Starting phenix.real_space_refine on Tue Apr 7 04:30:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffl_31568/04_2026/7ffl_31568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffl_31568/04_2026/7ffl_31568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ffl_31568/04_2026/7ffl_31568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffl_31568/04_2026/7ffl_31568_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ffl_31568/04_2026/7ffl_31568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffl_31568/04_2026/7ffl_31568.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 201 5.16 5 C 16302 2.51 5 N 4410 2.21 5 O 4851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25767 Number of models: 1 Model: "" Number of chains: 18 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: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "E" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} 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: 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: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} 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: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} 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: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "R" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} 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} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.09, per 1000 atoms: 0.24 Number of scatterers: 25767 At special positions: 0 Unit cell: (158.4, 199.32, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 201 16.00 O 4851 8.00 N 4410 7.00 C 16302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.04 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 D 29 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 55 " distance=2.00 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 42 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 55 " distance=1.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 64 " 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 H 29 " - pdb=" SG CYS H 42 " distance=2.03 Simple disulfide: pdb=" SG CYS H 37 " - pdb=" SG CYS H 55 " distance=1.25 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 64 " 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 - 3.00 Amino acid : True - 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 69 sheets defined 16.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.094A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.858A 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: 3.542A 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: 4.233A 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: 3.730A 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: 3.625A 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: 4.917A 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 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.902A pdb=" N SER E 59 " --> pdb=" O PHE E 56 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP E 60 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS E 62 " --> pdb=" O SER E 59 " (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: 3.760A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.648A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.566A 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: 3.586A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.758A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 55 through 62 removed outlier: 4.434A pdb=" N SER H 59 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP H 60 " --> pdb=" O ASP H 57 " (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: 3.701A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.545A 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: 3.785A pdb=" N VAL J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE J 356 " --> pdb=" O PRO J 352 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR J 357 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE J 368 " --> pdb=" O PRO J 364 " (cutoff:3.500A) removed outlier: 3.935A 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: 3.593A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.532A 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: 3.774A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.736A 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: 3.862A 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 410 through 416 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.873A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.591A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.098A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.654A 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: 8.263A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.784A 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: 3.545A 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: 4.752A 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: 4.261A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.737A 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: 6.307A 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: 3.647A 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: 3.699A 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: 6.405A 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 'D' and resid 34 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.640A pdb=" N VAL F 143 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.508A 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=AC8, 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: 8.538A 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: 5.774A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD1, 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=AD2, 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=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD4, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.337A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.065A 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=AD6, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AD7, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AD8, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AE1, 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=AE2, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AE3, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.587A pdb=" N GLN J 48 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL J 36 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG J 46 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J 65 " --> pdb=" O GLY J 54 " (cutoff:3.500A) Processing sheet with id=AE4, 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=AE5, first strand: chain 'J' and resid 147 through 149 Processing sheet with id=AE6, first strand: chain 'J' and resid 152 through 154 Processing sheet with id=AE7, first strand: chain 'J' and resid 237 through 238 removed outlier: 3.534A pdb=" N VAL J 237 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY J 253 " --> pdb=" O MET J 167 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 179 through 181 Processing sheet with id=AE9, first strand: chain 'J' and resid 196 through 200 removed outlier: 3.983A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 275 through 279 Processing sheet with id=AF2, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AF3, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AF4, 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: 4.510A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.383A 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) removed outlier: 6.279A pdb=" N THR Q 65 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AF6, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AF7, 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=AF8, 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=AF9, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AG1, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AG2, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AG3, 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: 4.804A 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: 9.904A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AG5, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AG6, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.629A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AG7, 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) Processing sheet with id=AG8, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.562A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AH1, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.655A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AH3, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AH4, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.496A 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: 6.156A 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=AH6, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.516A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.72 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: 8253 1.34 - 1.46: 6441 1.46 - 1.59: 11475 1.59 - 1.71: 0 1.71 - 1.84: 264 Bond restraints: 26433 Sorted by residual: bond pdb=" CB VAL G 148 " pdb=" CG2 VAL G 148 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.75e+00 bond pdb=" CB VAL C 148 " pdb=" CG2 VAL C 148 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.56e+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 6.54e+00 bond pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.83e+00 bond pdb=" C ASN G 264 " pdb=" N PRO G 265 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.74e+00 ... (remaining 26428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.48: 35937 7.48 - 14.96: 37 14.96 - 22.43: 1 22.43 - 29.91: 0 29.91 - 37.39: 1 Bond angle restraints: 35976 Sorted by residual: angle pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" C PRO R 409 " ideal model delta sigma weight residual 112.47 149.86 -37.39 2.06e+00 2.36e-01 3.29e+02 angle pdb=" N PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta sigma weight residual 110.49 132.07 -21.58 1.69e+00 3.50e-01 1.63e+02 angle pdb=" N LYS D 58 " pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 111.39 123.04 -11.65 1.38e+00 5.25e-01 7.12e+01 angle pdb=" N LYS H 58 " pdb=" CA LYS H 58 " pdb=" C LYS H 58 " ideal model delta sigma weight residual 111.54 120.30 -8.76 1.36e+00 5.41e-01 4.15e+01 angle pdb=" N PHE H 56 " pdb=" CA PHE H 56 " pdb=" C PHE H 56 " ideal model delta sigma weight residual 109.96 100.78 9.18 1.50e+00 4.44e-01 3.75e+01 ... (remaining 35971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 14964 14.33 - 28.65: 732 28.65 - 42.98: 189 42.98 - 57.31: 31 57.31 - 71.64: 20 Dihedral angle restraints: 15936 sinusoidal: 6261 harmonic: 9675 Sorted by residual: dihedral pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual 115.10 155.02 -39.92 0 2.50e+00 1.60e-01 2.55e+02 dihedral pdb=" C PRO R 409 " pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual -120.70 -155.07 34.37 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta harmonic sigma weight residual 122.80 157.10 -34.30 0 2.50e+00 1.60e-01 1.88e+02 ... (remaining 15933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 3981 0.403 - 0.806: 4 0.806 - 1.209: 0 1.209 - 1.612: 1 1.612 - 2.014: 1 Chirality restraints: 3987 Sorted by residual: chirality pdb=" CA PRO R 409 " pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CB PRO R 409 " both_signs ideal model delta sigma weight residual False 2.72 0.70 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA PHE R 410 " pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CB PHE R 410 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.63e+01 chirality pdb=" CA LYS D 58 " pdb=" N LYS D 58 " pdb=" C LYS D 58 " pdb=" CB LYS D 58 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 3984 not shown) Planarity restraints: 4647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " 0.068 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 2.21e-02 1.22e+01 pdb=" CG TRP J 236 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J 236 " -0.011 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 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 236 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 236 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 236 " -0.004 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 8.64e-02 1.19e+01 pdb=" N PRO B 265 " -0.149 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 4644 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 376 2.65 - 3.22: 21300 3.22 - 3.78: 37781 3.78 - 4.34: 51412 4.34 - 4.90: 86899 Nonbonded interactions: 197768 Sorted by model distance: nonbonded pdb=" OD1 ASP D 57 " pdb=" OG SER J 177 " model vdw 2.092 3.040 nonbonded pdb=" O HIS G 441 " pdb=" OXT ASN G 442 " model vdw 2.236 3.040 nonbonded pdb=" O ALA C 401 " pdb=" OH TYR R 359 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU B 120 " pdb=" OH TYR B 122 " model vdw 2.269 3.040 nonbonded pdb=" O ALA B 401 " pdb=" OH TYR Q 359 " model vdw 2.272 3.040 ... (remaining 197763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.011 0.996 26482 Z= 0.519 Angle : 1.064 61.632 36074 Z= 0.574 Chirality : 0.071 2.014 3987 Planarity : 0.008 0.102 4647 Dihedral : 9.546 71.636 9591 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.65 % Favored : 93.19 % Rotamer: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.20 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.12), residues: 3306 helix: -2.35 (0.18), residues: 435 sheet: -1.84 (0.16), residues: 909 loop : -2.50 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 21 TYR 0.039 0.003 TYR C 308 PHE 0.032 0.004 PHE Q 328 TRP 0.047 0.004 TRP J 236 HIS 0.010 0.002 HIS J 288 Details of bonding type rmsd covalent geometry : bond 0.00746 (26433) covalent geometry : angle 0.96430 (35976) SS BOND : bond 0.19264 ( 49) SS BOND : angle 8.70284 ( 98) hydrogen bonds : bond 0.21032 ( 756) hydrogen bonds : angle 8.41426 ( 1962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 649 time to evaluate : 0.931 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 180 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7298 (t) REVERT: A 200 TYR cc_start: 0.6210 (m-80) cc_final: 0.5619 (m-80) REVERT: A 267 TYR cc_start: 0.6714 (t80) cc_final: 0.6229 (t80) REVERT: B 55 MET cc_start: 0.8106 (mtm) cc_final: 0.7902 (mtm) REVERT: C 115 LEU cc_start: 0.8423 (tm) cc_final: 0.8192 (tp) REVERT: C 354 ILE cc_start: 0.8152 (pt) cc_final: 0.7800 (mt) REVERT: D 28 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7146 (mm-30) REVERT: E 43 ILE cc_start: 0.8924 (pt) cc_final: 0.8711 (pt) REVERT: F 193 HIS cc_start: 0.7965 (p-80) cc_final: 0.7571 (p-80) REVERT: J 356 ILE cc_start: 0.9038 (mt) cc_final: 0.8734 (mp) REVERT: J 390 CYS cc_start: 0.6584 (m) cc_final: 0.6128 (t) REVERT: R 21 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.6577 (mmm160) REVERT: S 184 MET cc_start: 0.6585 (ttm) cc_final: 0.6329 (ttm) REVERT: S 228 ARG cc_start: 0.3559 (mtt-85) cc_final: 0.3315 (mtp85) REVERT: S 256 VAL cc_start: 0.6193 (m) cc_final: 0.5901 (m) REVERT: S 266 LYS cc_start: 0.6712 (tttm) cc_final: 0.6208 (tptm) outliers start: 10 outliers final: 2 residues processed: 658 average time/residue: 0.1881 time to fit residues: 187.1528 Evaluate side-chains 351 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 348 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL 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: 327 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN B 43 ASN B 125 HIS B 140 HIS B 218 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 442 ASN C 235 GLN C 360 ASN C 368 GLN C 394 HIS C 442 ASN D 27 ASN D 30 ASN E 30 ASN F 137 ASN F 203 HIS G 125 HIS G 264 ASN G 360 ASN G 390 HIS G 394 HIS G 439 GLN ** G 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN H 30 ASN J 256 HIS J 353 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 152 GLN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 HIS R 405 ASN T 37 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113764 restraints weight = 37845.721| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.18 r_work: 0.3220 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26482 Z= 0.158 Angle : 0.653 9.726 36074 Z= 0.340 Chirality : 0.046 0.218 3987 Planarity : 0.006 0.076 4647 Dihedral : 6.053 73.373 3609 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.80 % Rotamer: Outliers : 2.16 % Allowed : 7.97 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.14), residues: 3306 helix: -0.43 (0.24), residues: 444 sheet: -1.23 (0.16), residues: 945 loop : -1.83 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 21 TYR 0.020 0.002 TYR C 308 PHE 0.022 0.002 PHE A 148 TRP 0.047 0.002 TRP J 236 HIS 0.008 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00366 (26433) covalent geometry : angle 0.65000 (35976) SS BOND : bond 0.00331 ( 49) SS BOND : angle 1.36143 ( 98) hydrogen bonds : bond 0.03728 ( 756) hydrogen bonds : angle 5.84138 ( 1962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 393 time to evaluate : 1.030 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: A 200 TYR cc_start: 0.6188 (m-80) cc_final: 0.5404 (m-80) REVERT: A 267 TYR cc_start: 0.7207 (t80) cc_final: 0.6675 (t80) REVERT: B 408 THR cc_start: 0.8444 (m) cc_final: 0.8242 (m) REVERT: C 115 LEU cc_start: 0.8760 (tm) cc_final: 0.8539 (tp) REVERT: C 354 ILE cc_start: 0.8674 (pt) cc_final: 0.8223 (mt) REVERT: D 28 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7211 (mm-30) REVERT: F 121 LYS cc_start: 0.8066 (tttm) cc_final: 0.7711 (ptmt) REVERT: F 148 PHE cc_start: 0.7952 (m-80) cc_final: 0.7661 (m-10) REVERT: G 288 THR cc_start: 0.8510 (m) cc_final: 0.8257 (p) REVERT: H 57 ASP cc_start: 0.7472 (p0) cc_final: 0.7243 (p0) REVERT: I 33 MET cc_start: 0.5884 (ttp) cc_final: 0.5681 (ttm) REVERT: J 224 GLU cc_start: 0.8552 (mp0) cc_final: 0.8332 (mp0) REVERT: J 342 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7592 (mm-30) REVERT: J 356 ILE cc_start: 0.9010 (mt) cc_final: 0.8784 (mp) REVERT: J 390 CYS cc_start: 0.6987 (m) cc_final: 0.6403 (t) REVERT: J 391 ARG cc_start: 0.6937 (mtp-110) cc_final: 0.6634 (ttm170) REVERT: Q 360 TYR cc_start: 0.8344 (t80) cc_final: 0.7296 (t80) REVERT: R 88 ARG cc_start: 0.6989 (mmt180) cc_final: 0.6508 (mmt90) REVERT: R 216 GLN cc_start: 0.8065 (tt0) cc_final: 0.7588 (tp40) REVERT: R 275 MET cc_start: 0.8580 (mtp) cc_final: 0.8323 (mtm) REVERT: S 118 MET cc_start: 0.7074 (tmm) cc_final: 0.6700 (tmm) REVERT: S 176 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7474 (mt-10) REVERT: S 184 MET cc_start: 0.8402 (ttm) cc_final: 0.7834 (ttt) REVERT: S 189 PHE cc_start: 0.8047 (m-80) cc_final: 0.7782 (m-10) REVERT: S 266 LYS cc_start: 0.8389 (tttm) cc_final: 0.8172 (tptm) REVERT: T 6 MET cc_start: 0.5039 (mpp) cc_final: 0.4454 (mmm) outliers start: 61 outliers final: 35 residues processed: 428 average time/residue: 0.1715 time to fit residues: 113.7048 Evaluate side-chains 361 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 236 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 386 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN F 204 HIS ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS G 441 HIS J 358 HIS Q 91 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 225 GLN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS R 219 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.159926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111830 restraints weight = 37537.470| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.57 r_work: 0.3091 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26482 Z= 0.264 Angle : 0.717 10.443 36074 Z= 0.371 Chirality : 0.049 0.328 3987 Planarity : 0.006 0.155 4647 Dihedral : 6.206 76.486 3608 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.74 % Rotamer: Outliers : 3.26 % Allowed : 10.41 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3306 helix: 0.48 (0.26), residues: 432 sheet: -0.99 (0.16), residues: 1026 loop : -1.65 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 21 TYR 0.025 0.002 TYR G 24 PHE 0.026 0.003 PHE Q 259 TRP 0.040 0.002 TRP J 236 HIS 0.014 0.002 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00646 (26433) covalent geometry : angle 0.71431 (35976) SS BOND : bond 0.00414 ( 49) SS BOND : angle 1.30180 ( 98) hydrogen bonds : bond 0.03980 ( 756) hydrogen bonds : angle 5.43158 ( 1962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 342 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6351 (pmm) REVERT: A 200 TYR cc_start: 0.6663 (m-80) cc_final: 0.5726 (m-80) REVERT: A 267 TYR cc_start: 0.7547 (t80) cc_final: 0.6991 (t80) REVERT: B 377 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7771 (mtmt) REVERT: B 396 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8708 (tp40) REVERT: C 151 GLU cc_start: 0.8267 (pm20) cc_final: 0.7972 (pm20) REVERT: C 354 ILE cc_start: 0.8858 (pt) cc_final: 0.8395 (mt) REVERT: D 28 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 52 LEU cc_start: 0.8515 (mt) cc_final: 0.8233 (mt) REVERT: F 148 PHE cc_start: 0.8107 (m-80) cc_final: 0.7689 (m-10) REVERT: G 99 GLU cc_start: 0.8668 (pt0) cc_final: 0.8222 (pm20) REVERT: H 57 ASP cc_start: 0.7766 (p0) cc_final: 0.7543 (p0) REVERT: I 33 MET cc_start: 0.5937 (ttp) cc_final: 0.5622 (tmm) REVERT: J 224 GLU cc_start: 0.8506 (mp0) cc_final: 0.8297 (mp0) REVERT: J 323 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7475 (mm-30) REVERT: J 342 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7539 (mm-30) REVERT: J 390 CYS cc_start: 0.7136 (m) cc_final: 0.6500 (t) REVERT: J 391 ARG cc_start: 0.7157 (mtp-110) cc_final: 0.6913 (ttm170) REVERT: P 33 MET cc_start: 0.6187 (ttp) cc_final: 0.5744 (ptm) REVERT: Q 167 MET cc_start: 0.7430 (tpp) cc_final: 0.6848 (mpp) REVERT: Q 186 VAL cc_start: 0.8276 (p) cc_final: 0.7995 (m) REVERT: Q 256 HIS cc_start: 0.8022 (p90) cc_final: 0.7808 (p90) REVERT: Q 357 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7612 (p) REVERT: Q 360 TYR cc_start: 0.8428 (t80) cc_final: 0.7597 (t80) REVERT: R 88 ARG cc_start: 0.6967 (mmt180) cc_final: 0.6181 (mmt180) REVERT: R 275 MET cc_start: 0.8784 (mtp) cc_final: 0.8556 (mtm) REVERT: R 313 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8273 (mt-10) REVERT: S 135 LYS cc_start: 0.7870 (mmmt) cc_final: 0.7353 (mmtt) REVERT: S 156 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7593 (tmtt) REVERT: S 184 MET cc_start: 0.8368 (ttm) cc_final: 0.7759 (ttt) REVERT: S 259 ASN cc_start: 0.7573 (t0) cc_final: 0.7051 (t0) outliers start: 92 outliers final: 66 residues processed: 407 average time/residue: 0.1672 time to fit residues: 106.6848 Evaluate side-chains 378 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 310 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain S residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 69 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 360 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 81 GLN J 288 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111227 restraints weight = 37435.017| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.41 r_work: 0.3117 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26482 Z= 0.205 Angle : 0.644 9.247 36074 Z= 0.334 Chirality : 0.046 0.267 3987 Planarity : 0.006 0.118 4647 Dihedral : 6.003 77.066 3608 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.43 % Rotamer: Outliers : 2.98 % Allowed : 11.58 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3306 helix: 0.88 (0.26), residues: 429 sheet: -0.86 (0.16), residues: 1032 loop : -1.48 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 21 TYR 0.019 0.002 TYR C 308 PHE 0.018 0.002 PHE Q 259 TRP 0.056 0.002 TRP J 236 HIS 0.013 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00499 (26433) covalent geometry : angle 0.64118 (35976) SS BOND : bond 0.00306 ( 49) SS BOND : angle 1.33555 ( 98) hydrogen bonds : bond 0.03513 ( 756) hydrogen bonds : angle 5.24844 ( 1962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 319 time to evaluate : 0.897 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: A 118 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6292 (pmm) REVERT: A 200 TYR cc_start: 0.6650 (m-80) cc_final: 0.5864 (m-80) REVERT: A 267 TYR cc_start: 0.7463 (t80) cc_final: 0.6960 (t80) REVERT: B 396 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8648 (tp40) REVERT: C 354 ILE cc_start: 0.8931 (pt) cc_final: 0.8484 (mt) REVERT: D 28 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7489 (mm-30) REVERT: G 99 GLU cc_start: 0.8543 (pt0) cc_final: 0.8136 (pm20) REVERT: H 57 ASP cc_start: 0.7658 (p0) cc_final: 0.7361 (p0) REVERT: I 33 MET cc_start: 0.5946 (ttp) cc_final: 0.5652 (tmm) REVERT: J 224 GLU cc_start: 0.8474 (mp0) cc_final: 0.8240 (mp0) REVERT: J 342 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7379 (mm-30) REVERT: J 356 ILE cc_start: 0.8951 (mt) cc_final: 0.8748 (mp) REVERT: J 390 CYS cc_start: 0.7373 (m) cc_final: 0.6497 (t) REVERT: J 391 ARG cc_start: 0.7039 (mtp-110) cc_final: 0.6757 (ttm170) REVERT: J 401 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.8010 (mtp180) REVERT: Q 60 ASN cc_start: 0.7665 (t0) cc_final: 0.7464 (m-40) REVERT: Q 167 MET cc_start: 0.7392 (tpp) cc_final: 0.6985 (mpp) REVERT: Q 186 VAL cc_start: 0.8263 (p) cc_final: 0.8028 (m) REVERT: Q 357 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7680 (p) REVERT: Q 360 TYR cc_start: 0.8438 (t80) cc_final: 0.7600 (t80) REVERT: R 88 ARG cc_start: 0.7016 (mmt180) cc_final: 0.6425 (mmt180) REVERT: R 275 MET cc_start: 0.8713 (mtp) cc_final: 0.8482 (mtm) REVERT: R 313 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8294 (mt-10) REVERT: S 135 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7401 (mmtm) REVERT: S 156 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7632 (tmtt) REVERT: S 184 MET cc_start: 0.8347 (ttm) cc_final: 0.7762 (ttt) REVERT: S 197 GLN cc_start: 0.8233 (pm20) cc_final: 0.7556 (tt0) REVERT: S 259 ASN cc_start: 0.7541 (t0) cc_final: 0.7152 (t0) outliers start: 84 outliers final: 62 residues processed: 373 average time/residue: 0.1661 time to fit residues: 98.3085 Evaluate side-chains 368 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 114 optimal weight: 30.0000 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 50.0000 chunk 238 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 147 optimal weight: 0.0870 chunk 234 optimal weight: 8.9990 chunk 67 optimal weight: 0.0970 chunk 217 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 ASN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN R 219 GLN R 353 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115518 restraints weight = 37463.190| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.62 r_work: 0.3155 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26482 Z= 0.095 Angle : 0.565 9.362 36074 Z= 0.292 Chirality : 0.044 0.227 3987 Planarity : 0.004 0.071 4647 Dihedral : 5.527 77.775 3608 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.57 % Favored : 95.31 % Rotamer: Outliers : 2.20 % Allowed : 13.18 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3306 helix: 0.97 (0.26), residues: 444 sheet: -0.49 (0.16), residues: 990 loop : -1.25 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 117 TYR 0.015 0.001 TYR G 308 PHE 0.022 0.001 PHE A 189 TRP 0.049 0.001 TRP J 236 HIS 0.005 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00205 (26433) covalent geometry : angle 0.56369 (35976) SS BOND : bond 0.00245 ( 49) SS BOND : angle 0.98919 ( 98) hydrogen bonds : bond 0.02967 ( 756) hydrogen bonds : angle 5.07156 ( 1962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 335 time to evaluate : 0.939 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 195 LYS cc_start: 0.6843 (mppt) cc_final: 0.6192 (ptpp) REVERT: A 200 TYR cc_start: 0.6683 (m-80) cc_final: 0.6049 (m-80) REVERT: A 207 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7276 (p) REVERT: A 267 TYR cc_start: 0.7302 (t80) cc_final: 0.6817 (t80) REVERT: B 31 ILE cc_start: 0.7891 (mt) cc_final: 0.7604 (mm) REVERT: B 396 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8597 (tp40) REVERT: C 354 ILE cc_start: 0.8884 (pt) cc_final: 0.8509 (mt) REVERT: D 28 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 57 ASP cc_start: 0.7392 (t70) cc_final: 0.7140 (t70) REVERT: F 121 LYS cc_start: 0.7586 (ptmt) cc_final: 0.7030 (ptmt) REVERT: F 199 TYR cc_start: 0.7230 (m-80) cc_final: 0.6847 (m-80) REVERT: F 254 SER cc_start: 0.7995 (p) cc_final: 0.7187 (m) REVERT: G 99 GLU cc_start: 0.8550 (pt0) cc_final: 0.8103 (pm20) REVERT: G 377 LYS cc_start: 0.8286 (tttm) cc_final: 0.7830 (ptpp) REVERT: H 57 ASP cc_start: 0.7657 (p0) cc_final: 0.7291 (p0) REVERT: I 33 MET cc_start: 0.5932 (ttp) cc_final: 0.5586 (tmm) REVERT: J 224 GLU cc_start: 0.8469 (mp0) cc_final: 0.8194 (mp0) REVERT: J 298 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8996 (ptt-90) REVERT: J 342 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7278 (mm-30) REVERT: J 390 CYS cc_start: 0.7343 (m) cc_final: 0.6479 (t) REVERT: J 391 ARG cc_start: 0.7098 (mtp-110) cc_final: 0.6812 (ttm170) REVERT: J 401 ARG cc_start: 0.8420 (mtt-85) cc_final: 0.8031 (mtp180) REVERT: Q 167 MET cc_start: 0.7445 (tpp) cc_final: 0.7221 (mpp) REVERT: Q 186 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7974 (m) REVERT: Q 360 TYR cc_start: 0.8440 (t80) cc_final: 0.7432 (t80) REVERT: R 88 ARG cc_start: 0.6902 (mmt180) cc_final: 0.6501 (mmt180) REVERT: R 267 THR cc_start: 0.9175 (t) cc_final: 0.8854 (m) REVERT: R 313 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8300 (mt-10) REVERT: S 135 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7461 (mmtm) REVERT: S 156 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7533 (tmtt) REVERT: S 184 MET cc_start: 0.8286 (ttm) cc_final: 0.7735 (ttt) REVERT: S 197 GLN cc_start: 0.8266 (pm20) cc_final: 0.7603 (tt0) REVERT: S 247 GLU cc_start: 0.2171 (tm-30) cc_final: 0.1754 (tm-30) REVERT: S 259 ASN cc_start: 0.7617 (t0) cc_final: 0.7285 (t0) outliers start: 62 outliers final: 38 residues processed: 375 average time/residue: 0.1662 time to fit residues: 98.5805 Evaluate side-chains 354 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 47 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 317 optimal weight: 30.0000 chunk 89 optimal weight: 40.0000 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 296 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109701 restraints weight = 37523.750| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.38 r_work: 0.3095 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26482 Z= 0.217 Angle : 0.638 8.245 36074 Z= 0.329 Chirality : 0.047 0.395 3987 Planarity : 0.005 0.128 4647 Dihedral : 5.837 87.714 3608 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.75 % Favored : 94.13 % Rotamer: Outliers : 3.05 % Allowed : 13.28 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3306 helix: 1.11 (0.26), residues: 441 sheet: -0.51 (0.16), residues: 1020 loop : -1.24 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 21 TYR 0.022 0.002 TYR A 177 PHE 0.016 0.002 PHE Q 259 TRP 0.063 0.002 TRP J 236 HIS 0.011 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00531 (26433) covalent geometry : angle 0.63600 (35976) SS BOND : bond 0.00266 ( 49) SS BOND : angle 1.09526 ( 98) hydrogen bonds : bond 0.03476 ( 756) hydrogen bonds : angle 5.10943 ( 1962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 323 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LYS cc_start: 0.7394 (mmmt) cc_final: 0.7145 (tppt) REVERT: A 200 TYR cc_start: 0.6890 (m-80) cc_final: 0.6379 (m-80) REVERT: A 207 VAL cc_start: 0.7573 (OUTLIER) cc_final: 0.7319 (p) REVERT: A 267 TYR cc_start: 0.7441 (t80) cc_final: 0.6936 (t80) REVERT: B 27 LEU cc_start: 0.6925 (tp) cc_final: 0.6725 (tp) REVERT: B 31 ILE cc_start: 0.8031 (mt) cc_final: 0.7784 (mm) REVERT: B 160 LYS cc_start: 0.7430 (tppt) cc_final: 0.7163 (tttp) REVERT: B 188 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8998 (m-30) REVERT: C 354 ILE cc_start: 0.8917 (pt) cc_final: 0.8522 (mt) REVERT: D 28 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7485 (mm-30) REVERT: D 57 ASP cc_start: 0.7709 (t70) cc_final: 0.7432 (t70) REVERT: F 148 PHE cc_start: 0.8385 (m-10) cc_final: 0.8010 (m-10) REVERT: F 254 SER cc_start: 0.8127 (p) cc_final: 0.7288 (m) REVERT: G 99 GLU cc_start: 0.8647 (pt0) cc_final: 0.8242 (pm20) REVERT: G 377 LYS cc_start: 0.8419 (tttm) cc_final: 0.7867 (ptpp) REVERT: H 57 ASP cc_start: 0.7688 (p0) cc_final: 0.7365 (p0) REVERT: I 33 MET cc_start: 0.5917 (ttp) cc_final: 0.5570 (tmm) REVERT: J 224 GLU cc_start: 0.8484 (mp0) cc_final: 0.8213 (mp0) REVERT: J 298 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.9036 (ptt-90) REVERT: J 323 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7368 (mm-30) REVERT: J 342 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7338 (mm-30) REVERT: J 391 ARG cc_start: 0.7214 (mtp-110) cc_final: 0.6924 (ttm170) REVERT: J 401 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.8157 (mtp180) REVERT: P 33 MET cc_start: 0.6668 (ttp) cc_final: 0.6376 (ptm) REVERT: Q 5 LEU cc_start: 0.7334 (mp) cc_final: 0.7058 (mm) REVERT: Q 167 MET cc_start: 0.7524 (tpp) cc_final: 0.7277 (mpp) REVERT: Q 360 TYR cc_start: 0.8429 (t80) cc_final: 0.7570 (t80) REVERT: R 88 ARG cc_start: 0.7430 (mmt180) cc_final: 0.6944 (mmt90) REVERT: R 275 MET cc_start: 0.8708 (mtp) cc_final: 0.8453 (mtm) REVERT: R 313 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8296 (mt-10) REVERT: S 135 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7417 (mmtm) REVERT: S 156 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7593 (tmtt) REVERT: S 184 MET cc_start: 0.8329 (ttm) cc_final: 0.7761 (ttt) REVERT: S 197 GLN cc_start: 0.8358 (pm20) cc_final: 0.7642 (tt0) REVERT: S 259 ASN cc_start: 0.7415 (t0) cc_final: 0.7136 (t0) outliers start: 86 outliers final: 71 residues processed: 382 average time/residue: 0.1658 time to fit residues: 100.7997 Evaluate side-chains 381 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 412 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 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain S residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 317 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 308 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 118 optimal weight: 0.2980 chunk 99 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 288 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.160726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118319 restraints weight = 37223.964| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.50 r_work: 0.3153 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26482 Z= 0.136 Angle : 0.586 7.926 36074 Z= 0.302 Chirality : 0.045 0.383 3987 Planarity : 0.005 0.069 4647 Dihedral : 5.632 86.566 3608 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 2.59 % Allowed : 14.06 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 3306 helix: 1.19 (0.26), residues: 441 sheet: -0.39 (0.16), residues: 1020 loop : -1.15 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 103 TYR 0.024 0.001 TYR A 177 PHE 0.022 0.001 PHE Q 6 TRP 0.057 0.002 TRP J 236 HIS 0.007 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00322 (26433) covalent geometry : angle 0.58444 (35976) SS BOND : bond 0.00183 ( 49) SS BOND : angle 0.92164 ( 98) hydrogen bonds : bond 0.03153 ( 756) hydrogen bonds : angle 5.06175 ( 1962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 PHE cc_start: 0.8813 (m-80) cc_final: 0.8518 (m-80) REVERT: A 156 LYS cc_start: 0.7312 (mmmt) cc_final: 0.7070 (tppt) REVERT: A 200 TYR cc_start: 0.6937 (m-80) cc_final: 0.6452 (m-80) REVERT: A 267 TYR cc_start: 0.7311 (t80) cc_final: 0.6864 (t80) REVERT: B 31 ILE cc_start: 0.8007 (mt) cc_final: 0.7744 (mm) REVERT: B 188 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8933 (m-30) REVERT: C 354 ILE cc_start: 0.8894 (pt) cc_final: 0.8502 (mt) REVERT: D 28 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7476 (mm-30) REVERT: D 57 ASP cc_start: 0.7603 (t70) cc_final: 0.7326 (t70) REVERT: F 148 PHE cc_start: 0.8398 (m-10) cc_final: 0.7984 (m-10) REVERT: F 193 HIS cc_start: 0.7227 (p-80) cc_final: 0.6790 (p-80) REVERT: F 199 TYR cc_start: 0.7239 (m-80) cc_final: 0.6884 (m-80) REVERT: F 254 SER cc_start: 0.8124 (p) cc_final: 0.7305 (m) REVERT: G 99 GLU cc_start: 0.8596 (pt0) cc_final: 0.8198 (pm20) REVERT: H 57 ASP cc_start: 0.7650 (p0) cc_final: 0.7260 (p0) REVERT: I 33 MET cc_start: 0.6015 (ttp) cc_final: 0.5590 (tmm) REVERT: J 224 GLU cc_start: 0.8418 (mp0) cc_final: 0.8092 (mp0) REVERT: J 298 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.9034 (ptt-90) REVERT: J 323 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7399 (mm-30) REVERT: J 342 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7257 (mm-30) REVERT: J 391 ARG cc_start: 0.7152 (mtp-110) cc_final: 0.6906 (ttm170) REVERT: J 401 ARG cc_start: 0.8497 (mtt-85) cc_final: 0.8038 (mtp-110) REVERT: P 6 MET cc_start: 0.4272 (tmm) cc_final: 0.4065 (tpt) REVERT: P 33 MET cc_start: 0.6330 (ttp) cc_final: 0.6020 (ptm) REVERT: Q 357 THR cc_start: 0.7871 (t) cc_final: 0.7590 (p) REVERT: Q 360 TYR cc_start: 0.8402 (t80) cc_final: 0.7548 (t80) REVERT: R 88 ARG cc_start: 0.6929 (mmt180) cc_final: 0.6382 (mmt90) REVERT: R 110 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8371 (mm) REVERT: R 313 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8194 (mt-10) REVERT: S 135 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7310 (mmtm) REVERT: S 156 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7587 (tmtt) REVERT: S 184 MET cc_start: 0.8355 (ttm) cc_final: 0.7816 (ttt) REVERT: S 197 GLN cc_start: 0.8299 (pm20) cc_final: 0.7654 (tt0) REVERT: S 259 ASN cc_start: 0.7410 (t0) cc_final: 0.7134 (t0) outliers start: 73 outliers final: 56 residues processed: 361 average time/residue: 0.1669 time to fit residues: 95.7458 Evaluate side-chains 366 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 307 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 275 MET Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR 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 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 178 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN G 50 HIS G 218 ASN ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN S 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112961 restraints weight = 37452.799| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.55 r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26482 Z= 0.129 Angle : 0.577 7.797 36074 Z= 0.298 Chirality : 0.045 0.371 3987 Planarity : 0.005 0.072 4647 Dihedral : 5.515 82.875 3608 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 2.66 % Allowed : 13.92 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3306 helix: 1.19 (0.26), residues: 444 sheet: -0.26 (0.16), residues: 1026 loop : -1.06 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 103 TYR 0.026 0.001 TYR A 177 PHE 0.018 0.001 PHE C 365 TRP 0.055 0.002 TRP J 236 HIS 0.006 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00307 (26433) covalent geometry : angle 0.57618 (35976) SS BOND : bond 0.00200 ( 49) SS BOND : angle 0.89598 ( 98) hydrogen bonds : bond 0.03111 ( 756) hydrogen bonds : angle 4.98626 ( 1962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.6160 (ptpt) cc_final: 0.5932 (tptt) REVERT: A 148 PHE cc_start: 0.8808 (m-80) cc_final: 0.8488 (m-80) REVERT: A 189 PHE cc_start: 0.7889 (m-80) cc_final: 0.7602 (m-10) REVERT: A 200 TYR cc_start: 0.6795 (m-80) cc_final: 0.6128 (m-80) REVERT: A 267 TYR cc_start: 0.7276 (t80) cc_final: 0.6871 (t80) REVERT: B 31 ILE cc_start: 0.8025 (mt) cc_final: 0.7760 (mm) REVERT: C 354 ILE cc_start: 0.8927 (pt) cc_final: 0.8527 (mt) REVERT: C 364 GLU cc_start: 0.7637 (tp30) cc_final: 0.7387 (mm-30) REVERT: C 370 CYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7736 (m) REVERT: D 28 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7443 (mm-30) REVERT: D 57 ASP cc_start: 0.7683 (t70) cc_final: 0.7424 (t70) REVERT: F 143 VAL cc_start: 0.7917 (m) cc_final: 0.7648 (t) REVERT: F 148 PHE cc_start: 0.8344 (m-10) cc_final: 0.8068 (m-10) REVERT: F 193 HIS cc_start: 0.7174 (p-80) cc_final: 0.6742 (p-80) REVERT: F 199 TYR cc_start: 0.7258 (m-80) cc_final: 0.6911 (m-80) REVERT: F 254 SER cc_start: 0.8143 (p) cc_final: 0.7300 (m) REVERT: G 99 GLU cc_start: 0.8665 (pt0) cc_final: 0.8216 (pm20) REVERT: G 364 GLU cc_start: 0.8159 (tt0) cc_final: 0.7749 (tt0) REVERT: H 57 ASP cc_start: 0.7653 (p0) cc_final: 0.7322 (p0) REVERT: I 33 MET cc_start: 0.6092 (ttp) cc_final: 0.5640 (tmm) REVERT: J 224 GLU cc_start: 0.8445 (mp0) cc_final: 0.8112 (mp0) REVERT: J 298 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.9052 (ptt-90) REVERT: J 323 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7472 (mm-30) REVERT: J 342 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7253 (mm-30) REVERT: J 391 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.7035 (ttm170) REVERT: J 401 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8061 (mtp-110) REVERT: P 33 MET cc_start: 0.6532 (ttp) cc_final: 0.6244 (ptm) REVERT: Q 357 THR cc_start: 0.7870 (t) cc_final: 0.7599 (p) REVERT: Q 360 TYR cc_start: 0.8423 (t80) cc_final: 0.7522 (t80) REVERT: R 88 ARG cc_start: 0.6974 (mmt180) cc_final: 0.6419 (mmt90) REVERT: R 313 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8315 (mt-10) REVERT: S 135 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7295 (mmtm) REVERT: S 156 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7621 (tmtt) REVERT: S 184 MET cc_start: 0.8315 (ttm) cc_final: 0.7772 (ttt) REVERT: S 197 GLN cc_start: 0.8262 (pm20) cc_final: 0.7653 (tt0) REVERT: S 259 ASN cc_start: 0.7400 (t0) cc_final: 0.7132 (t0) outliers start: 75 outliers final: 63 residues processed: 364 average time/residue: 0.1629 time to fit residues: 94.9987 Evaluate side-chains 375 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 275 MET Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 412 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 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 298 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN S 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114419 restraints weight = 37627.965| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.61 r_work: 0.3134 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26482 Z= 0.128 Angle : 0.575 10.386 36074 Z= 0.295 Chirality : 0.045 0.368 3987 Planarity : 0.005 0.070 4647 Dihedral : 5.447 80.460 3608 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 2.62 % Allowed : 14.31 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 3306 helix: 1.24 (0.26), residues: 444 sheet: -0.18 (0.16), residues: 1026 loop : -1.00 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 103 TYR 0.024 0.001 TYR A 177 PHE 0.013 0.001 PHE Q 6 TRP 0.052 0.001 TRP J 236 HIS 0.006 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00305 (26433) covalent geometry : angle 0.57390 (35976) SS BOND : bond 0.00185 ( 49) SS BOND : angle 0.91622 ( 98) hydrogen bonds : bond 0.03070 ( 756) hydrogen bonds : angle 4.94344 ( 1962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 315 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 PHE cc_start: 0.8813 (m-80) cc_final: 0.8431 (m-80) REVERT: A 200 TYR cc_start: 0.6855 (m-80) cc_final: 0.6207 (m-80) REVERT: A 267 TYR cc_start: 0.7243 (t80) cc_final: 0.6848 (t80) REVERT: B 31 ILE cc_start: 0.8036 (mt) cc_final: 0.7794 (mm) REVERT: C 354 ILE cc_start: 0.8909 (pt) cc_final: 0.8504 (mt) REVERT: C 370 CYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7702 (m) REVERT: C 377 LYS cc_start: 0.7847 (ttmt) cc_final: 0.7637 (ttmm) REVERT: D 28 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7458 (mm-30) REVERT: D 57 ASP cc_start: 0.7692 (t70) cc_final: 0.7389 (t70) REVERT: F 143 VAL cc_start: 0.7919 (m) cc_final: 0.7659 (t) REVERT: F 148 PHE cc_start: 0.8279 (m-10) cc_final: 0.8074 (m-10) REVERT: F 193 HIS cc_start: 0.7154 (p-80) cc_final: 0.6729 (p-80) REVERT: F 199 TYR cc_start: 0.7267 (m-80) cc_final: 0.6937 (m-80) REVERT: F 254 SER cc_start: 0.8157 (p) cc_final: 0.7313 (m) REVERT: G 99 GLU cc_start: 0.8687 (pt0) cc_final: 0.8216 (pm20) REVERT: G 364 GLU cc_start: 0.8156 (tt0) cc_final: 0.7726 (tt0) REVERT: H 57 ASP cc_start: 0.7669 (p0) cc_final: 0.7351 (p0) REVERT: I 33 MET cc_start: 0.6144 (ttp) cc_final: 0.5721 (tmm) REVERT: J 224 GLU cc_start: 0.8435 (mp0) cc_final: 0.8101 (mp0) REVERT: J 298 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.9058 (ptt-90) REVERT: J 323 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7484 (mm-30) REVERT: J 342 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7241 (mm-30) REVERT: J 391 ARG cc_start: 0.7290 (mtp-110) cc_final: 0.6962 (ttm170) REVERT: J 401 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.8066 (mtp-110) REVERT: P 33 MET cc_start: 0.6259 (ttp) cc_final: 0.5986 (ptm) REVERT: Q 159 GLN cc_start: 0.8650 (tp40) cc_final: 0.8397 (mm-40) REVERT: Q 357 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7591 (p) REVERT: Q 360 TYR cc_start: 0.8413 (t80) cc_final: 0.7521 (t80) REVERT: R 88 ARG cc_start: 0.6987 (mmt180) cc_final: 0.6426 (mmt90) REVERT: S 135 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7305 (mmtm) REVERT: S 156 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7686 (tmtt) REVERT: S 184 MET cc_start: 0.8309 (ttm) cc_final: 0.7772 (ttt) REVERT: S 197 GLN cc_start: 0.8273 (pm20) cc_final: 0.7661 (tt0) REVERT: S 259 ASN cc_start: 0.7313 (t0) cc_final: 0.7048 (t0) outliers start: 74 outliers final: 61 residues processed: 361 average time/residue: 0.1656 time to fit residues: 95.0309 Evaluate side-chains 371 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 275 MET Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 6 PHE 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 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 246 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 51 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 313 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.161688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113635 restraints weight = 37418.708| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.54 r_work: 0.3144 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26482 Z= 0.120 Angle : 0.575 9.999 36074 Z= 0.295 Chirality : 0.044 0.364 3987 Planarity : 0.004 0.071 4647 Dihedral : 5.402 79.593 3608 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 2.30 % Allowed : 14.67 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3306 helix: 1.26 (0.26), residues: 444 sheet: -0.11 (0.16), residues: 1017 loop : -0.97 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 88 TYR 0.022 0.001 TYR A 177 PHE 0.012 0.001 PHE Q 6 TRP 0.053 0.002 TRP J 236 HIS 0.006 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00284 (26433) covalent geometry : angle 0.57322 (35976) SS BOND : bond 0.00203 ( 49) SS BOND : angle 1.05318 ( 98) hydrogen bonds : bond 0.03025 ( 756) hydrogen bonds : angle 4.94270 ( 1962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 PHE cc_start: 0.8830 (m-80) cc_final: 0.8462 (m-80) REVERT: A 200 TYR cc_start: 0.6812 (m-80) cc_final: 0.6169 (m-80) REVERT: A 267 TYR cc_start: 0.7154 (t80) cc_final: 0.6720 (t80) REVERT: B 31 ILE cc_start: 0.8023 (mt) cc_final: 0.7780 (mm) REVERT: C 354 ILE cc_start: 0.8913 (pt) cc_final: 0.8497 (mt) REVERT: C 370 CYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7675 (m) REVERT: D 28 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7456 (mm-30) REVERT: D 57 ASP cc_start: 0.7560 (t70) cc_final: 0.7268 (t70) REVERT: F 143 VAL cc_start: 0.7937 (m) cc_final: 0.7716 (t) REVERT: F 193 HIS cc_start: 0.7226 (p-80) cc_final: 0.6801 (p-80) REVERT: F 199 TYR cc_start: 0.7264 (m-80) cc_final: 0.6942 (m-80) REVERT: F 254 SER cc_start: 0.8160 (p) cc_final: 0.7323 (m) REVERT: G 99 GLU cc_start: 0.8667 (pt0) cc_final: 0.8210 (pm20) REVERT: G 364 GLU cc_start: 0.8108 (tt0) cc_final: 0.7641 (tt0) REVERT: H 57 ASP cc_start: 0.7611 (p0) cc_final: 0.7252 (p0) REVERT: I 33 MET cc_start: 0.6168 (ttp) cc_final: 0.5745 (tmm) REVERT: J 224 GLU cc_start: 0.8420 (mp0) cc_final: 0.8080 (mp0) REVERT: J 298 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.9048 (ptt-90) REVERT: J 323 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7477 (mm-30) REVERT: J 342 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7233 (mm-30) REVERT: J 391 ARG cc_start: 0.7274 (mtp-110) cc_final: 0.6790 (ttm170) REVERT: J 401 ARG cc_start: 0.8465 (mtt-85) cc_final: 0.8090 (mtp-110) REVERT: P 33 MET cc_start: 0.6042 (ttp) cc_final: 0.5620 (ptm) REVERT: Q 159 GLN cc_start: 0.8665 (tp40) cc_final: 0.8408 (mm-40) REVERT: Q 357 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7585 (p) REVERT: Q 360 TYR cc_start: 0.8564 (t80) cc_final: 0.7542 (t80) REVERT: R 88 ARG cc_start: 0.7011 (mmt180) cc_final: 0.6467 (mmt90) REVERT: R 267 THR cc_start: 0.9222 (t) cc_final: 0.8971 (m) REVERT: S 135 LYS cc_start: 0.7774 (mmmt) cc_final: 0.7339 (mmtm) REVERT: S 156 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7699 (tmtt) REVERT: S 184 MET cc_start: 0.8306 (ttm) cc_final: 0.7776 (ttt) REVERT: S 197 GLN cc_start: 0.8273 (pm20) cc_final: 0.7674 (tt0) REVERT: S 259 ASN cc_start: 0.7315 (t0) cc_final: 0.7047 (t0) outliers start: 65 outliers final: 59 residues processed: 354 average time/residue: 0.1660 time to fit residues: 93.4346 Evaluate side-chains 364 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 302 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 275 MET Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 412 LEU Chi-restraints excluded: chain R residue 6 PHE 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 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 324 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 303 optimal weight: 8.9990 chunk 226 optimal weight: 0.0470 chunk 201 optimal weight: 6.9990 chunk 326 optimal weight: 50.0000 chunk 272 optimal weight: 2.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 ASN ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115656 restraints weight = 37289.240| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.56 r_work: 0.3126 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26482 Z= 0.166 Angle : 0.604 10.474 36074 Z= 0.312 Chirality : 0.046 0.365 3987 Planarity : 0.005 0.071 4647 Dihedral : 5.526 78.588 3608 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 2.44 % Allowed : 14.77 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 3306 helix: 1.20 (0.26), residues: 444 sheet: -0.22 (0.16), residues: 1044 loop : -0.97 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.021 0.002 TYR A 177 PHE 0.015 0.002 PHE J 6 TRP 0.049 0.002 TRP J 236 HIS 0.009 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00403 (26433) covalent geometry : angle 0.60192 (35976) SS BOND : bond 0.00235 ( 49) SS BOND : angle 1.05196 ( 98) hydrogen bonds : bond 0.03271 ( 756) hydrogen bonds : angle 5.01130 ( 1962) =============================================================================== Job complete usr+sys time: 9011.76 seconds wall clock time: 154 minutes 34.60 seconds (9274.60 seconds total)