cc_final: 0.8290 (ttm170) REVERT: E 205 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8928 (mm110) REVERT: E 466 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7255 (ttp-110) REVERT: F 397 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8504 (mm) outliers start: 62 outliers final: 37 residues processed: 239 average time/residue: 1.6503 time to fit residues: 422.2057 Evaluate side-chains 248 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU 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: 2.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.097353 restraints weight = 14705.993| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.33 r_work: 0.2808 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13924 Z= 0.211 Angle : 0.498 12.827 18797 Z= 0.265 Chirality : 0.041 0.127 2040 Planarity : 0.004 0.060 2425 Dihedral : 4.909 61.354 1931 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.64 % Favored : 98.25 % Rotamer: Outliers : 3.37 % Allowed : 25.00 % Favored : 71.63 % 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: 2.54 (0.21), residues: 1711 helix: 3.04 (0.16), residues: 947 sheet: -0.16 (0.32), residues: 282 loop : 0.06 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 385 HIS 0.004 0.001 HIS C 195 PHE 0.009 0.001 PHE C 63 TYR 0.012 0.001 TYR C 190 ARG 0.005 0.000 ARG D 66 =============================================================================== Job complete usr+sys time: 6272.59 seconds wall clock time: 111 minutes 55.50 seconds (6715.50 seconds total)