Starting phenix.real_space_refine on Thu Mar 21 10:55:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw9_27024/03_2024/8cw9_27024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw9_27024/03_2024/8cw9_27024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw9_27024/03_2024/8cw9_27024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw9_27024/03_2024/8cw9_27024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw9_27024/03_2024/8cw9_27024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw9_27024/03_2024/8cw9_27024.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9645 atoms to isotropic. 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 135 5.16 5 C 12708 2.51 5 N 3420 2.21 5 O 3966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20229 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3260 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3260 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 415} Chain breaks: 1 Chain: "F" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3260 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 415} Chain breaks: 1 Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 963 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 963 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.48, per 1000 atoms: 0.52 Number of scatterers: 20229 At special positions: 0 Unit cell: (148.989, 144.889, 124.386, 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 135 16.00 O 3966 8.00 N 3420 7.00 C 12708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 407 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 283 " - pdb=" SG CYS E 311 " distance=2.03 Simple disulfide: pdb=" SG CYS E 292 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 326 " - pdb=" SG CYS E 335 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 365 " - pdb=" SG CYS E 463 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 390 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 407 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 311 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 326 " - pdb=" SG CYS F 335 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 365 " - pdb=" SG CYS F 463 " distance=2.03 Simple disulfide: pdb=" SG CYS F 384 " - pdb=" SG CYS F 390 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 57 " " NAG E 601 " - " ASN E 57 " " NAG F 601 " - " ASN F 57 " Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 3.6 seconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 54 sheets defined 20.3% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.657A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.915A pdb=" N ILE A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 186 through 210 removed outlier: 4.025A pdb=" N ALA A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.515A pdb=" N VAL A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 84 Processing helix chain 'E' and resid 104 through 129 removed outlier: 4.008A pdb=" N ILE E 108 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 163 through 171 Processing helix chain 'E' and resid 171 through 177 removed outlier: 3.601A pdb=" N ARG E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 197 Processing helix chain 'E' and resid 197 through 209 Processing helix chain 'E' and resid 223 through 234 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 247 through 255 Processing helix chain 'E' and resid 344 through 347 Processing helix chain 'E' and resid 348 through 354 Processing helix chain 'E' and resid 441 through 446 Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'F' and resid 65 through 84 Processing helix chain 'F' and resid 104 through 129 removed outlier: 4.229A pdb=" N ILE F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 144 removed outlier: 4.275A pdb=" N LYS F 143 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR F 144 " --> pdb=" O CYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 187 through 210 removed outlier: 4.464A pdb=" N ARG F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 234 Processing helix chain 'F' and resid 237 through 246 Processing helix chain 'F' and resid 247 through 255 Processing helix chain 'F' and resid 344 through 347 Processing helix chain 'F' and resid 348 through 354 removed outlier: 3.512A pdb=" N ILE F 354 " --> pdb=" O CYS F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 446 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 279 removed outlier: 3.702A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.727A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 8.303A pdb=" N ARG A 156 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR A 45 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 158 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET A 270 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU A 259 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN A 272 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY A 257 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 293 removed outlier: 7.137A pdb=" N CYS A 365 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE A 456 " --> pdb=" O CYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.798A pdb=" N ILE A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN A 402 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.647A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG C 50 " --> pdb=" O VAL C 35A" (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 35A" --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP C 52 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET C 34 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG C 50 " --> pdb=" O VAL C 35A" (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 35A" --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP C 52 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET C 34 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.817A pdb=" N THR D 72 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.451A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 13 Processing sheet with id=AB7, first strand: chain 'E' and resid 278 through 279 removed outlier: 3.907A pdb=" N VAL E 278 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY E 34 " --> pdb=" O CYS E 283 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS E 283 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP E 309 " --> pdb=" O TYR E 320 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 317 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 327 through 329 removed outlier: 6.823A pdb=" N GLU E 21 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE E 437 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR E 23 " --> pdb=" O ILE E 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 146 through 150 removed outlier: 8.160A pdb=" N ARG E 156 " --> pdb=" O TRP E 43 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR E 45 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 158 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET E 270 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU E 259 " --> pdb=" O MET E 270 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN E 272 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY E 257 " --> pdb=" O GLN E 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 291 through 293 removed outlier: 7.095A pdb=" N CYS E 365 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE E 456 " --> pdb=" O CYS E 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 372 through 376 Processing sheet with id=AC3, first strand: chain 'E' and resid 398 through 402 removed outlier: 6.890A pdb=" N ILE E 392 " --> pdb=" O ILE E 400 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN E 402 " --> pdb=" O CYS E 390 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS E 390 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 278 through 279 removed outlier: 3.844A pdb=" N VAL F 278 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY F 34 " --> pdb=" O CYS F 283 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS F 283 " --> pdb=" O GLY F 34 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TRP F 309 " --> pdb=" O TYR F 320 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 328 through 329 Processing sheet with id=AC6, first strand: chain 'F' and resid 146 through 150 removed outlier: 9.191A pdb=" N TRP F 43 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LEU F 158 " --> pdb=" O TRP F 43 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR F 45 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR F 160 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL F 47 " --> pdb=" O THR F 160 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL F 162 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR F 49 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET F 270 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU F 259 " --> pdb=" O MET F 270 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN F 272 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY F 257 " --> pdb=" O GLN F 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 291 through 293 removed outlier: 7.248A pdb=" N CYS F 365 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE F 456 " --> pdb=" O CYS F 365 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 372 through 375 removed outlier: 3.518A pdb=" N CYS F 384 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 398 through 402 removed outlier: 6.973A pdb=" N ILE F 392 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN F 402 " --> pdb=" O CYS F 390 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS F 390 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.517A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N GLY G 10 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR G 121 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER G 33 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N GLY G 10 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR G 121 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N CYS G 96 " --> pdb=" O TRP G 114 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP G 114 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG G 98 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP H 52 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET H 34 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP H 52 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET H 34 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.533A pdb=" N SER I 70 " --> pdb=" O VAL I 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.668A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG I 50 " --> pdb=" O VAL I 35A" (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL I 35A" --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP I 52 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET I 34 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.668A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG I 50 " --> pdb=" O VAL I 35A" (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL I 35A" --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP I 52 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET I 34 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.780A pdb=" N ALA J 23 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS J 96 " --> pdb=" O TRP J 114 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP J 114 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG J 98 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.689A pdb=" N PHE K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.379A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 6 removed outlier: 5.633A pdb=" N GLN L 17 " --> pdb=" O GLY L 77 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.551A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.551A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.331A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AF3, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.571A pdb=" N SER N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.477A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS N 96 " --> pdb=" O TRP N 114 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP N 114 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG N 98 " --> pdb=" O ASP N 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.477A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.403A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 9 through 11 Processing sheet with id=AF9, first strand: chain 'O' and resid 18 through 22 removed outlier: 3.639A pdb=" N ALA O 73 " --> pdb=" O CYS O 22 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.76 Time building geometry restraints manager: 7.96 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: 6550 1.34 - 1.46: 4648 1.46 - 1.58: 9235 1.58 - 1.70: 0 1.70 - 1.83: 177 Bond restraints: 20610 Sorted by residual: bond pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.20e-03 1.18e+04 9.90e+00 bond pdb=" CA ARG F 367 " pdb=" C ARG F 367 " ideal model delta sigma weight residual 1.528 1.504 0.024 1.04e-02 9.25e+03 5.32e+00 bond pdb=" C ARG F 367 " pdb=" N HIS F 368 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.37e-02 5.33e+03 4.61e+00 bond pdb=" C1 NAG F 601 " pdb=" C2 NAG F 601 " ideal model delta sigma weight residual 1.532 1.496 0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C CYS F 365 " pdb=" N GLY F 366 " ideal model delta sigma weight residual 1.325 1.342 -0.017 1.06e-02 8.90e+03 2.58e+00 ... (remaining 20605 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.58: 541 106.58 - 113.44: 11257 113.44 - 120.29: 7133 120.29 - 127.15: 8849 127.15 - 134.00: 198 Bond angle restraints: 27978 Sorted by residual: angle pdb=" N GLY G 9 " pdb=" CA GLY G 9 " pdb=" C GLY G 9 " ideal model delta sigma weight residual 110.80 117.46 -6.66 1.71e+00 3.42e-01 1.52e+01 angle pdb=" CA GLY F 366 " pdb=" C GLY F 366 " pdb=" O GLY F 366 " ideal model delta sigma weight residual 121.48 117.88 3.60 9.90e-01 1.02e+00 1.32e+01 angle pdb=" N ARG F 367 " pdb=" CA ARG F 367 " pdb=" C ARG F 367 " ideal model delta sigma weight residual 109.71 104.66 5.05 1.41e+00 5.03e-01 1.28e+01 angle pdb=" CA CYS E 140 " pdb=" CB CYS E 140 " pdb=" SG CYS E 140 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.22e+01 angle pdb=" CA CYS F 140 " pdb=" CB CYS F 140 " pdb=" SG CYS F 140 " ideal model delta sigma weight residual 114.40 122.26 -7.86 2.30e+00 1.89e-01 1.17e+01 ... (remaining 27973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 11448 17.53 - 35.05: 833 35.05 - 52.58: 157 52.58 - 70.10: 51 70.10 - 87.63: 15 Dihedral angle restraints: 12504 sinusoidal: 4863 harmonic: 7641 Sorted by residual: dihedral pdb=" CB CYS F 365 " pdb=" SG CYS F 365 " pdb=" SG CYS F 463 " pdb=" CB CYS F 463 " ideal model delta sinusoidal sigma weight residual 93.00 157.75 -64.75 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS A 365 " pdb=" SG CYS A 365 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual 93.00 150.48 -57.48 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS E 365 " pdb=" SG CYS E 365 " pdb=" SG CYS E 463 " pdb=" CB CYS E 463 " ideal model delta sinusoidal sigma weight residual 93.00 149.22 -56.22 1 1.00e+01 1.00e-02 4.26e+01 ... (remaining 12501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2205 0.041 - 0.082: 728 0.082 - 0.122: 255 0.122 - 0.163: 43 0.163 - 0.204: 6 Chirality restraints: 3237 Sorted by residual: chirality pdb=" CA TRP I 100 " pdb=" N TRP I 100 " pdb=" C TRP I 100 " pdb=" CB TRP I 100 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASP A 280 " pdb=" N ASP A 280 " pdb=" C ASP A 280 " pdb=" CB ASP A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ASN M 54 " pdb=" N ASN M 54 " pdb=" C ASN M 54 " pdb=" CB ASN M 54 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 3234 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 367 " 0.260 9.50e-02 1.11e+02 1.17e-01 1.09e+01 pdb=" NE ARG E 367 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 367 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG E 367 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 367 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 56 " -0.253 9.50e-02 1.11e+02 1.14e-01 1.01e+01 pdb=" NE ARG O 56 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG O 56 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG O 56 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG O 56 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 63 " 0.221 9.50e-02 1.11e+02 1.00e-01 8.25e+00 pdb=" NE ARG M 63 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG M 63 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG M 63 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG M 63 " -0.001 2.00e-02 2.50e+03 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1300 2.74 - 3.28: 20986 3.28 - 3.82: 33876 3.82 - 4.36: 41780 4.36 - 4.90: 72124 Nonbonded interactions: 170066 Sorted by model distance: nonbonded pdb=" OG SER E 376 " pdb=" O GLY E 379 " model vdw 2.196 2.440 nonbonded pdb=" O PRO F 290 " pdb=" OH TYR F 385 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASN F 422 " pdb=" NH2 ARG G 100 " model vdw 2.212 2.520 nonbonded pdb=" OD1 ASN A 422 " pdb=" NH2 ARG J 100 " model vdw 2.243 2.520 nonbonded pdb=" O GLN A 307 " pdb=" OH TYR A 319 " model vdw 2.267 2.440 ... (remaining 170061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 4.610 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 54.960 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20610 Z= 0.149 Angle : 0.665 8.050 27978 Z= 0.371 Chirality : 0.046 0.204 3237 Planarity : 0.009 0.117 3564 Dihedral : 13.445 87.628 7473 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.14 % Rotamer: Outliers : 1.25 % Allowed : 4.99 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.23 (0.16), residues: 2622 helix: -1.71 (0.20), residues: 393 sheet: -0.22 (0.18), residues: 774 loop : -0.82 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 43 HIS 0.004 0.001 HIS E 435 PHE 0.018 0.002 PHE A 334 TYR 0.029 0.005 TYR A 44 ARG 0.028 0.004 ARG E 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 736 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6335 (tt0) cc_final: 0.5808 (tt0) REVERT: A 26 GLU cc_start: 0.7466 (pt0) cc_final: 0.7211 (pt0) REVERT: A 35 TYR cc_start: 0.7963 (m-80) cc_final: 0.7418 (m-80) REVERT: A 72 ASP cc_start: 0.6520 (m-30) cc_final: 0.6066 (m-30) REVERT: A 103 PHE cc_start: 0.7830 (m-80) cc_final: 0.7312 (m-10) REVERT: A 110 CYS cc_start: 0.4909 (m) cc_final: 0.3743 (m) REVERT: A 171 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7329 (mtmt) REVERT: A 234 MET cc_start: 0.8091 (ptp) cc_final: 0.7600 (ptm) REVERT: A 269 TYR cc_start: 0.7345 (p90) cc_final: 0.6927 (p90) REVERT: A 299 TYR cc_start: 0.8083 (m-80) cc_final: 0.7523 (m-80) REVERT: A 327 GLU cc_start: 0.7353 (pt0) cc_final: 0.6740 (pt0) REVERT: A 331 ASP cc_start: 0.7875 (t0) cc_final: 0.7432 (t0) REVERT: A 337 THR cc_start: 0.8111 (p) cc_final: 0.7596 (t) REVERT: A 359 TYR cc_start: 0.7307 (t80) cc_final: 0.7086 (t80) REVERT: A 367 ARG cc_start: 0.7573 (ptt-90) cc_final: 0.7352 (ptp90) REVERT: A 409 TYR cc_start: 0.8102 (t80) cc_final: 0.6970 (t80) REVERT: A 410 ILE cc_start: 0.8455 (mm) cc_final: 0.8236 (mm) REVERT: A 428 SER cc_start: 0.7573 (m) cc_final: 0.6997 (p) REVERT: A 433 GLU cc_start: 0.6972 (tt0) cc_final: 0.6767 (tt0) REVERT: A 440 ARG cc_start: 0.7188 (ttm170) cc_final: 0.6843 (ptm-80) REVERT: B 68 LYS cc_start: 0.7737 (tttm) cc_final: 0.7468 (ttpt) REVERT: C 34 MET cc_start: 0.6481 (mmt) cc_final: 0.6240 (mmt) REVERT: C 91 TYR cc_start: 0.6730 (m-80) cc_final: 0.6362 (m-80) REVERT: D 34 HIS cc_start: 0.5611 (m-70) cc_final: 0.4700 (m-70) REVERT: D 79 GLN cc_start: 0.7254 (pp30) cc_final: 0.6613 (pp30) REVERT: E 24 LEU cc_start: 0.8257 (mp) cc_final: 0.7985 (mp) REVERT: E 29 SER cc_start: 0.7822 (t) cc_final: 0.7520 (p) REVERT: E 51 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6707 (mm-30) REVERT: E 85 SER cc_start: 0.7181 (t) cc_final: 0.6800 (m) REVERT: E 129 ARG cc_start: 0.7364 (ptp-110) cc_final: 0.7117 (ttp80) REVERT: E 178 ASN cc_start: 0.7636 (m-40) cc_final: 0.7362 (m-40) REVERT: E 269 TYR cc_start: 0.7303 (p90) cc_final: 0.6791 (p90) REVERT: E 270 MET cc_start: 0.7365 (ptm) cc_final: 0.6958 (ptm) REVERT: E 349 GLU cc_start: 0.6909 (tp30) cc_final: 0.5663 (tp30) REVERT: E 353 ASN cc_start: 0.7219 (m-40) cc_final: 0.6224 (p0) REVERT: E 364 SER cc_start: 0.7042 (t) cc_final: 0.6336 (m) REVERT: E 400 ILE cc_start: 0.7989 (mt) cc_final: 0.7766 (mm) REVERT: E 410 ILE cc_start: 0.8164 (mm) cc_final: 0.7922 (mm) REVERT: E 412 ASN cc_start: 0.6770 (m-40) cc_final: 0.6362 (m-40) REVERT: E 433 GLU cc_start: 0.7096 (tt0) cc_final: 0.6813 (tt0) REVERT: E 438 LYS cc_start: 0.7708 (mttm) cc_final: 0.7464 (mttm) REVERT: E 442 VAL cc_start: 0.8306 (m) cc_final: 0.7914 (t) REVERT: F 27 SER cc_start: 0.8321 (t) cc_final: 0.7929 (p) REVERT: F 35 TYR cc_start: 0.7893 (m-80) cc_final: 0.7257 (m-80) REVERT: F 51 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6945 (mm-30) REVERT: F 56 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6582 (mt-10) REVERT: F 62 ASP cc_start: 0.7435 (t0) cc_final: 0.6984 (t0) REVERT: F 68 LYS cc_start: 0.8465 (tttp) cc_final: 0.7808 (tttm) REVERT: F 72 ASP cc_start: 0.6873 (m-30) cc_final: 0.6592 (m-30) REVERT: F 80 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6177 (mt-10) REVERT: F 85 SER cc_start: 0.7684 (t) cc_final: 0.7406 (m) REVERT: F 126 LYS cc_start: 0.7346 (mmtt) cc_final: 0.7045 (mmtp) REVERT: F 178 ASN cc_start: 0.7995 (m-40) cc_final: 0.7759 (m-40) REVERT: F 188 LYS cc_start: 0.7447 (ttmm) cc_final: 0.7225 (ttmm) REVERT: F 193 PHE cc_start: 0.7502 (t80) cc_final: 0.6872 (t80) REVERT: F 197 ASN cc_start: 0.7562 (p0) cc_final: 0.7201 (p0) REVERT: F 202 ASN cc_start: 0.7121 (m-40) cc_final: 0.6705 (m110) REVERT: F 222 MET cc_start: 0.8018 (ttp) cc_final: 0.7798 (ttm) REVERT: F 234 MET cc_start: 0.8259 (ptp) cc_final: 0.8049 (ptm) REVERT: F 244 MET cc_start: 0.7189 (mtm) cc_final: 0.6967 (mtt) REVERT: F 331 ASP cc_start: 0.7629 (t0) cc_final: 0.7266 (t0) REVERT: F 345 GLU cc_start: 0.6878 (tp30) cc_final: 0.6407 (tp30) REVERT: F 348 LYS cc_start: 0.7544 (ptpt) cc_final: 0.7308 (ptpt) REVERT: F 386 LYS cc_start: 0.7498 (mmtm) cc_final: 0.7194 (mmtm) REVERT: F 412 ASN cc_start: 0.6862 (m-40) cc_final: 0.6294 (m-40) REVERT: F 428 SER cc_start: 0.7426 (m) cc_final: 0.7078 (p) REVERT: F 437 ILE cc_start: 0.8493 (mm) cc_final: 0.8115 (mt) REVERT: F 440 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6922 (ptm160) REVERT: F 462 GLN cc_start: 0.7755 (tt0) cc_final: 0.7517 (tt0) REVERT: G 11 LEU cc_start: 0.7907 (tp) cc_final: 0.7685 (tp) REVERT: G 94 TYR cc_start: 0.7019 (m-80) cc_final: 0.6780 (m-80) REVERT: G 116 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7542 (mm-40) REVERT: H 45 LEU cc_start: 0.8219 (mp) cc_final: 0.7959 (mt) REVERT: H 52 ASP cc_start: 0.7337 (p0) cc_final: 0.7092 (p0) REVERT: H 87 THR cc_start: 0.7510 (m) cc_final: 0.7241 (p) REVERT: H 96 TYR cc_start: 0.8473 (t80) cc_final: 0.8077 (t80) REVERT: I 34 MET cc_start: 0.6484 (mmt) cc_final: 0.6093 (mmt) REVERT: J 5 VAL cc_start: 0.6930 (t) cc_final: 0.6718 (m) REVERT: J 65 LYS cc_start: 0.7841 (tttt) cc_final: 0.7519 (tttt) REVERT: J 108 THR cc_start: 0.7769 (t) cc_final: 0.7467 (t) REVERT: K 34 HIS cc_start: 0.5746 (m-70) cc_final: 0.5190 (m-70) REVERT: K 93 SER cc_start: 0.8687 (t) cc_final: 0.8263 (t) REVERT: L 48 MET cc_start: 0.6808 (mmm) cc_final: 0.6380 (mmm) REVERT: L 75 ILE cc_start: 0.8332 (mt) cc_final: 0.8106 (mt) REVERT: L 76 SER cc_start: 0.8494 (m) cc_final: 0.8193 (p) REVERT: L 87 TYR cc_start: 0.7654 (m-80) cc_final: 0.7428 (m-10) REVERT: M 47 LYS cc_start: 0.7317 (tttt) cc_final: 0.6981 (tttt) REVERT: M 53 ASN cc_start: 0.7063 (m-40) cc_final: 0.6747 (m110) REVERT: M 64 PHE cc_start: 0.6703 (m-80) cc_final: 0.6497 (m-80) REVERT: M 68 LYS cc_start: 0.8244 (tttm) cc_final: 0.7743 (ttpt) REVERT: N 5 VAL cc_start: 0.6424 (t) cc_final: 0.5946 (m) REVERT: N 93 ILE cc_start: 0.8228 (mt) cc_final: 0.7774 (tt) REVERT: N 111 PHE cc_start: 0.7865 (m-10) cc_final: 0.7640 (m-10) REVERT: N 119 LEU cc_start: 0.8017 (tp) cc_final: 0.7749 (tt) REVERT: O 35 VAL cc_start: 0.7822 (t) cc_final: 0.7500 (p) REVERT: O 37 TRP cc_start: 0.8187 (m100) cc_final: 0.7847 (m-90) REVERT: O 53 ASN cc_start: 0.7541 (m-40) cc_final: 0.7212 (m110) outliers start: 28 outliers final: 8 residues processed: 756 average time/residue: 0.3439 time to fit residues: 383.5934 Evaluate side-chains 608 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 600 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 463 CYS Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain J residue 59 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 204 optimal weight: 0.0070 chunk 79 optimal weight: 0.0470 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 307 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 GLN C 39 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 178 ASN E 272 GLN E 346 GLN F 139 ASN F 195 GLN ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20610 Z= 0.174 Angle : 0.616 8.100 27978 Z= 0.330 Chirality : 0.046 0.233 3237 Planarity : 0.004 0.050 3564 Dihedral : 5.943 44.605 2932 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.76 % Allowed : 12.66 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2622 helix: 0.47 (0.26), residues: 399 sheet: -0.16 (0.18), residues: 801 loop : 0.02 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 36 HIS 0.005 0.001 HIS K 34 PHE 0.015 0.002 PHE J 29 TYR 0.024 0.002 TYR A 385 ARG 0.007 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 634 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6136 (tt0) cc_final: 0.5930 (tt0) REVERT: A 35 TYR cc_start: 0.8076 (m-80) cc_final: 0.7527 (m-80) REVERT: A 62 ASP cc_start: 0.7628 (t0) cc_final: 0.7330 (t0) REVERT: A 72 ASP cc_start: 0.6708 (m-30) cc_final: 0.6198 (m-30) REVERT: A 103 PHE cc_start: 0.7871 (m-80) cc_final: 0.7640 (m-10) REVERT: A 126 LYS cc_start: 0.6713 (mmtt) cc_final: 0.6426 (mmmm) REVERT: A 164 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 171 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7331 (mtmt) REVERT: A 184 ILE cc_start: 0.7945 (mm) cc_final: 0.7252 (pt) REVERT: A 234 MET cc_start: 0.8027 (ptp) cc_final: 0.7664 (ptm) REVERT: A 269 TYR cc_start: 0.7658 (p90) cc_final: 0.7258 (p90) REVERT: A 327 GLU cc_start: 0.7438 (pt0) cc_final: 0.6833 (pt0) REVERT: A 364 SER cc_start: 0.7981 (t) cc_final: 0.7745 (p) REVERT: A 367 ARG cc_start: 0.7684 (ptt-90) cc_final: 0.7305 (ptp90) REVERT: A 376 SER cc_start: 0.8037 (m) cc_final: 0.7747 (p) REVERT: A 385 TYR cc_start: 0.7628 (m-80) cc_final: 0.7259 (m-10) REVERT: A 392 ILE cc_start: 0.8145 (pt) cc_final: 0.7934 (pt) REVERT: A 402 GLN cc_start: 0.7492 (tt0) cc_final: 0.7237 (tp40) REVERT: A 410 ILE cc_start: 0.8447 (mm) cc_final: 0.8205 (mm) REVERT: A 412 ASN cc_start: 0.7106 (m-40) cc_final: 0.6723 (m110) REVERT: A 428 SER cc_start: 0.7824 (m) cc_final: 0.7317 (p) REVERT: A 433 GLU cc_start: 0.6968 (tt0) cc_final: 0.6617 (tt0) REVERT: B 47 LYS cc_start: 0.7619 (tttt) cc_final: 0.7360 (tttt) REVERT: B 68 LYS cc_start: 0.7802 (tttm) cc_final: 0.7434 (ttpt) REVERT: C 34 MET cc_start: 0.6288 (mmt) cc_final: 0.6037 (mmt) REVERT: C 68 THR cc_start: 0.7075 (m) cc_final: 0.6715 (p) REVERT: C 91 TYR cc_start: 0.6511 (m-80) cc_final: 0.6237 (m-80) REVERT: D 34 HIS cc_start: 0.5901 (m-70) cc_final: 0.5008 (m-70) REVERT: E 29 SER cc_start: 0.7937 (t) cc_final: 0.7618 (p) REVERT: E 51 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6411 (mm-30) REVERT: E 70 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5955 (mm-30) REVERT: E 85 SER cc_start: 0.7428 (t) cc_final: 0.7120 (m) REVERT: E 126 LYS cc_start: 0.6994 (mmtt) cc_final: 0.6667 (mmtp) REVERT: E 143 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7574 (ttmt) REVERT: E 199 ARG cc_start: 0.7514 (ttt-90) cc_final: 0.7139 (ttt-90) REVERT: E 245 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7235 (mp) REVERT: E 318 VAL cc_start: 0.8552 (p) cc_final: 0.8175 (m) REVERT: E 335 CYS cc_start: 0.5782 (m) cc_final: 0.5480 (m) REVERT: E 364 SER cc_start: 0.7345 (t) cc_final: 0.7034 (p) REVERT: E 410 ILE cc_start: 0.8176 (mm) cc_final: 0.7962 (mm) REVERT: E 412 ASN cc_start: 0.6629 (m-40) cc_final: 0.6340 (m-40) REVERT: E 433 GLU cc_start: 0.7073 (tt0) cc_final: 0.6812 (tt0) REVERT: E 444 SER cc_start: 0.8408 (m) cc_final: 0.8188 (p) REVERT: F 27 SER cc_start: 0.8384 (t) cc_final: 0.8115 (p) REVERT: F 51 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6800 (mm-30) REVERT: F 62 ASP cc_start: 0.7374 (t0) cc_final: 0.6855 (t0) REVERT: F 68 LYS cc_start: 0.8454 (tttp) cc_final: 0.7889 (tttp) REVERT: F 72 ASP cc_start: 0.6916 (m-30) cc_final: 0.6597 (m-30) REVERT: F 126 LYS cc_start: 0.7340 (mmtt) cc_final: 0.7065 (mmtp) REVERT: F 134 VAL cc_start: 0.8573 (p) cc_final: 0.8351 (t) REVERT: F 222 MET cc_start: 0.7934 (ttp) cc_final: 0.7717 (ttm) REVERT: F 331 ASP cc_start: 0.7657 (t0) cc_final: 0.7360 (t0) REVERT: F 364 SER cc_start: 0.7500 (t) cc_final: 0.7222 (p) REVERT: F 412 ASN cc_start: 0.6907 (m-40) cc_final: 0.6700 (m110) REVERT: F 437 ILE cc_start: 0.8493 (mm) cc_final: 0.8110 (mt) REVERT: G 36 TRP cc_start: 0.7384 (m100) cc_final: 0.7144 (m100) REVERT: H 45 LEU cc_start: 0.8233 (mp) cc_final: 0.8013 (mt) REVERT: H 52 ASP cc_start: 0.7415 (p0) cc_final: 0.7162 (p0) REVERT: H 87 THR cc_start: 0.7369 (m) cc_final: 0.7103 (p) REVERT: I 34 MET cc_start: 0.6262 (mmt) cc_final: 0.5967 (mmt) REVERT: I 50 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7292 (ttp-170) REVERT: J 65 LYS cc_start: 0.7744 (tttt) cc_final: 0.7495 (tttt) REVERT: J 119 LEU cc_start: 0.7934 (tp) cc_final: 0.7612 (tt) REVERT: L 12 SER cc_start: 0.7953 (p) cc_final: 0.7746 (t) REVERT: L 39 LYS cc_start: 0.8438 (mttt) cc_final: 0.8084 (mttm) REVERT: L 52 SER cc_start: 0.7859 (m) cc_final: 0.7616 (p) REVERT: L 75 ILE cc_start: 0.8338 (mt) cc_final: 0.8094 (mt) REVERT: L 87 TYR cc_start: 0.7132 (m-80) cc_final: 0.6911 (m-10) REVERT: M 37 TRP cc_start: 0.8358 (m100) cc_final: 0.7724 (m100) REVERT: M 68 LYS cc_start: 0.8284 (tttm) cc_final: 0.7154 (tttt) REVERT: N 5 VAL cc_start: 0.6651 (t) cc_final: 0.6261 (m) REVERT: N 80 PHE cc_start: 0.7669 (m-80) cc_final: 0.6957 (m-80) REVERT: N 93 ILE cc_start: 0.8264 (mt) cc_final: 0.7721 (tt) REVERT: N 94 TYR cc_start: 0.7529 (m-80) cc_final: 0.7221 (m-80) REVERT: N 119 LEU cc_start: 0.8066 (tp) cc_final: 0.7762 (tt) REVERT: O 10 VAL cc_start: 0.8707 (p) cc_final: 0.8421 (t) REVERT: O 47 LYS cc_start: 0.7465 (tttt) cc_final: 0.7140 (tttt) REVERT: O 53 ASN cc_start: 0.7491 (m-40) cc_final: 0.7075 (m110) outliers start: 62 outliers final: 36 residues processed: 662 average time/residue: 0.3359 time to fit residues: 332.4614 Evaluate side-chains 630 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 592 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 GLN A 462 GLN C 56 ASN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN E 346 GLN E 353 ASN ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN O 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20610 Z= 0.247 Angle : 0.603 7.911 27978 Z= 0.324 Chirality : 0.047 0.247 3237 Planarity : 0.004 0.040 3564 Dihedral : 5.507 41.922 2926 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.06 % Allowed : 15.11 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2622 helix: 0.29 (0.25), residues: 435 sheet: -0.20 (0.18), residues: 771 loop : -0.03 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 114 HIS 0.006 0.002 HIS L 34 PHE 0.017 0.002 PHE J 29 TYR 0.021 0.002 TYR A 385 ARG 0.009 0.001 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 607 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7715 (t0) cc_final: 0.7462 (t0) REVERT: A 72 ASP cc_start: 0.6796 (m-30) cc_final: 0.6272 (m-30) REVERT: A 126 LYS cc_start: 0.6846 (mmtt) cc_final: 0.6472 (mmmm) REVERT: A 129 ARG cc_start: 0.7182 (ptp-110) cc_final: 0.6853 (ptm160) REVERT: A 164 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 269 TYR cc_start: 0.7736 (p90) cc_final: 0.7325 (p90) REVERT: A 337 THR cc_start: 0.7884 (p) cc_final: 0.7385 (t) REVERT: A 376 SER cc_start: 0.7965 (m) cc_final: 0.7671 (p) REVERT: A 385 TYR cc_start: 0.7562 (m-80) cc_final: 0.7182 (m-10) REVERT: A 386 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7676 (mmmt) REVERT: A 402 GLN cc_start: 0.7512 (tt0) cc_final: 0.7211 (tp40) REVERT: A 412 ASN cc_start: 0.7147 (m-40) cc_final: 0.6647 (m110) REVERT: A 428 SER cc_start: 0.7913 (m) cc_final: 0.7317 (p) REVERT: A 433 GLU cc_start: 0.7050 (tt0) cc_final: 0.6677 (tt0) REVERT: A 453 GLN cc_start: 0.7288 (tt0) cc_final: 0.7059 (tt0) REVERT: B 47 LYS cc_start: 0.7638 (tttt) cc_final: 0.7416 (tttt) REVERT: C 34 MET cc_start: 0.6335 (mmt) cc_final: 0.6076 (mmt) REVERT: C 68 THR cc_start: 0.7263 (m) cc_final: 0.6965 (p) REVERT: C 91 TYR cc_start: 0.6577 (m-80) cc_final: 0.6233 (m-80) REVERT: D 34 HIS cc_start: 0.5852 (m-70) cc_final: 0.5068 (m-70) REVERT: E 29 SER cc_start: 0.8006 (t) cc_final: 0.7694 (p) REVERT: E 51 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6401 (mm-30) REVERT: E 70 GLU cc_start: 0.6260 (mm-30) cc_final: 0.5917 (mm-30) REVERT: E 80 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6350 (tt0) REVERT: E 85 SER cc_start: 0.7073 (t) cc_final: 0.6847 (m) REVERT: E 126 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6905 (mmtp) REVERT: E 175 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6708 (mtm-85) REVERT: E 189 MET cc_start: 0.6461 (tpp) cc_final: 0.6228 (ttm) REVERT: E 233 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7948 (m-40) REVERT: E 243 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6815 (tp) REVERT: E 245 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7283 (mp) REVERT: E 250 MET cc_start: 0.6041 (mmm) cc_final: 0.5644 (tpt) REVERT: E 267 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8163 (m) REVERT: E 318 VAL cc_start: 0.8613 (p) cc_final: 0.8208 (m) REVERT: E 364 SER cc_start: 0.7360 (t) cc_final: 0.6962 (p) REVERT: E 410 ILE cc_start: 0.8217 (mm) cc_final: 0.7981 (mm) REVERT: E 433 GLU cc_start: 0.7153 (tt0) cc_final: 0.6875 (tt0) REVERT: F 27 SER cc_start: 0.8378 (t) cc_final: 0.8122 (p) REVERT: F 51 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6949 (mm-30) REVERT: F 62 ASP cc_start: 0.7506 (t0) cc_final: 0.6873 (t0) REVERT: F 72 ASP cc_start: 0.6973 (m-30) cc_final: 0.6669 (m-30) REVERT: F 126 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7229 (mmtp) REVERT: F 134 VAL cc_start: 0.8607 (p) cc_final: 0.8383 (t) REVERT: F 142 LYS cc_start: 0.7625 (mmtp) cc_final: 0.7418 (mttt) REVERT: F 183 ASP cc_start: 0.6584 (t0) cc_final: 0.6289 (t0) REVERT: F 188 LYS cc_start: 0.7406 (ttmm) cc_final: 0.7154 (ttpp) REVERT: F 202 ASN cc_start: 0.7129 (m-40) cc_final: 0.6786 (m110) REVERT: F 331 ASP cc_start: 0.7830 (t0) cc_final: 0.7279 (t70) REVERT: F 348 LYS cc_start: 0.7539 (ptpt) cc_final: 0.7179 (ptpp) REVERT: F 412 ASN cc_start: 0.6932 (m-40) cc_final: 0.6727 (m110) REVERT: F 437 ILE cc_start: 0.8474 (mm) cc_final: 0.8100 (mt) REVERT: G 36 TRP cc_start: 0.7300 (m100) cc_final: 0.7086 (m100) REVERT: G 94 TYR cc_start: 0.7073 (m-80) cc_final: 0.6862 (m-80) REVERT: H 45 LEU cc_start: 0.8345 (mp) cc_final: 0.8144 (mt) REVERT: H 52 ASP cc_start: 0.7366 (p0) cc_final: 0.7152 (p0) REVERT: H 69 ILE cc_start: 0.8351 (pt) cc_final: 0.8105 (mt) REVERT: H 87 THR cc_start: 0.7415 (m) cc_final: 0.7212 (p) REVERT: I 34 MET cc_start: 0.6305 (mmt) cc_final: 0.5801 (mmt) REVERT: J 65 LYS cc_start: 0.7779 (tttt) cc_final: 0.7554 (tttt) REVERT: K 98 PHE cc_start: 0.8045 (m-80) cc_final: 0.7533 (m-80) REVERT: L 39 LYS cc_start: 0.8494 (mttt) cc_final: 0.8221 (mttm) REVERT: L 52 SER cc_start: 0.7893 (m) cc_final: 0.7540 (t) REVERT: M 36 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6662 (m-70) REVERT: M 37 TRP cc_start: 0.8388 (m100) cc_final: 0.7730 (m100) REVERT: M 64 PHE cc_start: 0.7039 (m-80) cc_final: 0.6781 (m-80) REVERT: M 72 SER cc_start: 0.8093 (p) cc_final: 0.7866 (p) REVERT: N 35 ASN cc_start: 0.7368 (m-40) cc_final: 0.7073 (m110) REVERT: N 45 LEU cc_start: 0.8169 (mp) cc_final: 0.7963 (mt) REVERT: N 93 ILE cc_start: 0.8242 (mt) cc_final: 0.7703 (tt) REVERT: N 94 TYR cc_start: 0.7526 (m-80) cc_final: 0.7213 (m-80) REVERT: O 10 VAL cc_start: 0.8761 (p) cc_final: 0.8492 (t) REVERT: O 47 LYS cc_start: 0.7553 (tttt) cc_final: 0.7224 (tttt) outliers start: 91 outliers final: 64 residues processed: 651 average time/residue: 0.3100 time to fit residues: 307.9260 Evaluate side-chains 641 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 571 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 36 HIS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 28 ASN Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 0.0870 chunk 178 optimal weight: 0.2980 chunk 123 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 113 optimal weight: 4.9990 chunk 159 optimal weight: 0.3980 chunk 238 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 225 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 195 GLN A 272 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 GLN A 462 GLN B 36 HIS B 39 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN F 368 HIS F 455 GLN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20610 Z= 0.148 Angle : 0.563 8.281 27978 Z= 0.296 Chirality : 0.045 0.302 3237 Planarity : 0.004 0.039 3564 Dihedral : 4.978 40.646 2924 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.19 % Allowed : 16.13 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2622 helix: 0.78 (0.26), residues: 417 sheet: -0.12 (0.18), residues: 753 loop : 0.10 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 35 HIS 0.004 0.001 HIS M 36 PHE 0.032 0.001 PHE I 27 TYR 0.019 0.001 TYR J 104 ARG 0.006 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 616 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6364 (tt0) cc_final: 0.6164 (tt0) REVERT: A 24 LEU cc_start: 0.7918 (mt) cc_final: 0.7691 (mp) REVERT: A 79 ARG cc_start: 0.7863 (ttp-110) cc_final: 0.7643 (mtm-85) REVERT: A 126 LYS cc_start: 0.6670 (mmtt) cc_final: 0.6322 (mmmm) REVERT: A 139 ASN cc_start: 0.7890 (m-40) cc_final: 0.7587 (m-40) REVERT: A 142 LYS cc_start: 0.7748 (mmtp) cc_final: 0.7471 (mmtp) REVERT: A 269 TYR cc_start: 0.7735 (p90) cc_final: 0.7248 (p90) REVERT: A 324 LYS cc_start: 0.7202 (mtpt) cc_final: 0.6913 (mtpt) REVERT: A 327 GLU cc_start: 0.7265 (pt0) cc_final: 0.6979 (pt0) REVERT: A 349 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6399 (mt-10) REVERT: A 364 SER cc_start: 0.7650 (t) cc_final: 0.7280 (m) REVERT: A 386 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7628 (mmmt) REVERT: A 402 GLN cc_start: 0.7460 (tt0) cc_final: 0.7190 (tp40) REVERT: A 412 ASN cc_start: 0.6895 (m-40) cc_final: 0.6453 (m110) REVERT: A 428 SER cc_start: 0.7897 (m) cc_final: 0.7369 (p) REVERT: A 433 GLU cc_start: 0.7023 (tt0) cc_final: 0.6667 (tt0) REVERT: B 37 TRP cc_start: 0.8089 (m100) cc_final: 0.7694 (m-90) REVERT: B 47 LYS cc_start: 0.7602 (tttt) cc_final: 0.7397 (tttt) REVERT: C 34 MET cc_start: 0.6097 (mmt) cc_final: 0.5877 (mmt) REVERT: C 68 THR cc_start: 0.7330 (m) cc_final: 0.7016 (p) REVERT: C 91 TYR cc_start: 0.6511 (m-80) cc_final: 0.6220 (m-80) REVERT: D 34 HIS cc_start: 0.5810 (m-70) cc_final: 0.5084 (m-70) REVERT: E 29 SER cc_start: 0.7932 (t) cc_final: 0.7640 (p) REVERT: E 51 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6325 (mm-30) REVERT: E 70 GLU cc_start: 0.6353 (mm-30) cc_final: 0.5898 (mm-30) REVERT: E 80 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6297 (tt0) REVERT: E 233 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7736 (m-40) REVERT: E 245 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7276 (mp) REVERT: E 267 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8185 (m) REVERT: E 318 VAL cc_start: 0.8562 (p) cc_final: 0.8178 (m) REVERT: E 410 ILE cc_start: 0.8219 (mm) cc_final: 0.7976 (mm) REVERT: E 433 GLU cc_start: 0.7140 (tt0) cc_final: 0.6845 (tt0) REVERT: F 26 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7248 (mt-10) REVERT: F 47 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7799 (m) REVERT: F 51 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6911 (mm-30) REVERT: F 62 ASP cc_start: 0.7425 (t0) cc_final: 0.6798 (t0) REVERT: F 68 LYS cc_start: 0.8370 (tttp) cc_final: 0.7880 (tttp) REVERT: F 72 ASP cc_start: 0.6973 (m-30) cc_final: 0.6669 (m-30) REVERT: F 126 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7155 (mmtp) REVERT: F 183 ASP cc_start: 0.6557 (t0) cc_final: 0.6204 (t0) REVERT: F 202 ASN cc_start: 0.7109 (m-40) cc_final: 0.6701 (m110) REVERT: F 234 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7807 (ttm) REVERT: F 331 ASP cc_start: 0.7733 (t0) cc_final: 0.7337 (t0) REVERT: F 386 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7526 (mmtm) REVERT: F 412 ASN cc_start: 0.6900 (m-40) cc_final: 0.6693 (m-40) REVERT: F 421 ASP cc_start: 0.6672 (p0) cc_final: 0.6340 (p0) REVERT: F 437 ILE cc_start: 0.8445 (mm) cc_final: 0.8063 (mm) REVERT: G 36 TRP cc_start: 0.7156 (m100) cc_final: 0.6926 (m100) REVERT: G 93 ILE cc_start: 0.8132 (mt) cc_final: 0.7886 (tt) REVERT: G 94 TYR cc_start: 0.7003 (m-80) cc_final: 0.6702 (m-80) REVERT: H 12 VAL cc_start: 0.8651 (t) cc_final: 0.8274 (m) REVERT: H 45 LEU cc_start: 0.8223 (mp) cc_final: 0.8011 (mt) REVERT: H 52 ASP cc_start: 0.7348 (p0) cc_final: 0.7108 (p0) REVERT: H 69 ILE cc_start: 0.8264 (pt) cc_final: 0.7895 (mt) REVERT: H 102 LEU cc_start: 0.7870 (mp) cc_final: 0.7641 (mt) REVERT: I 34 MET cc_start: 0.6053 (mmt) cc_final: 0.5652 (mmt) REVERT: I 50 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7271 (ttp-170) REVERT: J 65 LYS cc_start: 0.7799 (tttt) cc_final: 0.7557 (tttt) REVERT: J 81 LEU cc_start: 0.7659 (tp) cc_final: 0.7352 (mp) REVERT: L 39 LYS cc_start: 0.8453 (mttt) cc_final: 0.8168 (mttm) REVERT: L 52 SER cc_start: 0.7762 (m) cc_final: 0.7439 (t) REVERT: L 87 TYR cc_start: 0.7235 (m-80) cc_final: 0.6960 (m-10) REVERT: M 37 TRP cc_start: 0.8375 (m100) cc_final: 0.7555 (m100) REVERT: M 64 PHE cc_start: 0.7012 (m-80) cc_final: 0.6781 (m-80) REVERT: M 72 SER cc_start: 0.8079 (p) cc_final: 0.7822 (p) REVERT: N 32 TYR cc_start: 0.7454 (m-80) cc_final: 0.7212 (m-80) REVERT: N 35 ASN cc_start: 0.7133 (m-40) cc_final: 0.6800 (m110) REVERT: N 93 ILE cc_start: 0.8167 (mt) cc_final: 0.7639 (tt) REVERT: N 119 LEU cc_start: 0.8063 (tp) cc_final: 0.7696 (tt) REVERT: O 5 THR cc_start: 0.7533 (m) cc_final: 0.7273 (m) REVERT: O 10 VAL cc_start: 0.8725 (p) cc_final: 0.8456 (t) REVERT: O 47 LYS cc_start: 0.7556 (tttt) cc_final: 0.7209 (tttt) REVERT: O 51 TYR cc_start: 0.7710 (p90) cc_final: 0.7315 (p90) REVERT: O 53 ASN cc_start: 0.7527 (m-40) cc_final: 0.7228 (m-40) outliers start: 94 outliers final: 62 residues processed: 658 average time/residue: 0.3331 time to fit residues: 328.9528 Evaluate side-chains 650 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 583 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6373 > 50: distance: 18 - 22: 4.319 distance: 22 - 23: 16.514 distance: 22 - 163: 3.902 distance: 23 - 24: 10.191 distance: 23 - 26: 11.413 distance: 24 - 25: 11.808 distance: 24 - 29: 33.556 distance: 26 - 27: 7.953 distance: 26 - 28: 19.948 distance: 29 - 30: 39.700 distance: 30 - 31: 18.600 distance: 30 - 33: 13.412 distance: 31 - 32: 22.055 distance: 31 - 35: 7.211 distance: 35 - 36: 15.482 distance: 35 - 41: 33.535 distance: 36 - 37: 5.747 distance: 36 - 39: 11.244 distance: 37 - 38: 8.983 distance: 37 - 42: 15.026 distance: 39 - 40: 35.120 distance: 40 - 41: 25.503 distance: 42 - 43: 22.639 distance: 43 - 44: 4.960 distance: 44 - 45: 27.278 distance: 44 - 46: 11.708 distance: 46 - 47: 16.856 distance: 47 - 48: 4.290 distance: 47 - 50: 10.348 distance: 48 - 49: 4.105 distance: 48 - 55: 9.700 distance: 50 - 51: 29.832 distance: 51 - 52: 18.598 distance: 52 - 53: 8.402 distance: 52 - 54: 10.870 distance: 55 - 56: 11.243 distance: 56 - 57: 8.870 distance: 56 - 59: 19.213 distance: 57 - 58: 9.200 distance: 57 - 62: 5.093 distance: 59 - 60: 14.892 distance: 59 - 61: 24.551 distance: 62 - 129: 11.707 distance: 63 - 64: 10.751 distance: 63 - 66: 13.461 distance: 64 - 65: 11.127 distance: 64 - 67: 12.024 distance: 65 - 126: 10.920 distance: 67 - 68: 18.216 distance: 68 - 69: 12.406 distance: 68 - 71: 9.800 distance: 69 - 70: 11.629 distance: 69 - 78: 7.906 distance: 71 - 72: 28.089 distance: 72 - 73: 39.105 distance: 73 - 74: 7.361 distance: 75 - 76: 3.592 distance: 75 - 77: 14.414 distance: 78 - 79: 3.377 distance: 78 - 116: 6.683 distance: 79 - 80: 9.316 distance: 79 - 82: 7.869 distance: 80 - 81: 13.604 distance: 80 - 86: 14.201 distance: 81 - 113: 15.616 distance: 82 - 83: 6.159 distance: 82 - 84: 7.119 distance: 86 - 87: 15.270 distance: 86 - 92: 9.303 distance: 87 - 88: 8.669 distance: 87 - 90: 8.337 distance: 88 - 89: 15.625 distance: 88 - 93: 8.708 distance: 90 - 91: 6.910 distance: 91 - 92: 8.774