Starting phenix.real_space_refine on Sat Jun 28 18:10:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fff_31567/06_2025/7fff_31567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fff_31567/06_2025/7fff_31567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fff_31567/06_2025/7fff_31567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fff_31567/06_2025/7fff_31567.map" model { file = "/net/cci-nas-00/data/ceres_data/7fff_31567/06_2025/7fff_31567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fff_31567/06_2025/7fff_31567.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 268 5.16 5 C 21736 2.51 5 N 5880 2.21 5 O 6468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34356 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "L" 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: "M" 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: "N" 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: "O" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} 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: "M" 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: 18.57, per 1000 atoms: 0.54 Number of scatterers: 34356 At special positions: 0 Unit cell: (209.88, 158.4, 217.8, 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 4 19.99 S 268 16.00 O 6468 8.00 N 5880 7.00 C 21736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=65, symmetry=0 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-981 " - pdb=" SG CYS J-877 " distance=2.03 Simple disulfide: pdb=" SG CYS J-978 " - pdb=" SG CYS J-973 " distance=2.03 Simple disulfide: pdb=" SG CYS J-910 " - pdb=" SG CYS J-896 " distance=2.02 Simple disulfide: pdb=" SG CYS J-849 " - pdb=" SG CYS J-734 " distance=2.03 Simple disulfide: pdb=" SG CYS J-800 " - pdb=" SG CYS J-774 " distance=2.03 Simple disulfide: pdb=" SG CYS J-798 " - pdb=" SG CYS J-780 " distance=2.03 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 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 T 7 " - pdb=" SG CYS T 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 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 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 P 7 " - pdb=" SG CYS P 16 " 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 L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 42 " distance=2.03 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 55 " distance=1.09 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 64 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " 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: 7.35 Conformation dependent library (CDL) restraints added in 4.2 seconds 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8264 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 95 sheets defined 16.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.802A pdb=" N ARG K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) 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 '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: 3.702A 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 -998 through -993 Processing helix chain 'J' and resid -920 through -918 No H-bonds generated for 'chain 'J' and resid -920 through -918' Processing helix chain 'J' and resid -825 through -823 No H-bonds generated for 'chain 'J' and resid -825 through -823' Processing helix chain 'J' and resid -778 through -776 No H-bonds generated for 'chain 'J' and resid -778 through -776' Processing helix chain 'J' and resid -649 through -637 removed outlier: 3.785A pdb=" N VAL J-645 " --> pdb=" O LEU J-649 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE J-644 " --> pdb=" O PRO J-648 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR J-643 " --> pdb=" O HIS J-647 " (cutoff:3.500A) Processing helix chain 'J' and resid -637 through -602 removed outlier: 3.863A pdb=" N ILE J-632 " --> pdb=" O PRO J-636 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU J-631 " --> pdb=" O MET J-635 " (cutoff:3.500A) Processing helix chain 'J' and resid -591 through -584 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: 4.234A pdb=" N ALA B 418 " --> pdb=" O LEU B 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 '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: 3.655A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.533A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.773A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain '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: 3.702A 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: 4.239A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (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 '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: 4.918A 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 '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: 3.901A 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 'P' and resid 28 through 37 removed outlier: 3.592A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.206A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) 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: 3.644A 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 'L' and resid 26 through 37 removed outlier: 3.785A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 48 No H-bonds generated for 'chain 'M' and resid 46 through 48' Processing helix chain 'M' and resid 55 through 59 removed outlier: 3.973A pdb=" N SER M 59 " --> pdb=" O PHE M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.805A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.515A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.616A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.502A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.572A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.900A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 439 Processing sheet with id=AA1, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.658A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.705A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.494A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 213 through 217 current: chain 'K' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.656A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AA8, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AA9, 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=AA9 Processing sheet with id=AB1, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.495A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AB3, 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=AB4, 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=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AB6, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AB7, 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: 4.064A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AB9, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AC1, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AC2, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AC3, 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=AC4, first strand: chain 'J' and resid -983 through -981 Processing sheet with id=AC5, first strand: chain 'J' and resid -967 through -963 removed outlier: 6.587A pdb=" N GLN J-952 " --> pdb=" O GLU J-966 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL J-964 " --> pdb=" O ARG J-954 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG J-954 " --> pdb=" O VAL J-964 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER J-950 " --> pdb=" O ASP J-931 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP J-931 " --> pdb=" O SER J-950 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J-935 " --> pdb=" O GLY J-946 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid -917 through -915 removed outlier: 3.504A pdb=" N ILE J-890 " --> pdb=" O VAL J-875 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid -853 through -851 Processing sheet with id=AC8, first strand: chain 'J' and resid -848 through -846 Processing sheet with id=AC9, first strand: chain 'J' and resid -763 through -762 removed outlier: 3.534A pdb=" N VAL J-763 " --> pdb=" O HIS J-832 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY J-747 " --> pdb=" O MET J-833 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid -821 through -819 Processing sheet with id=AD2, first strand: chain 'J' and resid -804 through -800 removed outlier: 3.983A pdb=" N LEU J-803 " --> pdb=" O TYR J-771 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid -725 through -721 Processing sheet with id=AD4, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AD5, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AD6, 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=AD7, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.751A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.117A 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=AD8, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AD9, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AE1, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AE2, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.306A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AE3, 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=AE4, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AE5, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AE6, 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) Processing sheet with id=AE7, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AE8, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.624A 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: 9.384A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR Q 65 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AF1, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AF2, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.786A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AF3, 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=AF4, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AF5, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AF6, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.733A 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=AF7, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.099A 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: 6.783A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AF8, 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: 6.507A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AF9, 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=AG1, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AG2, 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=AG3, 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=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.698A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AG6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AG7, 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=AG8, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AG9, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AH1, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AH2, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AH3, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AH4, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AH5, 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: 5.525A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AH7, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AH8, 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=AH9, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.879A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL R 188 " --> pdb=" O LYS R 215 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.563A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AI3, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AI4, first strand: chain 'M' and resid 34 through 36 Processing sheet with id=AI5, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 35 through 37 removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AI8, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AI9, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AJ1, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.714A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.684A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AJ4, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AJ5, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AJ6, first strand: chain 'O' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 27 through 42 current: chain 'O' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 141 through 147 current: chain 'O' and resid 183 through 185 Processing sheet with id=AJ7, first strand: chain 'O' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 51 through 55 current: chain 'O' and resid 101 through 110 No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.889A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AK1, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AK2, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AK3, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.012A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AK5, first strand: chain 'O' and resid 364 through 369 1017 hydrogen bonds defined for protein. 2625 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: 14.87 Time building geometry restraints manager: 9.04 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: 11020 1.34 - 1.46: 8594 1.46 - 1.59: 15277 1.59 - 1.72: 1 1.72 - 1.84: 352 Bond restraints: 35244 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.089 1.08e-02 8.57e+03 6.74e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.310 -0.076 1.21e-02 6.83e+03 3.90e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.89e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.065 1.22e-02 6.72e+03 2.81e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.505 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 35239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.48: 47918 7.48 - 14.97: 46 14.97 - 22.45: 3 22.45 - 29.93: 0 29.93 - 37.42: 1 Bond angle restraints: 47968 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 112.47 149.89 -37.42 2.06e+00 2.36e-01 3.30e+02 angle pdb=" N PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta sigma weight residual 110.49 132.06 -21.57 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 111.39 123.03 -11.64 1.38e+00 5.25e-01 7.12e+01 angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.32 -15.88 1.93e+00 2.68e-01 6.77e+01 angle pdb=" N LYS H 58 " pdb=" CA LYS H 58 " pdb=" C LYS H 58 " ideal model delta sigma weight residual 111.54 120.31 -8.77 1.36e+00 5.41e-01 4.16e+01 ... (remaining 47963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 20397 17.61 - 35.22: 671 35.22 - 52.82: 141 52.82 - 70.43: 30 70.43 - 88.04: 8 Dihedral angle restraints: 21247 sinusoidal: 8347 harmonic: 12900 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 115.10 155.01 -39.91 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 -155.06 34.36 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 122.80 157.11 -34.31 0 2.50e+00 1.60e-01 1.88e+02 ... (remaining 21244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 5310 0.403 - 0.806: 4 0.806 - 1.209: 0 1.209 - 1.612: 1 1.612 - 2.015: 1 Chirality restraints: 5316 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 5313 not shown) Planarity restraints: 6196 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=" C ASN O 264 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J-764 " 0.039 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP J-764 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J-764 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP J-764 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J-764 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J-764 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J-764 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP J-764 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J-764 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J-764 " 0.018 2.00e-02 2.50e+03 ... (remaining 6193 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 146 2.52 - 3.11: 23006 3.11 - 3.71: 49451 3.71 - 4.30: 70655 4.30 - 4.90: 120782 Nonbonded interactions: 264040 Sorted by model distance: nonbonded pdb=" OH TYR K 173 " pdb=" NE2 GLN O 439 " model vdw 1.924 3.120 nonbonded pdb=" NZ LYS K 156 " pdb=" OE2 GLU A 133 " model vdw 2.002 3.120 nonbonded pdb=" OG SER J-823 " pdb=" OD1 ASP D 57 " model vdw 2.091 3.040 nonbonded pdb=" O ASN O 442 " pdb=" ND2 ASN O 442 " model vdw 2.111 3.120 nonbonded pdb=" O HIS G 441 " pdb=" OXT ASN G 442 " model vdw 2.236 3.040 ... (remaining 264035 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 'K' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'N' 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: 3.000 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: 0.040 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 74.650 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 0.997 35309 Z= 0.541 Angle : 1.050 61.625 48098 Z= 0.567 Chirality : 0.068 2.015 5316 Planarity : 0.008 0.102 6196 Dihedral : 9.593 88.037 12788 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.22 % Rotamer: Outliers : 0.40 % Allowed : 2.52 % Favored : 97.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.11), residues: 4408 helix: -2.14 (0.17), residues: 548 sheet: -1.70 (0.13), residues: 1429 loop : -2.51 (0.10), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP J-764 HIS 0.011 0.002 HIS N 28 PHE 0.032 0.004 PHE Q 328 TYR 0.039 0.003 TYR C 308 ARG 0.015 0.001 ARG Q 21 Details of bonding type rmsd hydrogen bonds : bond 0.20784 ( 1017) hydrogen bonds : angle 8.33862 ( 2625) SS BOND : bond 0.20374 ( 65) SS BOND : angle 8.28552 ( 130) covalent geometry : bond 0.00745 (35244) covalent geometry : angle 0.95904 (47968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 801 time to evaluate : 4.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 159 ASN cc_start: 0.4531 (t0) cc_final: 0.4241 (t160) REVERT: K 193 HIS cc_start: 0.6886 (p-80) cc_final: 0.6531 (p90) REVERT: K 215 THR cc_start: 0.6433 (p) cc_final: 0.6000 (p) REVERT: K 270 GLU cc_start: 0.6727 (tt0) cc_final: 0.6342 (pm20) REVERT: S 256 VAL cc_start: 0.5820 (m) cc_final: 0.5526 (m) REVERT: S 261 LYS cc_start: 0.6548 (mmtt) cc_final: 0.6270 (mtmm) REVERT: S 266 LYS cc_start: 0.6495 (tttm) cc_final: 0.5909 (tmtp) REVERT: G 212 ASP cc_start: 0.7539 (t0) cc_final: 0.7314 (p0) REVERT: B 29 ILE cc_start: 0.7555 (mt) cc_final: 0.7203 (mm) REVERT: B 369 ILE cc_start: 0.8473 (tt) cc_final: 0.8267 (tt) REVERT: T 23 TYR cc_start: 0.6250 (t80) cc_final: 0.5677 (t80) REVERT: Q 112 MET cc_start: 0.8772 (ttm) cc_final: 0.8383 (ttm) REVERT: A 148 PHE cc_start: 0.8275 (m-10) cc_final: 0.8072 (m-80) REVERT: R 360 TYR cc_start: 0.8474 (t80) cc_final: 0.8181 (t80) REVERT: N 9 TYR cc_start: 0.8366 (m-80) cc_final: 0.8107 (m-80) REVERT: N 42 ASP cc_start: 0.7649 (m-30) cc_final: 0.7348 (m-30) REVERT: N 112 MET cc_start: 0.9013 (ttm) cc_final: 0.8793 (ttp) REVERT: N 365 MET cc_start: 0.7668 (ttt) cc_final: 0.7355 (pmt) REVERT: O 115 LEU cc_start: 0.8481 (tm) cc_final: 0.8263 (mm) REVERT: O 442 ASN cc_start: 0.6350 (OUTLIER) cc_final: 0.6017 (t0) outliers start: 15 outliers final: 4 residues processed: 809 average time/residue: 1.5982 time to fit residues: 1547.2769 Evaluate side-chains 416 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 411 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 7.9990 chunk 330 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 HIS G 264 ASN G 394 HIS G 396 GLN H 27 ASN H 30 ASN J-848 GLN ** J-775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-744 HIS J-647 HIS J-639 HIS B 10 GLN B 43 ASN B 235 GLN B 360 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN D 27 ASN D 30 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 ASN Q 212 ASN Q 225 GLN Q 232 GLN Q 239 ASN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS F 203 HIS C 130 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN C 442 ASN E 27 ASN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN R 347 ASN R 361 HIS R 405 ASN M 27 ASN M 30 ASN N 7 ASN N 52 GLN N 96 HIS ** N 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 353 HIS ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS O 392 GLN O 394 HIS O 442 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.177606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121790 restraints weight = 46380.027| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.54 r_work: 0.3237 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35309 Z= 0.178 Angle : 0.666 11.221 48098 Z= 0.348 Chirality : 0.046 0.208 5316 Planarity : 0.006 0.089 6196 Dihedral : 6.458 160.296 4819 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 3.48 % Allowed : 11.08 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.12), residues: 4408 helix: -0.23 (0.22), residues: 562 sheet: -1.11 (0.13), residues: 1443 loop : -1.87 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP J-764 HIS 0.007 0.001 HIS Q 305 PHE 0.021 0.002 PHE A 189 TYR 0.024 0.002 TYR O 308 ARG 0.007 0.001 ARG Q 67 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 1017) hydrogen bonds : angle 5.79037 ( 2625) SS BOND : bond 0.00341 ( 65) SS BOND : angle 1.47046 ( 130) covalent geometry : bond 0.00423 (35244) covalent geometry : angle 0.66216 (47968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 465 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.5821 (ptt) cc_final: 0.4639 (tpp) REVERT: K 151 MET cc_start: 0.8150 (mmp) cc_final: 0.7611 (mmp) REVERT: K 153 VAL cc_start: 0.8928 (t) cc_final: 0.8664 (p) REVERT: K 193 HIS cc_start: 0.7909 (p-80) cc_final: 0.7487 (p90) REVERT: K 208 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: K 215 THR cc_start: 0.8654 (p) cc_final: 0.8166 (p) REVERT: K 270 GLU cc_start: 0.8248 (tt0) cc_final: 0.7610 (pm20) REVERT: S 131 MET cc_start: 0.6903 (mmm) cc_final: 0.6666 (mmm) REVERT: S 135 LYS cc_start: 0.7024 (mptt) cc_final: 0.6768 (mmtp) REVERT: S 169 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7094 (mtmt) REVERT: S 199 TYR cc_start: 0.6249 (m-10) cc_final: 0.5858 (m-80) REVERT: S 223 LYS cc_start: 0.8440 (tttt) cc_final: 0.8124 (tptt) REVERT: S 251 THR cc_start: 0.7411 (p) cc_final: 0.7020 (t) REVERT: G 10 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: G 52 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8638 (tttp) REVERT: G 319 LYS cc_start: 0.7728 (ttpm) cc_final: 0.7461 (ttpt) REVERT: G 361 ILE cc_start: 0.8033 (mt) cc_final: 0.7730 (tt) REVERT: H 57 ASP cc_start: 0.7426 (p0) cc_final: 0.7161 (p0) REVERT: J -775 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: J -687 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: J -609 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6855 (ttm170) REVERT: B 97 ASP cc_start: 0.7975 (m-30) cc_final: 0.7698 (m-30) REVERT: B 207 THR cc_start: 0.8289 (m) cc_final: 0.8020 (t) REVERT: B 433 MET cc_start: 0.5690 (pp-130) cc_final: 0.5104 (ptp) REVERT: D 41 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.8099 (ttt-90) REVERT: D 58 LYS cc_start: 0.8408 (mppt) cc_final: 0.8143 (mppt) REVERT: T 23 TYR cc_start: 0.5909 (t80) cc_final: 0.5041 (t80) REVERT: Q 130 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8774 (pttp) REVERT: Q 137 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: Q 144 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8188 (mt-10) REVERT: Q 213 LYS cc_start: 0.7439 (mttt) cc_final: 0.6876 (mmtp) REVERT: A 118 MET cc_start: 0.6163 (pmt) cc_final: 0.5590 (pmt) REVERT: A 207 VAL cc_start: 0.8169 (m) cc_final: 0.7966 (p) REVERT: F 131 MET cc_start: 0.7850 (mmp) cc_final: 0.7618 (mmm) REVERT: F 266 LYS cc_start: 0.8368 (tttt) cc_final: 0.8140 (tptm) REVERT: C 61 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8150 (ttmt) REVERT: C 73 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7482 (mtt-85) REVERT: C 140 HIS cc_start: 0.7820 (m90) cc_final: 0.7163 (m90) REVERT: C 160 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7705 (ttmt) REVERT: C 300 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: C 324 LYS cc_start: 0.6838 (mtmt) cc_final: 0.6508 (mtmm) REVERT: E 36 MET cc_start: 0.8281 (tpp) cc_final: 0.8006 (tpp) REVERT: R 8 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: R 79 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7591 (tp) REVERT: R 342 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7378 (mp0) REVERT: R 360 TYR cc_start: 0.8758 (t80) cc_final: 0.8384 (t80) REVERT: R 377 ILE cc_start: 0.7537 (mt) cc_final: 0.7303 (mm) REVERT: N 5 LEU cc_start: 0.6156 (mp) cc_final: 0.5834 (pp) REVERT: N 66 MET cc_start: 0.9334 (ttt) cc_final: 0.9037 (ttt) REVERT: N 365 MET cc_start: 0.8746 (ttt) cc_final: 0.7661 (pmt) REVERT: O 2 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: O 73 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7112 (mtp180) REVERT: O 175 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.7999 (ttp-110) outliers start: 131 outliers final: 41 residues processed: 535 average time/residue: 1.4213 time to fit residues: 920.8227 Evaluate side-chains 428 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 373 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -775 GLN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 293 optimal weight: 9.9990 chunk 261 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 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** Q 361 HIS C 130 GLN C 360 ASN C 394 HIS C 396 GLN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.178454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124318 restraints weight = 46096.946| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.33 r_work: 0.3240 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35309 Z= 0.181 Angle : 0.646 13.500 48098 Z= 0.334 Chirality : 0.046 0.367 5316 Planarity : 0.005 0.087 6196 Dihedral : 5.674 73.274 4811 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 3.45 % Allowed : 13.18 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4408 helix: 0.47 (0.23), residues: 569 sheet: -0.79 (0.13), residues: 1443 loop : -1.60 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP J-764 HIS 0.007 0.001 HIS Q 305 PHE 0.023 0.002 PHE R 6 TYR 0.026 0.002 TYR O 308 ARG 0.008 0.001 ARG Q 103 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1017) hydrogen bonds : angle 5.35672 ( 2625) SS BOND : bond 0.00325 ( 65) SS BOND : angle 1.46141 ( 130) covalent geometry : bond 0.00442 (35244) covalent geometry : angle 0.64214 (47968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 406 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.5976 (ptt) cc_final: 0.4724 (tpp) REVERT: K 151 MET cc_start: 0.8296 (mmp) cc_final: 0.7662 (mmp) REVERT: K 153 VAL cc_start: 0.8956 (t) cc_final: 0.8612 (p) REVERT: K 193 HIS cc_start: 0.7998 (p-80) cc_final: 0.7625 (p90) REVERT: K 208 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: K 226 SER cc_start: 0.8358 (t) cc_final: 0.7687 (m) REVERT: K 270 GLU cc_start: 0.8249 (tt0) cc_final: 0.7678 (pm20) REVERT: S 120 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6327 (mpt) REVERT: S 131 MET cc_start: 0.7013 (mmm) cc_final: 0.6769 (mmm) REVERT: S 172 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8124 (tmmt) REVERT: S 199 TYR cc_start: 0.6360 (m-10) cc_final: 0.5885 (m-80) REVERT: S 223 LYS cc_start: 0.8499 (tttt) cc_final: 0.8203 (tptt) REVERT: S 251 THR cc_start: 0.7650 (p) cc_final: 0.7360 (t) REVERT: S 257 MET cc_start: 0.7728 (ptp) cc_final: 0.7500 (mpp) REVERT: S 266 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7817 (tmtp) REVERT: G 52 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8677 (tttp) REVERT: G 99 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: G 241 GLU cc_start: 0.8420 (tp30) cc_final: 0.8220 (tp30) REVERT: G 319 LYS cc_start: 0.7791 (ttpm) cc_final: 0.7516 (ttpt) REVERT: H 57 ASP cc_start: 0.7379 (p0) cc_final: 0.7084 (p0) REVERT: J -687 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: J -609 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6813 (ttm170) REVERT: B 282 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6456 (tp) REVERT: T 23 TYR cc_start: 0.6221 (t80) cc_final: 0.5235 (t80) REVERT: Q 130 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8792 (pttp) REVERT: Q 137 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: Q 144 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8205 (mt-10) REVERT: Q 159 GLN cc_start: 0.8342 (tt0) cc_final: 0.7924 (tp40) REVERT: Q 213 LYS cc_start: 0.7698 (mttt) cc_final: 0.7208 (mmtp) REVERT: A 118 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5460 (pmt) REVERT: A 146 LYS cc_start: 0.5251 (OUTLIER) cc_final: 0.4930 (ptpt) REVERT: A 184 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6399 (mpt) REVERT: F 131 MET cc_start: 0.7918 (mmp) cc_final: 0.7658 (mmm) REVERT: F 190 LYS cc_start: 0.8283 (mtmt) cc_final: 0.8043 (mmmt) REVERT: F 195 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.6096 (pttm) REVERT: F 257 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.5693 (ptm) REVERT: C 115 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8388 (tp) REVERT: C 139 GLU cc_start: 0.7717 (pp20) cc_final: 0.7450 (pp20) REVERT: C 140 HIS cc_start: 0.7438 (m90) cc_final: 0.6952 (m90) REVERT: C 364 GLU cc_start: 0.8151 (tp30) cc_final: 0.7611 (tp30) REVERT: C 377 LYS cc_start: 0.7325 (ttmm) cc_final: 0.6915 (tttm) REVERT: E 38 SER cc_start: 0.8933 (t) cc_final: 0.8508 (m) REVERT: R 8 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: R 60 ASN cc_start: 0.7221 (m110) cc_final: 0.6988 (m110) REVERT: R 323 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: R 360 TYR cc_start: 0.8792 (t80) cc_final: 0.8451 (t80) REVERT: R 377 ILE cc_start: 0.7732 (mt) cc_final: 0.7517 (mm) REVERT: R 402 LEU cc_start: 0.7471 (mt) cc_final: 0.7236 (mp) REVERT: N 66 MET cc_start: 0.9376 (ttt) cc_final: 0.9065 (ttt) REVERT: N 201 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7064 (tm-30) REVERT: N 231 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8556 (mm) REVERT: N 291 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8714 (p0) REVERT: N 365 MET cc_start: 0.8735 (ttt) cc_final: 0.7641 (pmt) REVERT: O 2 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: O 73 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7146 (mtp180) REVERT: O 175 ARG cc_start: 0.8456 (ttt-90) cc_final: 0.8059 (ttp-110) outliers start: 130 outliers final: 52 residues processed: 492 average time/residue: 1.3114 time to fit residues: 784.9078 Evaluate side-chains 440 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 365 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 126 LYS Chi-restraints excluded: chain S residue 146 LYS Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 266 LYS Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 50 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 203 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 HIS ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119371 restraints weight = 46248.018| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.36 r_work: 0.3180 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35309 Z= 0.203 Angle : 0.652 11.144 48098 Z= 0.336 Chirality : 0.047 0.462 5316 Planarity : 0.005 0.094 6196 Dihedral : 5.646 75.984 4811 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.40 % Favored : 94.51 % Rotamer: Outliers : 4.44 % Allowed : 13.34 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4408 helix: 0.87 (0.23), residues: 569 sheet: -0.64 (0.13), residues: 1463 loop : -1.46 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP J-764 HIS 0.007 0.001 HIS R 156 PHE 0.016 0.002 PHE N 328 TYR 0.027 0.002 TYR O 308 ARG 0.006 0.001 ARG N 120 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 1017) hydrogen bonds : angle 5.20158 ( 2625) SS BOND : bond 0.00352 ( 65) SS BOND : angle 1.45675 ( 130) covalent geometry : bond 0.00499 (35244) covalent geometry : angle 0.64814 (47968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 383 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6185 (ptt) cc_final: 0.5954 (ppp) REVERT: K 151 MET cc_start: 0.8282 (mmp) cc_final: 0.7655 (mmp) REVERT: K 153 VAL cc_start: 0.8957 (t) cc_final: 0.8609 (p) REVERT: K 223 LYS cc_start: 0.8775 (tppt) cc_final: 0.8552 (tppt) REVERT: K 226 SER cc_start: 0.8486 (t) cc_final: 0.7812 (m) REVERT: K 270 GLU cc_start: 0.8084 (tt0) cc_final: 0.7494 (pm20) REVERT: S 131 MET cc_start: 0.6988 (mmm) cc_final: 0.6616 (mmm) REVERT: S 169 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7125 (mtmt) REVERT: S 172 LYS cc_start: 0.8530 (tmmm) cc_final: 0.8307 (tmmt) REVERT: S 251 THR cc_start: 0.7835 (p) cc_final: 0.7600 (t) REVERT: S 257 MET cc_start: 0.7465 (ptp) cc_final: 0.7257 (mpp) REVERT: S 266 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7842 (tmtp) REVERT: G 2 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: G 10 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: G 99 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: G 293 THR cc_start: 0.8274 (m) cc_final: 0.7946 (t) REVERT: G 319 LYS cc_start: 0.7701 (ttpm) cc_final: 0.6803 (tptp) REVERT: G 366 ARG cc_start: 0.8459 (ttp80) cc_final: 0.7640 (ttp80) REVERT: G 370 CYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7518 (m) REVERT: H 57 ASP cc_start: 0.7405 (p0) cc_final: 0.7149 (p0) REVERT: J -768 GLN cc_start: 0.8545 (mt0) cc_final: 0.8008 (tt0) REVERT: J -687 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: J -609 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6686 (ttm170) REVERT: B 10 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: B 97 ASP cc_start: 0.8040 (m-30) cc_final: 0.7741 (p0) REVERT: B 282 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6552 (tp) REVERT: T 23 TYR cc_start: 0.5804 (t80) cc_final: 0.5189 (t80) REVERT: Q 4 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: Q 130 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8800 (mtmm) REVERT: Q 137 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: Q 144 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8221 (mt-10) REVERT: Q 159 GLN cc_start: 0.8420 (tt0) cc_final: 0.7918 (tp40) REVERT: Q 167 MET cc_start: 0.7974 (mmt) cc_final: 0.6967 (mmt) REVERT: Q 213 LYS cc_start: 0.7887 (mttt) cc_final: 0.7315 (mmtp) REVERT: A 118 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.5659 (pmm) REVERT: A 146 LYS cc_start: 0.4825 (OUTLIER) cc_final: 0.4520 (ptpt) REVERT: A 184 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6415 (mpt) REVERT: F 195 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6137 (pttm) REVERT: F 257 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5540 (ptm) REVERT: C 140 HIS cc_start: 0.7319 (m90) cc_final: 0.6902 (m90) REVERT: C 160 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7704 (ttmt) REVERT: C 364 GLU cc_start: 0.8266 (tp30) cc_final: 0.7671 (tp30) REVERT: C 375 THR cc_start: 0.8617 (m) cc_final: 0.8389 (t) REVERT: E 38 SER cc_start: 0.8905 (t) cc_final: 0.8519 (m) REVERT: R 6 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6997 (t80) REVERT: R 8 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: R 60 ASN cc_start: 0.6983 (m110) cc_final: 0.6636 (m110) REVERT: R 323 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: R 360 TYR cc_start: 0.8722 (t80) cc_final: 0.8326 (t80) REVERT: R 402 LEU cc_start: 0.7353 (mt) cc_final: 0.7105 (mp) REVERT: L 44 ASP cc_start: 0.7109 (t0) cc_final: 0.6868 (m-30) REVERT: N 20 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.7945 (mp) REVERT: N 66 MET cc_start: 0.9373 (ttt) cc_final: 0.9073 (ttt) REVERT: N 160 ASN cc_start: 0.7350 (t0) cc_final: 0.6941 (t0) REVERT: N 365 MET cc_start: 0.8719 (ttt) cc_final: 0.7558 (pmt) REVERT: O 2 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: O 18 ILE cc_start: 0.9062 (pt) cc_final: 0.8861 (pp) REVERT: O 175 ARG cc_start: 0.8544 (ttt-90) cc_final: 0.8188 (ttp-110) outliers start: 167 outliers final: 78 residues processed: 503 average time/residue: 1.2694 time to fit residues: 783.2494 Evaluate side-chains 450 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 349 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain S residue 126 LYS 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 168 LYS Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 266 LYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL 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 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 374 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 404 optimal weight: 0.7980 chunk 251 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 204 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 259 ASN ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J-920 HIS J-919 GLN J-767 ASN J-642 HIS B 386 HIS Q 288 HIS ** N 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 157 ASN O 360 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.171591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117763 restraints weight = 46361.125| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.26 r_work: 0.3140 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 35309 Z= 0.279 Angle : 0.712 11.551 48098 Z= 0.367 Chirality : 0.049 0.493 5316 Planarity : 0.006 0.115 6196 Dihedral : 5.862 79.324 4811 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.06 % Favored : 93.83 % Rotamer: Outliers : 5.02 % Allowed : 13.50 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4408 helix: 1.26 (0.24), residues: 541 sheet: -0.62 (0.14), residues: 1384 loop : -1.40 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP J-764 HIS 0.010 0.002 HIS N 41 PHE 0.018 0.002 PHE N 328 TYR 0.029 0.002 TYR O 308 ARG 0.008 0.001 ARG Q 103 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 1017) hydrogen bonds : angle 5.20813 ( 2625) SS BOND : bond 0.00387 ( 65) SS BOND : angle 1.53371 ( 130) covalent geometry : bond 0.00689 (35244) covalent geometry : angle 0.70884 (47968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 369 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6360 (ptt) cc_final: 0.6090 (ppp) REVERT: K 151 MET cc_start: 0.8193 (mmp) cc_final: 0.7516 (mmp) REVERT: K 153 VAL cc_start: 0.8975 (t) cc_final: 0.8736 (p) REVERT: K 223 LYS cc_start: 0.8844 (tppt) cc_final: 0.8594 (tppt) REVERT: K 226 SER cc_start: 0.8724 (t) cc_final: 0.7899 (m) REVERT: K 257 MET cc_start: 0.8783 (ptp) cc_final: 0.8482 (mpp) REVERT: K 270 GLU cc_start: 0.7984 (tt0) cc_final: 0.7503 (pm20) REVERT: S 131 MET cc_start: 0.6839 (mmm) cc_final: 0.6428 (mmm) REVERT: S 135 LYS cc_start: 0.7123 (mmtp) cc_final: 0.6603 (mptt) REVERT: S 169 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7104 (mtmt) REVERT: S 172 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8155 (tmmt) REVERT: S 257 MET cc_start: 0.7610 (ptp) cc_final: 0.7364 (ptp) REVERT: G 10 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: G 99 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: G 293 THR cc_start: 0.8339 (m) cc_final: 0.8015 (t) REVERT: G 300 GLU cc_start: 0.5945 (pm20) cc_final: 0.5716 (pm20) REVERT: G 319 LYS cc_start: 0.7744 (ttpm) cc_final: 0.7129 (ttmt) REVERT: G 366 ARG cc_start: 0.8460 (ttp80) cc_final: 0.7579 (ttp80) REVERT: G 370 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7339 (m) REVERT: H 57 ASP cc_start: 0.7429 (p0) cc_final: 0.7208 (p0) REVERT: J -768 GLN cc_start: 0.8567 (mt0) cc_final: 0.8125 (tt0) REVERT: J -687 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: J -609 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6684 (ttm170) REVERT: J -588 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6864 (mp) REVERT: B 7 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7860 (ttp) REVERT: B 10 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: B 166 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7749 (tp) REVERT: B 282 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6621 (tp) REVERT: B 305 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5753 (mt-10) REVERT: D 41 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7812 (ttt-90) REVERT: D 63 GLU cc_start: 0.7404 (mp0) cc_final: 0.6970 (tp30) REVERT: Q 4 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: Q 120 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8127 (ttp80) REVERT: Q 130 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8832 (mtmm) REVERT: Q 137 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: Q 144 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8163 (mt-10) REVERT: Q 159 GLN cc_start: 0.8446 (tt0) cc_final: 0.7935 (tp40) REVERT: Q 213 LYS cc_start: 0.7921 (mttt) cc_final: 0.7403 (mmtp) REVERT: Q 255 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8653 (mt) REVERT: A 118 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5911 (pmm) REVERT: A 146 LYS cc_start: 0.4804 (OUTLIER) cc_final: 0.4563 (ptpt) REVERT: A 184 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6307 (mpt) REVERT: F 195 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6270 (pttm) REVERT: F 257 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5560 (ptm) REVERT: C 72 TYR cc_start: 0.8605 (m-80) cc_final: 0.8244 (m-80) REVERT: C 140 HIS cc_start: 0.7209 (m90) cc_final: 0.6840 (m90) REVERT: C 160 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7541 (tttm) REVERT: C 206 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7857 (tpt170) REVERT: C 289 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7337 (mtm110) REVERT: C 364 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: C 366 ARG cc_start: 0.8738 (ttp-170) cc_final: 0.8501 (ttp-170) REVERT: C 396 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: E 38 SER cc_start: 0.8988 (t) cc_final: 0.8645 (m) REVERT: R 6 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7172 (t80) REVERT: R 8 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7703 (mt-10) REVERT: R 60 ASN cc_start: 0.6995 (m110) cc_final: 0.6743 (m-40) REVERT: R 111 THR cc_start: 0.8411 (m) cc_final: 0.7978 (m) REVERT: R 164 TYR cc_start: 0.8256 (m-80) cc_final: 0.7969 (m-80) REVERT: R 239 ASN cc_start: 0.8566 (t0) cc_final: 0.8246 (t0) REVERT: R 323 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: R 360 TYR cc_start: 0.8705 (t80) cc_final: 0.8305 (t80) REVERT: R 388 LEU cc_start: 0.7041 (tp) cc_final: 0.6840 (tp) REVERT: R 402 LEU cc_start: 0.7360 (mt) cc_final: 0.7139 (mp) REVERT: N 66 MET cc_start: 0.9406 (ttp) cc_final: 0.9133 (ttt) REVERT: N 160 ASN cc_start: 0.7194 (t0) cc_final: 0.6927 (t0) REVERT: N 187 THR cc_start: 0.8117 (m) cc_final: 0.7684 (p) REVERT: N 365 MET cc_start: 0.8814 (ttt) cc_final: 0.7607 (pmt) REVERT: O 2 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8612 (mm-30) REVERT: O 175 ARG cc_start: 0.8536 (ttt-90) cc_final: 0.8244 (ttp-110) outliers start: 189 outliers final: 100 residues processed: 500 average time/residue: 1.3690 time to fit residues: 840.5621 Evaluate side-chains 478 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 348 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain S residue 126 LYS 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 168 LYS Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -860 THR Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -631 LEU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain J residue -588 LEU Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 120 ARG Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU 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 221 THR Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain R residue 368 ILE Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 88 ARG Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 160 LYS Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 104 optimal weight: 0.8980 chunk 310 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 331 optimal weight: 4.9990 chunk 424 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 280 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 431 optimal weight: 0.7980 chunk 386 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 ASN J-919 GLN J-767 ASN Q 60 ASN A 159 ASN A 203 HIS R 159 GLN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.174839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121156 restraints weight = 46302.274| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.17 r_work: 0.3203 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35309 Z= 0.116 Angle : 0.593 10.146 48098 Z= 0.305 Chirality : 0.045 0.458 5316 Planarity : 0.005 0.072 6196 Dihedral : 5.417 78.250 4811 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 3.53 % Allowed : 15.52 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4408 helix: 1.30 (0.24), residues: 559 sheet: -0.41 (0.14), residues: 1358 loop : -1.30 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP J-764 HIS 0.004 0.001 HIS R 168 PHE 0.018 0.001 PHE R 217 TYR 0.025 0.001 TYR R 363 ARG 0.007 0.000 ARG Q 88 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 1017) hydrogen bonds : angle 4.97702 ( 2625) SS BOND : bond 0.00228 ( 65) SS BOND : angle 1.31169 ( 130) covalent geometry : bond 0.00265 (35244) covalent geometry : angle 0.58978 (47968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 377 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 132 LEU cc_start: 0.8543 (tp) cc_final: 0.8208 (mt) REVERT: K 151 MET cc_start: 0.8026 (mmp) cc_final: 0.7452 (mmp) REVERT: K 153 VAL cc_start: 0.8919 (t) cc_final: 0.8567 (p) REVERT: K 226 SER cc_start: 0.8704 (t) cc_final: 0.7963 (m) REVERT: S 131 MET cc_start: 0.6841 (mmm) cc_final: 0.6549 (mmm) REVERT: S 135 LYS cc_start: 0.7199 (mmtp) cc_final: 0.6651 (mptt) REVERT: S 169 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6846 (mtmt) REVERT: S 172 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8215 (tmmt) REVERT: G 99 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: G 293 THR cc_start: 0.8172 (m) cc_final: 0.7964 (t) REVERT: G 319 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7060 (ttmt) REVERT: G 366 ARG cc_start: 0.8418 (ttp80) cc_final: 0.7711 (ttp80) REVERT: H 57 ASP cc_start: 0.7414 (p0) cc_final: 0.7128 (p0) REVERT: J -984 MET cc_start: 0.8825 (mtp) cc_final: 0.8570 (mtm) REVERT: J -768 GLN cc_start: 0.8524 (mt0) cc_final: 0.8071 (tt0) REVERT: J -687 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: J -609 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6682 (ttm170) REVERT: B 29 ILE cc_start: 0.7685 (mt) cc_final: 0.7337 (mm) REVERT: B 282 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6664 (tp) REVERT: B 305 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5672 (mt-10) REVERT: B 341 GLU cc_start: 0.8188 (pm20) cc_final: 0.7693 (pm20) REVERT: D 41 ARG cc_start: 0.8267 (ttt-90) cc_final: 0.8037 (ttt-90) REVERT: Q 4 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: Q 130 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8764 (mtmm) REVERT: Q 137 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: Q 144 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8299 (mt-10) REVERT: Q 159 GLN cc_start: 0.8383 (tt0) cc_final: 0.7973 (tp40) REVERT: Q 210 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (p) REVERT: Q 213 LYS cc_start: 0.7738 (mttt) cc_final: 0.7328 (mmtp) REVERT: A 118 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6285 (pmm) REVERT: A 168 LYS cc_start: 0.6229 (ttpp) cc_final: 0.6018 (ttpp) REVERT: A 184 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6315 (mpt) REVERT: C 72 TYR cc_start: 0.8558 (m-80) cc_final: 0.8179 (m-80) REVERT: C 97 ASP cc_start: 0.7429 (m-30) cc_final: 0.7139 (p0) REVERT: C 140 HIS cc_start: 0.7272 (m90) cc_final: 0.6922 (m90) REVERT: C 160 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7452 (tttm) REVERT: C 281 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8901 (t70) REVERT: C 289 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7781 (mtm110) REVERT: C 364 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: C 366 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8538 (ttp-170) REVERT: E 38 SER cc_start: 0.8950 (t) cc_final: 0.8633 (m) REVERT: R 6 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7195 (t80) REVERT: R 8 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: R 60 ASN cc_start: 0.6980 (m110) cc_final: 0.6710 (m-40) REVERT: R 164 TYR cc_start: 0.8265 (m-80) cc_final: 0.7998 (m-80) REVERT: R 197 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7167 (pt) REVERT: R 239 ASN cc_start: 0.8374 (t0) cc_final: 0.8049 (t0) REVERT: R 323 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: R 360 TYR cc_start: 0.8726 (t80) cc_final: 0.8382 (t80) REVERT: R 402 LEU cc_start: 0.7358 (mt) cc_final: 0.7153 (mp) REVERT: N 9 TYR cc_start: 0.8660 (m-80) cc_final: 0.8416 (m-80) REVERT: N 20 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8072 (mp) REVERT: N 66 MET cc_start: 0.9338 (ttp) cc_final: 0.9088 (ttt) REVERT: N 160 ASN cc_start: 0.7911 (t0) cc_final: 0.7533 (t0) REVERT: N 365 MET cc_start: 0.8731 (ttt) cc_final: 0.7604 (pmt) REVERT: O 2 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8317 (mm-30) REVERT: O 18 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8450 (pp) REVERT: O 175 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8202 (ttp-110) outliers start: 133 outliers final: 57 residues processed: 467 average time/residue: 1.4552 time to fit residues: 825.9751 Evaluate side-chains 425 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 345 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain T residue 33 MET Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 251 LEU Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 364 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 R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 20 optimal weight: 0.6980 chunk 307 optimal weight: 9.9990 chunk 312 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 421 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 399 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS J-848 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 396 GLN Q 60 ASN C 222 GLN C 396 GLN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN R 358 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.174861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120222 restraints weight = 46440.354| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.43 r_work: 0.3207 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35309 Z= 0.120 Angle : 0.597 10.844 48098 Z= 0.306 Chirality : 0.045 0.494 5316 Planarity : 0.005 0.069 6196 Dihedral : 5.267 78.305 4811 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 3.06 % Allowed : 16.58 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 4408 helix: 1.43 (0.24), residues: 559 sheet: -0.31 (0.14), residues: 1360 loop : -1.21 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP J-764 HIS 0.004 0.001 HIS R 168 PHE 0.021 0.001 PHE R 217 TYR 0.023 0.001 TYR O 308 ARG 0.006 0.000 ARG Q 88 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 1017) hydrogen bonds : angle 4.88104 ( 2625) SS BOND : bond 0.00219 ( 65) SS BOND : angle 1.20715 ( 130) covalent geometry : bond 0.00281 (35244) covalent geometry : angle 0.59444 (47968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 362 time to evaluate : 4.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 151 MET cc_start: 0.8121 (mmp) cc_final: 0.7621 (mmp) REVERT: K 153 VAL cc_start: 0.8924 (t) cc_final: 0.8568 (p) REVERT: K 226 SER cc_start: 0.8664 (t) cc_final: 0.7861 (m) REVERT: K 257 MET cc_start: 0.8702 (ptp) cc_final: 0.8476 (mpp) REVERT: S 131 MET cc_start: 0.6834 (mmm) cc_final: 0.6533 (mmm) REVERT: S 135 LYS cc_start: 0.7266 (mmtp) cc_final: 0.6675 (mptt) REVERT: S 169 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6859 (mtmt) REVERT: S 172 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8163 (tmmt) REVERT: G 99 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: G 293 THR cc_start: 0.8132 (m) cc_final: 0.7913 (t) REVERT: G 300 GLU cc_start: 0.6148 (pm20) cc_final: 0.5842 (pm20) REVERT: G 319 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7055 (ttmt) REVERT: G 361 ILE cc_start: 0.7781 (mt) cc_final: 0.7555 (tt) REVERT: G 366 ARG cc_start: 0.8352 (ttp80) cc_final: 0.7661 (ttp80) REVERT: H 57 ASP cc_start: 0.7471 (p0) cc_final: 0.7159 (p0) REVERT: I 33 MET cc_start: 0.5414 (ttp) cc_final: 0.4959 (ttm) REVERT: J -984 MET cc_start: 0.8850 (mtp) cc_final: 0.8575 (mtm) REVERT: J -799 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8535 (tm-30) REVERT: J -783 PHE cc_start: 0.8432 (m-80) cc_final: 0.8177 (m-80) REVERT: J -768 GLN cc_start: 0.8488 (mt0) cc_final: 0.8009 (tt0) REVERT: J -687 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: J -609 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6676 (ttm170) REVERT: B 10 GLN cc_start: 0.8457 (tt0) cc_final: 0.8163 (pp30) REVERT: B 29 ILE cc_start: 0.7585 (mt) cc_final: 0.7258 (mm) REVERT: B 305 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5543 (mt-10) REVERT: B 341 GLU cc_start: 0.8193 (pm20) cc_final: 0.7748 (pm20) REVERT: Q 4 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: Q 137 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: Q 159 GLN cc_start: 0.8387 (tt0) cc_final: 0.8021 (tp40) REVERT: Q 213 LYS cc_start: 0.7778 (mttt) cc_final: 0.7358 (mmtp) REVERT: Q 273 GLU cc_start: 0.8247 (mp0) cc_final: 0.7906 (mp0) REVERT: A 118 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6432 (pmm) REVERT: A 120 MET cc_start: 0.6031 (pmm) cc_final: 0.5652 (pmm) REVERT: A 168 LYS cc_start: 0.6242 (ttpp) cc_final: 0.6025 (ttpp) REVERT: C 72 TYR cc_start: 0.8562 (m-80) cc_final: 0.8169 (m-80) REVERT: C 97 ASP cc_start: 0.7483 (m-30) cc_final: 0.7135 (p0) REVERT: C 140 HIS cc_start: 0.7167 (m90) cc_final: 0.6872 (m90) REVERT: C 160 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7682 (ttmt) REVERT: C 289 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7486 (mtm110) REVERT: C 364 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: C 370 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7781 (m) REVERT: E 38 SER cc_start: 0.8978 (t) cc_final: 0.8665 (m) REVERT: R 6 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7196 (t80) REVERT: R 8 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: R 60 ASN cc_start: 0.7024 (m110) cc_final: 0.6755 (m-40) REVERT: R 164 TYR cc_start: 0.8253 (m-80) cc_final: 0.7998 (m-80) REVERT: R 197 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7127 (pt) REVERT: R 232 GLN cc_start: 0.8376 (tt0) cc_final: 0.8129 (tt0) REVERT: R 239 ASN cc_start: 0.8372 (t0) cc_final: 0.8077 (t0) REVERT: R 323 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: R 360 TYR cc_start: 0.8733 (t80) cc_final: 0.8379 (t80) REVERT: R 397 LEU cc_start: 0.7043 (mt) cc_final: 0.6705 (mp) REVERT: N 66 MET cc_start: 0.9374 (ttp) cc_final: 0.9050 (ttt) REVERT: N 160 ASN cc_start: 0.7915 (t0) cc_final: 0.7523 (t0) REVERT: N 365 MET cc_start: 0.8745 (ttt) cc_final: 0.7640 (pmt) REVERT: O 2 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: O 175 ARG cc_start: 0.8491 (ttt-90) cc_final: 0.8216 (ttp-110) outliers start: 115 outliers final: 62 residues processed: 437 average time/residue: 1.8015 time to fit residues: 982.3608 Evaluate side-chains 416 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain T residue 33 MET Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 251 LEU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 364 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 R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 342 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 406 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 405 optimal weight: 0.8980 chunk 254 optimal weight: 0.0770 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 HIS Q 60 ASN Q 233 ASN C 140 HIS C 222 GLN R 159 GLN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 353 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119749 restraints weight = 46270.748| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.39 r_work: 0.3198 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35309 Z= 0.131 Angle : 0.601 11.199 48098 Z= 0.307 Chirality : 0.045 0.466 5316 Planarity : 0.005 0.070 6196 Dihedral : 5.224 79.225 4811 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 2.90 % Allowed : 16.76 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4408 helix: 1.63 (0.24), residues: 555 sheet: -0.25 (0.14), residues: 1373 loop : -1.17 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP J-764 HIS 0.005 0.001 HIS R 168 PHE 0.024 0.001 PHE R 217 TYR 0.023 0.001 TYR O 308 ARG 0.006 0.000 ARG N 120 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 1017) hydrogen bonds : angle 4.85786 ( 2625) SS BOND : bond 0.00214 ( 65) SS BOND : angle 1.15531 ( 130) covalent geometry : bond 0.00314 (35244) covalent geometry : angle 0.59888 (47968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 358 time to evaluate : 5.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 132 LEU cc_start: 0.8499 (tp) cc_final: 0.8264 (mt) REVERT: K 151 MET cc_start: 0.8102 (mmp) cc_final: 0.7635 (mmp) REVERT: K 153 VAL cc_start: 0.8918 (t) cc_final: 0.8558 (p) REVERT: K 226 SER cc_start: 0.8701 (t) cc_final: 0.7947 (m) REVERT: K 257 MET cc_start: 0.8683 (ptp) cc_final: 0.8443 (mpp) REVERT: K 270 GLU cc_start: 0.7917 (tt0) cc_final: 0.7500 (pm20) REVERT: S 131 MET cc_start: 0.6830 (mmm) cc_final: 0.6533 (mmm) REVERT: S 135 LYS cc_start: 0.7228 (mmtp) cc_final: 0.6649 (mptt) REVERT: S 169 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6869 (mtmt) REVERT: S 172 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8167 (tmmt) REVERT: G 2 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: G 99 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: G 293 THR cc_start: 0.8142 (m) cc_final: 0.7916 (t) REVERT: G 300 GLU cc_start: 0.5993 (pm20) cc_final: 0.5788 (pm20) REVERT: G 319 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7033 (ttmt) REVERT: G 361 ILE cc_start: 0.7859 (mt) cc_final: 0.7587 (tt) REVERT: G 366 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7643 (ttp80) REVERT: G 370 CYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7247 (m) REVERT: H 57 ASP cc_start: 0.7463 (p0) cc_final: 0.7148 (p0) REVERT: J -984 MET cc_start: 0.8907 (mtp) cc_final: 0.8588 (mtm) REVERT: J -799 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8508 (tm-30) REVERT: J -783 PHE cc_start: 0.8395 (m-80) cc_final: 0.8151 (m-80) REVERT: J -768 GLN cc_start: 0.8483 (mt0) cc_final: 0.8014 (tt0) REVERT: J -687 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: J -609 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6674 (ttm170) REVERT: B 10 GLN cc_start: 0.8533 (tt0) cc_final: 0.8298 (tm-30) REVERT: B 282 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6411 (tp) REVERT: B 305 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5729 (mt-10) REVERT: Q 4 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: Q 137 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: Q 159 GLN cc_start: 0.8385 (tt0) cc_final: 0.8014 (tp40) REVERT: Q 213 LYS cc_start: 0.7871 (mttt) cc_final: 0.7367 (mmtp) REVERT: A 118 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6589 (pmm) REVERT: A 120 MET cc_start: 0.6088 (pmm) cc_final: 0.5731 (pmm) REVERT: C 72 TYR cc_start: 0.8549 (m-80) cc_final: 0.8162 (m-80) REVERT: C 97 ASP cc_start: 0.7521 (m-30) cc_final: 0.7140 (p0) REVERT: C 140 HIS cc_start: 0.7448 (m-70) cc_final: 0.7177 (m90) REVERT: C 160 LYS cc_start: 0.7874 (ttmt) cc_final: 0.7649 (ttmt) REVERT: C 281 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8863 (t70) REVERT: C 289 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7761 (ttp80) REVERT: C 364 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: C 411 THR cc_start: 0.7953 (m) cc_final: 0.7494 (p) REVERT: E 38 SER cc_start: 0.8994 (t) cc_final: 0.8682 (m) REVERT: R 6 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7109 (t80) REVERT: R 8 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: R 60 ASN cc_start: 0.7107 (m110) cc_final: 0.6842 (m-40) REVERT: R 111 THR cc_start: 0.8421 (m) cc_final: 0.7936 (m) REVERT: R 164 TYR cc_start: 0.8237 (m-80) cc_final: 0.7984 (m-80) REVERT: R 197 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7143 (pt) REVERT: R 239 ASN cc_start: 0.8361 (t0) cc_final: 0.8073 (t0) REVERT: R 323 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: R 360 TYR cc_start: 0.8742 (t80) cc_final: 0.8451 (t80) REVERT: R 397 LEU cc_start: 0.6951 (mt) cc_final: 0.6573 (mp) REVERT: N 66 MET cc_start: 0.9394 (ttp) cc_final: 0.9109 (ttt) REVERT: N 160 ASN cc_start: 0.7899 (t0) cc_final: 0.7497 (t0) REVERT: N 187 THR cc_start: 0.8028 (m) cc_final: 0.7595 (p) REVERT: N 365 MET cc_start: 0.8713 (ttt) cc_final: 0.7634 (pmt) REVERT: O 2 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: O 18 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8562 (pp) REVERT: O 24 TYR cc_start: 0.9047 (m-80) cc_final: 0.8827 (m-80) REVERT: O 175 ARG cc_start: 0.8493 (ttt-90) cc_final: 0.8221 (ttp-110) outliers start: 109 outliers final: 67 residues processed: 433 average time/residue: 1.5347 time to fit residues: 819.9186 Evaluate side-chains 431 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 343 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain T residue 33 MET Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 140 THR Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 251 LEU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 364 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 R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9323 > 50: distance: 72 - 77: 3.924 distance: 77 - 78: 6.278 distance: 77 - 178: 4.494 distance: 78 - 79: 10.794 distance: 78 - 81: 9.410 distance: 79 - 80: 11.739 distance: 79 - 84: 13.542 distance: 80 - 175: 12.457 distance: 81 - 82: 11.014 distance: 81 - 83: 11.835 distance: 84 - 85: 18.305 distance: 85 - 86: 13.889 distance: 85 - 88: 10.254 distance: 86 - 87: 8.284 distance: 86 - 92: 26.862 distance: 88 - 89: 11.969 distance: 89 - 90: 6.223 distance: 89 - 91: 9.464 distance: 92 - 93: 14.434 distance: 93 - 94: 25.095 distance: 93 - 96: 9.874 distance: 94 - 95: 34.208 distance: 94 - 101: 53.697 distance: 96 - 97: 6.295 distance: 97 - 98: 6.865 distance: 98 - 99: 16.792 distance: 98 - 100: 12.674 distance: 101 - 102: 55.932 distance: 102 - 103: 40.696 distance: 102 - 105: 32.759 distance: 103 - 104: 19.310 distance: 103 - 112: 14.198 distance: 105 - 106: 19.093 distance: 106 - 107: 18.799 distance: 107 - 108: 15.948 distance: 108 - 109: 7.820 distance: 109 - 110: 7.135 distance: 109 - 111: 4.452 distance: 112 - 113: 14.784 distance: 112 - 118: 10.151 distance: 113 - 114: 9.989 distance: 113 - 116: 19.113 distance: 114 - 115: 17.305 distance: 114 - 119: 18.171 distance: 116 - 117: 5.948 distance: 117 - 118: 16.798 distance: 119 - 120: 17.420 distance: 120 - 121: 12.657 distance: 120 - 123: 15.991 distance: 121 - 122: 30.856 distance: 121 - 128: 8.223 distance: 123 - 124: 5.612 distance: 124 - 125: 13.086 distance: 125 - 126: 18.287 distance: 126 - 127: 14.039 distance: 128 - 129: 23.208 distance: 129 - 130: 21.092 distance: 129 - 132: 25.096 distance: 130 - 131: 32.180 distance: 130 - 133: 25.965 distance: 133 - 134: 27.623 distance: 134 - 135: 19.308 distance: 135 - 136: 18.407 distance: 135 - 137: 12.266 distance: 137 - 138: 7.473 distance: 138 - 139: 7.877 distance: 138 - 141: 19.193 distance: 139 - 140: 13.437 distance: 139 - 142: 14.162 distance: 142 - 143: 17.926 distance: 143 - 146: 11.854 distance: 144 - 145: 6.482 distance: 146 - 147: 14.017 distance: 146 - 148: 13.712 distance: 147 - 149: 5.529