Starting phenix.real_space_refine on Mon Feb 19 13:36:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffq_31571/02_2024/7ffq_31571.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffq_31571/02_2024/7ffq_31571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffq_31571/02_2024/7ffq_31571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffq_31571/02_2024/7ffq_31571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffq_31571/02_2024/7ffq_31571.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffq_31571/02_2024/7ffq_31571.pdb" } resolution = 3.5 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= 0.001 sd= 0.006 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 180 5.16 5 C 15736 2.51 5 N 4243 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 161": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J ARG 419": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q ARG 281": "NH1" <-> "NH2" Residue "Q ARG 419": "NH1" <-> "NH2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 103": "NH1" <-> "NH2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24808 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 28, 'TRANS': 411} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3257 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 30, 'TRANS': 385} Chain breaks: 1 Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3243 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 30, 'TRANS': 383} Chain breaks: 1 Chain: "R" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3249 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain breaks: 1 Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Time building chain proxies: 13.68, per 1000 atoms: 0.55 Number of scatterers: 24808 At special positions: 0 Unit cell: (187.44, 201.96, 142.56, 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 180 16.00 O 4649 8.00 N 4243 7.00 C 15736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.04 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 266 " distance=2.03 Simple disulfide: pdb=" SG CYS J 200 " - pdb=" SG CYS J 226 " distance=2.03 Simple disulfide: pdb=" SG CYS J 202 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.64 Conformation dependent library (CDL) restraints added in 4.8 seconds 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 67 sheets defined 16.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.092A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.857A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.238A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.541A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 404 through 438 removed outlier: 4.834A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.729A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.662A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 404 through 439 removed outlier: 3.665A pdb=" N LEU C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.743A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.647A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.567A pdb=" N ARG F 185 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 289 through 293 removed outlier: 3.589A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.757A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.968A pdb=" N VAL I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.543A pdb=" N LYS I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 351 through 363 removed outlier: 3.784A pdb=" N VAL J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE J 356 " --> pdb=" O PRO J 352 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR J 357 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 398 removed outlier: 3.864A pdb=" N ILE J 368 " --> pdb=" O PRO J 364 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU J 369 " --> pdb=" O MET J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 416 Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.592A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.207A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.530A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.773A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 8 through 12 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.735A pdb=" N ILE R 356 " --> pdb=" O PRO R 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 398 removed outlier: 3.863A pdb=" N ILE R 368 " --> pdb=" O PRO R 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 369 " --> pdb=" O MET R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 409 through 416 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.100A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.655A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.734A pdb=" N TYR A 139 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 143 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.098A pdb=" N ALA A 206 " --> pdb=" O PRO A 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 214 through 217 current: chain 'A' and resid 239 through 247 removed outlier: 7.859A pdb=" N ALA A 239 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 147 current: chain 'B' and resid 183 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.753A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 103 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 101 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.308A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.646A pdb=" N CYS B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 147 current: chain 'C' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 55 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.697A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.406A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC3, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AC4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC5, first strand: chain 'F' and resid 146 through 148 removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 168 through 170 Processing sheet with id=AC7, first strand: chain 'F' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 190 through 191 current: chain 'F' and resid 205 through 209 removed outlier: 8.539A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 214 through 217 current: chain 'F' and resid 236 through 246 removed outlier: 5.775A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 27 through 31 current: chain 'G' and resid 119 through 137 removed outlier: 3.505A pdb=" N THR G 144 " --> pdb=" O LEU G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 141 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD1, first strand: chain 'G' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 55 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD3, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.339A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AD6, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AD7, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'I' and resid 6 through 8 removed outlier: 3.616A pdb=" N PHE I 14 " --> pdb=" O CYS I 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AE1, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.588A pdb=" N GLN J 48 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL J 36 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG J 46 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.504A pdb=" N ILE J 110 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 147 through 149 Processing sheet with id=AE4, first strand: chain 'J' and resid 152 through 154 Processing sheet with id=AE5, first strand: chain 'J' and resid 237 through 238 removed outlier: 3.532A pdb=" N VAL J 237 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY J 253 " --> pdb=" O MET J 167 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 179 through 181 Processing sheet with id=AE7, first strand: chain 'J' and resid 196 through 200 removed outlier: 3.982A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 275 through 279 Processing sheet with id=AE9, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AF1, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AF2, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.623A pdb=" N GLN Q 48 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AF4, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AF5, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.785A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 179 through 181 removed outlier: 4.120A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AF8, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AF9, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.795A pdb=" N GLN R 48 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL R 36 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG R 46 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AG3, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AG4, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.631A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.879A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL R 188 " --> pdb=" O LYS R 215 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.563A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AG8, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.656A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AH1, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AH2, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.707A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.493A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.518A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 1947 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: 8.16 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7919 1.34 - 1.47: 6269 1.47 - 1.59: 11027 1.59 - 1.72: 0 1.72 - 1.84: 240 Bond restraints: 25455 Sorted by residual: bond pdb=" CB VAL G 148 " pdb=" CG2 VAL G 148 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.47e+00 bond pdb=" CB VAL C 148 " pdb=" CG2 VAL C 148 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.78e+00 bond pdb=" CB VAL G 42 " pdb=" CG1 VAL G 42 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.46e+00 bond pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.96e+00 bond pdb=" C ASN G 264 " pdb=" N PRO G 265 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.88e+00 ... (remaining 25450 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.36: 722 105.36 - 112.60: 13316 112.60 - 119.83: 8375 119.83 - 127.06: 11846 127.06 - 134.30: 396 Bond angle restraints: 34655 Sorted by residual: angle pdb=" N GLU R 148 " pdb=" CA GLU R 148 " pdb=" C GLU R 148 " ideal model delta sigma weight residual 107.69 119.40 -11.71 2.01e+00 2.48e-01 3.39e+01 angle pdb=" N THR R 140 " pdb=" CA THR R 140 " pdb=" C THR R 140 " ideal model delta sigma weight residual 114.56 108.29 6.27 1.27e+00 6.20e-01 2.44e+01 angle pdb=" C ILE B 369 " pdb=" N CYS B 370 " pdb=" CA CYS B 370 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C LEU A 132 " pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 120.38 127.01 -6.63 1.46e+00 4.69e-01 2.06e+01 angle pdb=" C SER R 87 " pdb=" N ARG R 88 " pdb=" CA ARG R 88 " ideal model delta sigma weight residual 122.48 129.83 -7.35 1.62e+00 3.81e-01 2.06e+01 ... (remaining 34650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 14425 14.31 - 28.63: 689 28.63 - 42.94: 165 42.94 - 57.25: 21 57.25 - 71.57: 17 Dihedral angle restraints: 15317 sinusoidal: 5996 harmonic: 9321 Sorted by residual: dihedral pdb=" CA ILE G 369 " pdb=" C ILE G 369 " pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta harmonic sigma weight residual -180.00 -130.00 -50.00 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA ASN B 264 " pdb=" C ASN B 264 " pdb=" N PRO B 265 " pdb=" CA PRO B 265 " ideal model delta harmonic sigma weight residual 180.00 131.45 48.55 0 5.00e+00 4.00e-02 9.43e+01 dihedral pdb=" CA ASN C 264 " pdb=" C ASN C 264 " pdb=" N PRO C 265 " pdb=" CA PRO C 265 " ideal model delta harmonic sigma weight residual 180.00 137.04 42.96 0 5.00e+00 4.00e-02 7.38e+01 ... (remaining 15314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3412 0.092 - 0.183: 426 0.183 - 0.274: 22 0.274 - 0.366: 2 0.366 - 0.457: 2 Chirality restraints: 3864 Sorted by residual: chirality pdb=" CB ILE B 369 " pdb=" CA ILE B 369 " pdb=" CG1 ILE B 369 " pdb=" CG2 ILE B 369 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CG LEU I 31 " pdb=" CB LEU I 31 " pdb=" CD1 LEU I 31 " pdb=" CD2 LEU I 31 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA HIS Q 156 " pdb=" N HIS Q 156 " pdb=" C HIS Q 156 " pdb=" CB HIS Q 156 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3861 not shown) Planarity restraints: 4455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 265 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 236 " 0.039 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP J 236 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J 236 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 236 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 236 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 236 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 236 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP J 236 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 264 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO B 265 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.049 5.00e-02 4.00e+02 ... (remaining 4452 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5848 2.79 - 3.32: 20103 3.32 - 3.85: 39713 3.85 - 4.37: 44392 4.37 - 4.90: 79612 Nonbonded interactions: 189668 Sorted by model distance: nonbonded pdb=" OE1 GLU B 120 " pdb=" OH TYR B 122 " model vdw 2.267 2.440 nonbonded pdb=" O ALA C 401 " pdb=" OH TYR R 359 " model vdw 2.268 2.440 nonbonded pdb=" O ALA B 401 " pdb=" OH TYR Q 359 " model vdw 2.274 2.440 nonbonded pdb=" OG SER C 403 " pdb=" O PRO R 348 " model vdw 2.279 2.440 nonbonded pdb=" OH TYR C 51 " pdb=" O ALA C 236 " model vdw 2.279 2.440 ... (remaining 189663 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 'F' selection = chain 'S' } ncs_group { reference = (chain 'B' and resid 1 through 440) selection = (chain 'C' and resid 1 through 440) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } ncs_group { reference = (chain 'J' and (resid 1 through 55 or resid 62 through 419)) selection = (chain 'Q' and (resid 1 through 55 or resid 62 through 419)) selection = (chain 'R' and (resid 1 through 55 or resid 62 through 419)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.200 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 66.360 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.007 0.102 25455 Z= 0.497 Angle : 0.929 13.174 34655 Z= 0.507 Chirality : 0.058 0.457 3864 Planarity : 0.008 0.102 4455 Dihedral : 9.309 71.568 9225 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 0.18 % Allowed : 2.14 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.10 % 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: -3.45 (0.12), residues: 3178 helix: -2.39 (0.18), residues: 434 sheet: -1.78 (0.15), residues: 928 loop : -2.61 (0.12), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP J 236 HIS 0.010 0.002 HIS B 381 PHE 0.030 0.004 PHE Q 328 TYR 0.040 0.003 TYR C 308 ARG 0.016 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 676 time to evaluate : 2.880 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 214 PHE cc_start: 0.7499 (m-80) cc_final: 0.6694 (m-80) REVERT: B 109 MET cc_start: 0.6488 (ptt) cc_final: 0.6154 (ptt) REVERT: B 113 ASP cc_start: 0.8209 (m-30) cc_final: 0.7997 (m-30) REVERT: B 310 SER cc_start: 0.8360 (t) cc_final: 0.8090 (m) REVERT: C 136 THR cc_start: 0.8415 (m) cc_final: 0.8034 (p) REVERT: C 211 SER cc_start: 0.8926 (m) cc_final: 0.8489 (p) REVERT: C 389 THR cc_start: 0.8327 (p) cc_final: 0.8013 (p) REVERT: C 437 THR cc_start: 0.6501 (m) cc_final: 0.6019 (m) REVERT: Q 94 ASP cc_start: 0.5553 (t0) cc_final: 0.5258 (t0) REVERT: R 147 VAL cc_start: 0.8963 (m) cc_final: 0.8516 (p) REVERT: S 130 ILE cc_start: 0.3548 (mm) cc_final: 0.3314 (mt) REVERT: S 153 VAL cc_start: -0.0326 (t) cc_final: -0.1069 (t) REVERT: S 166 LYS cc_start: 0.7397 (tttt) cc_final: 0.7013 (pptt) outliers start: 5 outliers final: 2 residues processed: 679 average time/residue: 0.3906 time to fit residues: 401.0798 Evaluate side-chains 345 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 343 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain G residue 263 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 249 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 360 ASN B 362 HIS ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN C 43 ASN C 130 GLN C 304 ASN C 390 HIS ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 442 ASN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 HIS G 43 ASN G 235 GLN G 264 ASN G 360 ASN G 368 GLN G 394 HIS ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 239 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 HIS Q 160 ASN Q 168 HIS ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS R 121 HIS R 156 HIS R 216 GLN ** R 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25455 Z= 0.254 Angle : 0.636 8.903 34655 Z= 0.335 Chirality : 0.045 0.175 3864 Planarity : 0.006 0.095 4455 Dihedral : 5.963 73.259 3476 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 3.10 % Allowed : 8.44 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -2.18 (0.14), residues: 3178 helix: -0.33 (0.25), residues: 435 sheet: -1.19 (0.16), residues: 961 loop : -1.91 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 236 HIS 0.007 0.001 HIS F 152 PHE 0.027 0.002 PHE P 14 TYR 0.026 0.002 TYR G 434 ARG 0.009 0.001 ARG Q 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 385 time to evaluate : 3.189 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 204 HIS cc_start: 0.4661 (m170) cc_final: 0.4368 (m170) REVERT: B 109 MET cc_start: 0.7001 (ptt) cc_final: 0.6611 (ptt) REVERT: B 153 PRO cc_start: 0.7578 (Cg_exo) cc_final: 0.7356 (Cg_endo) REVERT: B 160 LYS cc_start: 0.8332 (tttp) cc_final: 0.8039 (tttp) REVERT: B 310 SER cc_start: 0.8757 (t) cc_final: 0.8532 (m) REVERT: C 136 THR cc_start: 0.8265 (m) cc_final: 0.7981 (p) REVERT: C 211 SER cc_start: 0.8805 (m) cc_final: 0.8492 (p) REVERT: C 389 THR cc_start: 0.8719 (p) cc_final: 0.8498 (p) REVERT: F 130 ILE cc_start: 0.4613 (mm) cc_final: 0.4401 (mt) REVERT: G 73 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7509 (mpt-90) REVERT: Q 401 ARG cc_start: 0.6756 (ptt-90) cc_final: 0.6524 (ptp90) REVERT: R 181 LEU cc_start: 0.7110 (tp) cc_final: 0.6819 (tp) REVERT: S 166 LYS cc_start: 0.7218 (tttt) cc_final: 0.6700 (pptt) REVERT: S 209 TYR cc_start: 0.4896 (t80) cc_final: 0.4652 (t80) outliers start: 84 outliers final: 53 residues processed: 443 average time/residue: 0.3748 time to fit residues: 261.1515 Evaluate side-chains 353 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 300 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 353 HIS Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 236 TRP Chi-restraints excluded: chain R residue 256 HIS Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 180 VAL Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 79 optimal weight: 0.0040 chunk 289 optimal weight: 0.8980 chunk 312 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 30.0000 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 235 GLN B 331 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 360 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 HIS Q 216 GLN ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 353 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25455 Z= 0.169 Angle : 0.571 9.302 34655 Z= 0.296 Chirality : 0.043 0.270 3864 Planarity : 0.005 0.069 4455 Dihedral : 5.494 74.413 3476 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 3.02 % Allowed : 10.95 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -1.55 (0.15), residues: 3178 helix: 0.41 (0.26), residues: 441 sheet: -0.78 (0.16), residues: 971 loop : -1.56 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 236 HIS 0.008 0.001 HIS C 140 PHE 0.049 0.001 PHE Q 217 TYR 0.018 0.001 TYR G 434 ARG 0.004 0.000 ARG Q 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 342 time to evaluate : 2.932 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: C 136 THR cc_start: 0.8449 (m) cc_final: 0.8113 (p) REVERT: C 211 SER cc_start: 0.8770 (m) cc_final: 0.8517 (p) REVERT: F 130 ILE cc_start: 0.5160 (mm) cc_final: 0.4911 (mt) REVERT: F 202 TRP cc_start: 0.5012 (t60) cc_final: 0.3719 (t60) REVERT: G 73 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7365 (mpt-90) REVERT: J 88 ARG cc_start: 0.5806 (mmt180) cc_final: 0.5601 (mmt180) REVERT: R 148 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7445 (mm-30) REVERT: R 387 TRP cc_start: 0.7566 (t60) cc_final: 0.7178 (t60) REVERT: S 120 MET cc_start: 0.6383 (tmm) cc_final: 0.5850 (mmt) REVERT: S 166 LYS cc_start: 0.7139 (tttt) cc_final: 0.6695 (pptt) outliers start: 82 outliers final: 53 residues processed: 401 average time/residue: 0.3569 time to fit residues: 226.3771 Evaluate side-chains 337 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 284 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 168 HIS Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 225 GLN Chi-restraints excluded: chain Q residue 226 CYS Chi-restraints excluded: chain Q residue 241 ASP Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 236 TRP Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 180 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 290 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 386 HIS G 386 HIS ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 239 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 GLN ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS R 96 HIS ** R 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25455 Z= 0.315 Angle : 0.633 8.278 34655 Z= 0.332 Chirality : 0.046 0.251 3864 Planarity : 0.005 0.076 4455 Dihedral : 5.655 74.979 3476 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.01 % Favored : 93.90 % Rotamer: Outliers : 3.43 % Allowed : 12.27 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -1.33 (0.15), residues: 3178 helix: 0.89 (0.26), residues: 434 sheet: -0.68 (0.16), residues: 1005 loop : -1.48 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP Q 236 HIS 0.026 0.001 HIS Q 168 PHE 0.018 0.002 PHE J 389 TYR 0.018 0.002 TYR Q 9 ARG 0.005 0.001 ARG G 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 327 time to evaluate : 2.982 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: A 209 TYR cc_start: 0.7901 (t80) cc_final: 0.7655 (t80) REVERT: A 257 MET cc_start: 0.8316 (ptp) cc_final: 0.8091 (ptp) REVERT: B 7 MET cc_start: 0.7485 (tmm) cc_final: 0.7144 (ttp) REVERT: C 88 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: C 136 THR cc_start: 0.8529 (m) cc_final: 0.8221 (p) REVERT: C 211 SER cc_start: 0.8764 (m) cc_final: 0.8475 (p) REVERT: F 202 TRP cc_start: 0.6226 (t60) cc_final: 0.5697 (t60) REVERT: G 73 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7525 (mpt-90) REVERT: I 29 GLU cc_start: 0.7978 (mp0) cc_final: 0.7741 (mp0) REVERT: R 88 ARG cc_start: 0.6451 (mmt180) cc_final: 0.6248 (mmt180) REVERT: R 387 TRP cc_start: 0.7511 (t60) cc_final: 0.7157 (t60) REVERT: S 131 MET cc_start: 0.6343 (mmp) cc_final: 0.6136 (ppp) outliers start: 93 outliers final: 76 residues processed: 399 average time/residue: 0.3572 time to fit residues: 224.0197 Evaluate side-chains 361 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 284 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain R residue 392 SER Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 CYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 180 VAL Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 126 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 156 optimal weight: 6.9990 chunk 275 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN G 392 GLN J 347 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 353 HIS ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25455 Z= 0.241 Angle : 0.582 9.146 34655 Z= 0.300 Chirality : 0.044 0.149 3864 Planarity : 0.004 0.066 4455 Dihedral : 5.472 75.699 3476 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 3.28 % Allowed : 13.16 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -1.18 (0.15), residues: 3178 helix: 0.99 (0.27), residues: 440 sheet: -0.61 (0.16), residues: 1008 loop : -1.37 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 409 HIS 0.005 0.001 HIS Q 168 PHE 0.025 0.002 PHE F 189 TYR 0.020 0.001 TYR G 308 ARG 0.004 0.001 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 312 time to evaluate : 2.908 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: A 257 MET cc_start: 0.8370 (ptp) cc_final: 0.8004 (ptp) REVERT: C 88 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8093 (mpp) REVERT: C 136 THR cc_start: 0.8522 (m) cc_final: 0.8196 (p) REVERT: C 211 SER cc_start: 0.8684 (m) cc_final: 0.8482 (p) REVERT: C 324 LYS cc_start: 0.7332 (ttpt) cc_final: 0.6832 (ttpt) REVERT: F 130 ILE cc_start: 0.5980 (mm) cc_final: 0.5644 (mt) REVERT: F 189 PHE cc_start: 0.6526 (m-80) cc_final: 0.5886 (m-10) REVERT: F 257 MET cc_start: 0.6388 (ptp) cc_final: 0.6104 (ptp) REVERT: I 29 GLU cc_start: 0.8058 (mp0) cc_final: 0.7785 (mp0) REVERT: I 34 LEU cc_start: 0.8758 (mt) cc_final: 0.8483 (mt) REVERT: J 199 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: J 239 ASN cc_start: 0.8635 (t0) cc_final: 0.8311 (t0) REVERT: Q 70 MET cc_start: 0.8563 (tpp) cc_final: 0.8275 (tpp) REVERT: R 387 TRP cc_start: 0.7487 (t60) cc_final: 0.7096 (t60) REVERT: S 131 MET cc_start: 0.6344 (mmp) cc_final: 0.6128 (ppp) outliers start: 89 outliers final: 58 residues processed: 377 average time/residue: 0.3594 time to fit residues: 213.1922 Evaluate side-chains 349 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 289 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain S residue 141 CYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 20.0000 chunk 276 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 349 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN F 116 GLN G 125 HIS G 368 GLN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 GLN ** R 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25455 Z= 0.340 Angle : 0.640 8.092 34655 Z= 0.331 Chirality : 0.046 0.194 3864 Planarity : 0.005 0.074 4455 Dihedral : 5.706 80.790 3475 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 3.98 % Allowed : 13.05 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.19 (0.15), residues: 3178 helix: 1.00 (0.26), residues: 443 sheet: -0.58 (0.16), residues: 974 loop : -1.39 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 409 HIS 0.007 0.001 HIS J 28 PHE 0.020 0.002 PHE I 14 TYR 0.021 0.002 TYR G 308 ARG 0.006 0.001 ARG Q 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 323 time to evaluate : 2.895 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: A 131 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4675 (mmp) REVERT: B 229 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8793 (tt) REVERT: B 387 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9188 (mt) REVERT: C 136 THR cc_start: 0.8587 (m) cc_final: 0.8370 (p) REVERT: C 366 ARG cc_start: 0.8167 (ptm160) cc_final: 0.7824 (ptm160) REVERT: F 130 ILE cc_start: 0.6503 (mm) cc_final: 0.6192 (mt) REVERT: F 189 PHE cc_start: 0.6804 (m-80) cc_final: 0.6175 (m-80) REVERT: F 214 PHE cc_start: 0.7792 (m-80) cc_final: 0.7385 (m-80) REVERT: J 199 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: J 400 TYR cc_start: 0.7452 (m-80) cc_final: 0.7182 (m-80) REVERT: Q 241 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7967 (p0) REVERT: Q 287 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8979 (mt) REVERT: R 88 ARG cc_start: 0.6516 (mmt180) cc_final: 0.5997 (mmt180) REVERT: R 387 TRP cc_start: 0.7622 (t60) cc_final: 0.7275 (t60) REVERT: S 135 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7733 (mmtp) REVERT: S 173 TYR cc_start: 0.4521 (m-80) cc_final: 0.4271 (m-10) REVERT: S 189 PHE cc_start: 0.2538 (m-10) cc_final: 0.2164 (m-10) REVERT: T 14 PHE cc_start: 0.6675 (p90) cc_final: 0.6394 (p90) outliers start: 108 outliers final: 74 residues processed: 405 average time/residue: 0.3771 time to fit residues: 238.7130 Evaluate side-chains 374 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 294 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 241 ASP Chi-restraints excluded: chain Q residue 287 LEU Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 385 SER Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 224 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 171 optimal weight: 0.1980 chunk 306 optimal weight: 30.0000 chunk 191 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 392 GLN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25455 Z= 0.234 Angle : 0.580 7.993 34655 Z= 0.299 Chirality : 0.044 0.166 3864 Planarity : 0.004 0.065 4455 Dihedral : 5.502 78.714 3475 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 3.39 % Allowed : 14.60 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -1.11 (0.15), residues: 3178 helix: 1.05 (0.26), residues: 443 sheet: -0.56 (0.16), residues: 1006 loop : -1.33 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 409 HIS 0.019 0.001 HIS C 140 PHE 0.016 0.001 PHE I 14 TYR 0.020 0.001 TYR G 308 ARG 0.010 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 313 time to evaluate : 3.216 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: A 131 MET cc_start: 0.5579 (mpp) cc_final: 0.4837 (mmp) REVERT: B 229 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8703 (tt) REVERT: C 88 MET cc_start: 0.7674 (mtt) cc_final: 0.7387 (mtt) REVERT: C 136 THR cc_start: 0.8491 (m) cc_final: 0.8159 (p) REVERT: C 324 LYS cc_start: 0.7495 (ttpt) cc_final: 0.7039 (ttpt) REVERT: C 366 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7771 (ptm160) REVERT: F 189 PHE cc_start: 0.6781 (m-80) cc_final: 0.6345 (m-80) REVERT: F 214 PHE cc_start: 0.7653 (m-80) cc_final: 0.7254 (m-80) REVERT: I 34 LEU cc_start: 0.8835 (mt) cc_final: 0.8555 (mt) REVERT: J 199 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: J 256 HIS cc_start: 0.7418 (p-80) cc_final: 0.7175 (p-80) REVERT: P 33 MET cc_start: 0.7978 (ptp) cc_final: 0.6973 (ptt) REVERT: R 88 ARG cc_start: 0.6405 (mmt180) cc_final: 0.5953 (mmt180) REVERT: R 387 TRP cc_start: 0.7574 (t60) cc_final: 0.7208 (t60) outliers start: 92 outliers final: 73 residues processed: 389 average time/residue: 0.3686 time to fit residues: 223.7152 Evaluate side-chains 366 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 291 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 238 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 28 optimal weight: 0.0770 chunk 240 optimal weight: 9.9990 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN B 130 GLN ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 392 GLN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25455 Z= 0.327 Angle : 0.622 9.278 34655 Z= 0.321 Chirality : 0.046 0.176 3864 Planarity : 0.005 0.072 4455 Dihedral : 5.630 81.275 3475 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.23 % Rotamer: Outliers : 3.46 % Allowed : 14.52 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -1.19 (0.15), residues: 3178 helix: 1.17 (0.27), residues: 437 sheet: -0.60 (0.16), residues: 1001 loop : -1.43 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 202 HIS 0.009 0.001 HIS S 152 PHE 0.015 0.002 PHE I 14 TYR 0.027 0.002 TYR F 209 ARG 0.011 0.001 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 313 time to evaluate : 3.235 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 131 MET cc_start: 0.5567 (mpp) cc_final: 0.4998 (mmp) REVERT: A 151 MET cc_start: 0.6048 (mmm) cc_final: 0.5559 (mmp) REVERT: A 168 LYS cc_start: 0.7384 (tppt) cc_final: 0.6937 (mptt) REVERT: B 55 MET cc_start: 0.7382 (mtm) cc_final: 0.7167 (ptp) REVERT: B 229 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8709 (tt) REVERT: B 387 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9243 (mt) REVERT: C 136 THR cc_start: 0.8709 (m) cc_final: 0.8471 (p) REVERT: C 366 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7828 (ptm160) REVERT: F 189 PHE cc_start: 0.6863 (m-80) cc_final: 0.6395 (m-80) REVERT: G 276 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9030 (mt) REVERT: I 29 GLU cc_start: 0.7870 (mp0) cc_final: 0.7316 (mp0) REVERT: J 199 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: J 256 HIS cc_start: 0.7439 (p-80) cc_final: 0.7097 (p-80) REVERT: P 33 MET cc_start: 0.7801 (ptp) cc_final: 0.6842 (ptt) REVERT: R 88 ARG cc_start: 0.6496 (mmt180) cc_final: 0.5956 (mmt180) REVERT: R 387 TRP cc_start: 0.7607 (t60) cc_final: 0.7244 (t60) REVERT: S 120 MET cc_start: 0.7233 (tmm) cc_final: 0.6621 (mtt) outliers start: 94 outliers final: 76 residues processed: 391 average time/residue: 0.3406 time to fit residues: 209.6000 Evaluate side-chains 386 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 306 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 225 ASP Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 285 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 392 GLN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 349 GLN F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 20 ASN G 130 GLN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25455 Z= 0.182 Angle : 0.572 9.516 34655 Z= 0.291 Chirality : 0.044 0.218 3864 Planarity : 0.004 0.063 4455 Dihedral : 5.336 79.702 3475 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.69 % Allowed : 15.78 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -1.04 (0.15), residues: 3178 helix: 1.04 (0.26), residues: 449 sheet: -0.47 (0.17), residues: 995 loop : -1.30 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 202 HIS 0.003 0.001 HIS F 204 PHE 0.018 0.001 PHE I 14 TYR 0.019 0.001 TYR F 209 ARG 0.007 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 319 time to evaluate : 2.949 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: A 228 ARG cc_start: 0.5994 (mtt180) cc_final: 0.5721 (mtp-110) REVERT: B 387 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9236 (mt) REVERT: C 136 THR cc_start: 0.8717 (m) cc_final: 0.8474 (p) REVERT: C 366 ARG cc_start: 0.8066 (ptm160) cc_final: 0.7770 (ptm160) REVERT: F 189 PHE cc_start: 0.6852 (m-80) cc_final: 0.6476 (m-80) REVERT: I 29 GLU cc_start: 0.7843 (mp0) cc_final: 0.7480 (mp0) REVERT: P 33 MET cc_start: 0.7814 (ptp) cc_final: 0.6802 (ptt) REVERT: Q 70 MET cc_start: 0.8286 (tpp) cc_final: 0.7348 (tpt) REVERT: R 88 ARG cc_start: 0.6342 (mmt180) cc_final: 0.5824 (mmt180) REVERT: R 387 TRP cc_start: 0.7486 (t60) cc_final: 0.7105 (t60) REVERT: S 116 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6299 (mp10) REVERT: S 120 MET cc_start: 0.7243 (tmm) cc_final: 0.6616 (mtt) REVERT: S 184 MET cc_start: 0.7187 (ptp) cc_final: 0.6677 (ptt) REVERT: S 191 TYR cc_start: 0.4360 (p90) cc_final: 0.3805 (p90) REVERT: T 14 PHE cc_start: 0.6571 (p90) cc_final: 0.6260 (p90) REVERT: T 31 LEU cc_start: 0.7064 (mp) cc_final: 0.6676 (mp) outliers start: 73 outliers final: 62 residues processed: 382 average time/residue: 0.3680 time to fit residues: 220.8796 Evaluate side-chains 353 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 289 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 408 ILE Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain S residue 116 GLN Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.0870 chunk 302 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 316 optimal weight: 20.0000 chunk 291 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 392 GLN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN Q 168 HIS S 116 GLN ** S 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25455 Z= 0.183 Angle : 0.576 9.337 34655 Z= 0.292 Chirality : 0.044 0.218 3864 Planarity : 0.004 0.069 4455 Dihedral : 5.263 80.082 3475 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 2.51 % Allowed : 16.26 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -0.96 (0.15), residues: 3178 helix: 1.04 (0.26), residues: 448 sheet: -0.38 (0.17), residues: 995 loop : -1.24 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 202 HIS 0.007 0.001 HIS Q 168 PHE 0.018 0.001 PHE I 14 TYR 0.024 0.001 TYR B 434 ARG 0.009 0.000 ARG G 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 299 time to evaluate : 2.852 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: A 151 MET cc_start: 0.5772 (mmm) cc_final: 0.5416 (mmp) REVERT: A 228 ARG cc_start: 0.6118 (mtt180) cc_final: 0.5753 (mtp-110) REVERT: B 387 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9231 (mt) REVERT: C 136 THR cc_start: 0.8665 (m) cc_final: 0.8425 (p) REVERT: C 366 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7764 (ptm160) REVERT: F 189 PHE cc_start: 0.6796 (m-80) cc_final: 0.6458 (m-80) REVERT: G 20 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (m110) REVERT: I 29 GLU cc_start: 0.7873 (mp0) cc_final: 0.7600 (mp0) REVERT: P 33 MET cc_start: 0.7750 (ptp) cc_final: 0.6844 (ptt) REVERT: Q 70 MET cc_start: 0.8252 (tpp) cc_final: 0.7266 (tpt) REVERT: R 88 ARG cc_start: 0.6321 (mmt180) cc_final: 0.5780 (mmt180) REVERT: R 387 TRP cc_start: 0.7438 (t60) cc_final: 0.7035 (t60) REVERT: S 116 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6307 (mp10) REVERT: S 120 MET cc_start: 0.7285 (tmm) cc_final: 0.6654 (mtt) REVERT: S 184 MET cc_start: 0.7262 (ptp) cc_final: 0.6814 (ptt) REVERT: T 31 LEU cc_start: 0.7105 (mp) cc_final: 0.6869 (mp) REVERT: T 35 SER cc_start: 0.8012 (m) cc_final: 0.7645 (t) outliers start: 68 outliers final: 61 residues processed: 356 average time/residue: 0.3657 time to fit residues: 204.6341 Evaluate side-chains 357 residues out of total 2713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 293 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 168 HIS Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 408 ILE Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain S residue 116 GLN Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 232 optimal weight: 0.1980 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 259 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 392 GLN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 235 GLN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN S 116 GLN ** S 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100247 restraints weight = 48422.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100629 restraints weight = 26114.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101083 restraints weight = 18142.925| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25455 Z= 0.270 Angle : 0.601 13.441 34655 Z= 0.306 Chirality : 0.045 0.244 3864 Planarity : 0.005 0.065 4455 Dihedral : 5.334 80.945 3475 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.10 % Favored : 93.80 % Rotamer: Outliers : 2.76 % Allowed : 16.51 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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: -0.98 (0.15), residues: 3178 helix: 1.11 (0.26), residues: 442 sheet: -0.41 (0.16), residues: 1001 loop : -1.26 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 236 HIS 0.013 0.001 HIS Q 168 PHE 0.019 0.001 PHE I 14 TYR 0.021 0.001 TYR Q 360 ARG 0.008 0.001 ARG A 149 =============================================================================== Job complete usr+sys time: 5143.95 seconds wall clock time: 94 minutes 43.99 seconds (5683.99 seconds total)