Starting phenix.real_space_refine on Mon Jul 6 06:16:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_31567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_31567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_31567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_31567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_31567.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_31567.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fff_31567/07_2026/7fff_31567.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 7.19, per 1000 atoms: 0.21 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: 2.40 Conformation dependent library (CDL) restraints added in 1.7 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: 1.37 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: 10.54 Time building geometry restraints manager: 3.36 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: 0.01 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: 4.090 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.690 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (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 ARG 0.015 0.001 ARG Q 21 TYR 0.039 0.003 TYR C 308 PHE 0.032 0.004 PHE Q 328 TRP 0.047 0.004 TRP J-764 HIS 0.011 0.002 HIS N 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.32 (35244) covalent geometry : angle 0.95904 / 0.53 (47968) SS BOND : bond 0.20374 / 12.59 ( 65) SS BOND : angle 8.28552 / 6.51 ( 130) hydrogen bonds : bond 0.20784 / 13.85 ( 1017) hydrogen bonds : angle 8.33862 / 5.70 ( 2625) *********************** 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 : 1.459 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: 0.6715 time to fit residues: 644.3953 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 : 1.220 ------------------------------------------------------------------------------- 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 432 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 361 HIS F 203 HIS ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 HIS 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 353 HIS O 3 HIS ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 442 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119536 restraints weight = 46534.279| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.26 r_work: 0.3197 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 35309 Z= 0.257 Angle : 0.728 11.417 48098 Z= 0.380 Chirality : 0.049 0.233 5316 Planarity : 0.007 0.092 6196 Dihedral : 6.648 161.317 4819 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 3.75 % Allowed : 11.16 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.12), residues: 4408 helix: -0.22 (0.22), residues: 563 sheet: -1.15 (0.13), residues: 1453 loop : -1.88 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 67 TYR 0.029 0.002 TYR O 308 PHE 0.020 0.002 PHE A 189 TRP 0.060 0.002 TRP J-764 HIS 0.010 0.002 HIS Q 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 (35244) covalent geometry : angle 0.72425 / 0.38 (47968) SS BOND : bond 0.00475 / 0.32 ( 65) SS BOND : angle 1.64937 / 1.03 ( 130) hydrogen bonds : bond 0.04087 / 2.70 ( 1017) hydrogen bonds : angle 5.79008 / 3.95 ( 2625) *********************** 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 582 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 441 time to evaluate : 1.249 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: K 118 MET cc_start: 0.5851 (ptt) cc_final: 0.4672 (tpp) REVERT: K 151 MET cc_start: 0.8059 (mmp) cc_final: 0.7482 (mmp) REVERT: K 153 VAL cc_start: 0.8974 (t) cc_final: 0.8709 (p) REVERT: K 176 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8148 (mt-10) REVERT: K 193 HIS cc_start: 0.7964 (p-80) cc_final: 0.7535 (p90) REVERT: K 208 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6395 (pm20) REVERT: K 215 THR cc_start: 0.8620 (p) cc_final: 0.8119 (p) REVERT: K 257 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8153 (ptp) REVERT: K 270 GLU cc_start: 0.8276 (tt0) cc_final: 0.7689 (pm20) REVERT: S 120 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.6103 (mpt) REVERT: S 131 MET cc_start: 0.6943 (mmm) cc_final: 0.6739 (mmm) REVERT: S 169 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7115 (mtmt) REVERT: S 199 TYR cc_start: 0.6350 (m-10) cc_final: 0.5899 (m-80) REVERT: S 223 LYS cc_start: 0.8482 (tttt) cc_final: 0.8179 (tptt) REVERT: S 251 THR cc_start: 0.7522 (p) cc_final: 0.7185 (t) REVERT: G 10 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: G 99 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: J -775 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: J -687 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: J -609 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6865 (ttm170) REVERT: B 97 ASP cc_start: 0.7936 (m-30) cc_final: 0.7642 (m-30) REVERT: B 433 MET cc_start: 0.5840 (pp-130) cc_final: 0.5220 (ptm) REVERT: D 41 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.8082 (ttt-90) REVERT: Q 113 GLU cc_start: 0.8313 (pt0) cc_final: 0.8090 (pt0) REVERT: Q 130 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8842 (pttp) REVERT: Q 137 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: Q 144 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8142 (mt-10) REVERT: Q 213 LYS cc_start: 0.7573 (mttt) cc_final: 0.7074 (mmtp) REVERT: A 118 MET cc_start: 0.6155 (pmt) cc_final: 0.5610 (pmt) REVERT: A 207 VAL cc_start: 0.8160 (m) cc_final: 0.7950 (p) REVERT: F 131 MET cc_start: 0.7845 (mmp) cc_final: 0.7588 (mmm) REVERT: F 176 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5725 (tm-30) REVERT: F 257 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5436 (ptm) REVERT: F 266 LYS cc_start: 0.8386 (tttt) cc_final: 0.8142 (tptm) REVERT: C 140 HIS cc_start: 0.7884 (m90) cc_final: 0.7225 (m90) REVERT: C 160 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7737 (ttmt) REVERT: C 300 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: C 364 GLU cc_start: 0.7840 (tp30) cc_final: 0.7387 (tp30) REVERT: C 377 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6912 (tttm) REVERT: R 8 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: R 79 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7683 (tp) REVERT: R 323 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: R 360 TYR cc_start: 0.8786 (t80) cc_final: 0.8366 (t80) REVERT: R 377 ILE cc_start: 0.7570 (mt) cc_final: 0.7333 (mm) REVERT: R 402 LEU cc_start: 0.7439 (mt) cc_final: 0.7171 (mp) REVERT: M 36 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8743 (ttt) REVERT: N 53 TYR cc_start: 0.9033 (m-80) cc_final: 0.8790 (m-80) REVERT: N 66 MET cc_start: 0.9345 (ttt) cc_final: 0.9008 (ttt) REVERT: N 112 MET cc_start: 0.9376 (ttm) cc_final: 0.9167 (tpp) REVERT: N 365 MET cc_start: 0.8775 (ttt) cc_final: 0.7612 (pmt) REVERT: O 2 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8553 (mm-30) REVERT: O 18 ILE cc_start: 0.9025 (pt) cc_final: 0.8799 (pp) REVERT: O 175 ARG cc_start: 0.8488 (ttt-90) cc_final: 0.8061 (ttp-110) outliers start: 141 outliers final: 48 residues processed: 519 average time/residue: 0.6176 time to fit residues: 387.7932 Evaluate side-chains 428 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 361 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 410 LEU 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 95 PHE 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 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 303 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain F residue 176 GLU 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 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 R residue 323 GLU Chi-restraints excluded: chain M residue 36 MET 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 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 160 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 0.4980 chunk 134 optimal weight: 8.9990 chunk 427 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 236 optimal weight: 0.5980 chunk 409 optimal weight: 2.9990 chunk 379 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 412 optimal weight: 0.7980 chunk 407 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 360 ASN H 30 ASN B 394 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS C 360 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 HIS N 152 GLN O 130 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 GLN O 394 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126367 restraints weight = 46246.297| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.50 r_work: 0.3267 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35309 Z= 0.123 Angle : 0.609 11.495 48098 Z= 0.316 Chirality : 0.045 0.375 5316 Planarity : 0.005 0.075 6196 Dihedral : 5.653 72.526 4814 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 3.27 % Allowed : 13.23 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.12), residues: 4408 helix: 0.50 (0.23), residues: 569 sheet: -0.77 (0.13), residues: 1435 loop : -1.58 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J-912 TYR 0.024 0.001 TYR O 308 PHE 0.030 0.001 PHE R 6 TRP 0.050 0.001 TRP J-764 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (35244) covalent geometry : angle 0.60537 / 0.31 (47968) SS BOND : bond 0.00390 / 0.26 ( 65) SS BOND : angle 1.39745 / 0.86 ( 130) hydrogen bonds : bond 0.03269 / 2.13 ( 1017) hydrogen bonds : angle 5.36520 / 3.66 ( 2625) *********************** 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 541 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 418 time to evaluate : 1.351 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: K 151 MET cc_start: 0.8272 (mmp) cc_final: 0.7692 (mmp) REVERT: K 153 VAL cc_start: 0.8931 (t) cc_final: 0.8622 (p) REVERT: K 193 HIS cc_start: 0.7993 (p-80) cc_final: 0.7623 (p90) REVERT: K 223 LYS cc_start: 0.8711 (tppt) cc_final: 0.8502 (tppt) REVERT: K 257 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8295 (ptp) REVERT: K 270 GLU cc_start: 0.8228 (tt0) cc_final: 0.7651 (pm20) REVERT: S 120 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5806 (mpt) REVERT: S 131 MET cc_start: 0.6999 (mmm) cc_final: 0.6783 (mmm) REVERT: S 135 LYS cc_start: 0.6776 (mptt) cc_final: 0.6543 (mmtp) REVERT: S 199 TYR cc_start: 0.6409 (m-10) cc_final: 0.5930 (m-80) REVERT: S 223 LYS cc_start: 0.8496 (tttt) cc_final: 0.8203 (tptt) REVERT: S 251 THR cc_start: 0.7577 (p) cc_final: 0.7247 (t) REVERT: S 257 MET cc_start: 0.7830 (ptp) cc_final: 0.7471 (mpp) REVERT: G 319 LYS cc_start: 0.7868 (ttpm) cc_final: 0.7577 (ttpt) REVERT: G 361 ILE cc_start: 0.7971 (mt) cc_final: 0.7650 (tt) REVERT: H 57 ASP cc_start: 0.7249 (p0) cc_final: 0.6936 (p0) REVERT: J -775 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: J -687 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: J -609 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6817 (ttm170) REVERT: B 282 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6594 (tp) REVERT: T 23 TYR cc_start: 0.6354 (t80) cc_final: 0.5229 (t80) REVERT: Q 74 ILE cc_start: 0.8681 (mt) cc_final: 0.8379 (mp) REVERT: Q 130 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8753 (pttp) REVERT: Q 137 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: Q 144 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8212 (mt-10) REVERT: Q 159 GLN cc_start: 0.8330 (tt0) cc_final: 0.8022 (tp40) REVERT: Q 211 ILE cc_start: 0.8111 (tt) cc_final: 0.7827 (tp) REVERT: Q 213 LYS cc_start: 0.7568 (mttt) cc_final: 0.7114 (mmtp) REVERT: A 118 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5756 (pmt) REVERT: A 146 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.4994 (ptpt) REVERT: F 176 GLU cc_start: 0.6437 (tp30) cc_final: 0.5881 (tm-30) REVERT: F 190 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8061 (mmmt) REVERT: F 192 THR cc_start: 0.7955 (t) cc_final: 0.7743 (m) REVERT: F 195 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6118 (pttm) REVERT: F 257 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5750 (ptm) REVERT: C 73 ARG cc_start: 0.7772 (mtp180) cc_final: 0.7560 (mtt-85) REVERT: C 115 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (tp) REVERT: C 139 GLU cc_start: 0.7849 (pp20) cc_final: 0.7596 (pp20) REVERT: C 140 HIS cc_start: 0.7441 (m90) cc_final: 0.6979 (m90) REVERT: C 364 GLU cc_start: 0.8055 (tp30) cc_final: 0.7556 (tp30) REVERT: E 38 SER cc_start: 0.8937 (t) cc_final: 0.8484 (m) REVERT: P 6 MET cc_start: 0.4531 (tpp) cc_final: 0.4235 (ttp) REVERT: R 8 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: R 60 ASN cc_start: 0.7291 (m110) cc_final: 0.7024 (m110) REVERT: R 70 MET cc_start: 0.8507 (tpt) cc_final: 0.8305 (mmm) REVERT: R 79 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7738 (tp) REVERT: R 197 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7327 (pt) REVERT: R 360 TYR cc_start: 0.8844 (t80) cc_final: 0.8502 (t80) REVERT: R 377 ILE cc_start: 0.7813 (mt) cc_final: 0.7574 (mm) REVERT: R 402 LEU cc_start: 0.7468 (mt) cc_final: 0.7207 (mp) REVERT: M 36 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8382 (ttt) REVERT: N 66 MET cc_start: 0.9234 (ttt) cc_final: 0.8934 (ttt) REVERT: N 365 MET cc_start: 0.8745 (ttt) cc_final: 0.7700 (pmt) REVERT: O 2 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8297 (mm-30) REVERT: O 175 ARG cc_start: 0.8249 (ttt-90) cc_final: 0.7845 (ttp-110) outliers start: 123 outliers final: 40 residues processed: 503 average time/residue: 0.5987 time to fit residues: 365.3504 Evaluate side-chains 418 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 360 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 146 LYS Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS 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 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 B residue 151 GLU Chi-restraints excluded: chain B residue 282 ILE 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 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 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 115 LEU Chi-restraints excluded: chain C residue 128 SER 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 79 LEU 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 307 THR Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 52 LEU 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 O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL 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 305 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 370 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 127 optimal weight: 0.0060 chunk 396 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 203 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-642 HIS B 386 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 288 HIS R 232 GLN O 130 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 = 0.4089 r_free = 0.4089 target = 0.173431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118812 restraints weight = 46194.534| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.14 r_work: 0.3178 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35309 Z= 0.219 Angle : 0.662 9.745 48098 Z= 0.341 Chirality : 0.047 0.467 5316 Planarity : 0.005 0.104 6196 Dihedral : 5.704 75.373 4814 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 4.38 % Allowed : 13.44 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.12), residues: 4408 helix: 0.88 (0.23), residues: 569 sheet: -0.67 (0.13), residues: 1476 loop : -1.46 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 103 TYR 0.027 0.002 TYR O 308 PHE 0.017 0.002 PHE A 148 TRP 0.055 0.002 TRP J-764 HIS 0.008 0.001 HIS N 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (35244) covalent geometry : angle 0.65907 / 0.34 (47968) SS BOND : bond 0.00380 / 0.25 ( 65) SS BOND : angle 1.43399 / 0.87 ( 130) hydrogen bonds : bond 0.03427 / 2.25 ( 1017) hydrogen bonds : angle 5.21745 / 3.56 ( 2625) *********************** 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 545 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 380 time to evaluate : 1.124 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: 0.5663 (OUTLIER) cc_final: 0.5434 (ppp) REVERT: K 151 MET cc_start: 0.8298 (mmp) cc_final: 0.7622 (mmp) REVERT: K 153 VAL cc_start: 0.8957 (t) cc_final: 0.8610 (p) REVERT: K 215 THR cc_start: 0.8650 (p) cc_final: 0.8408 (t) REVERT: K 223 LYS cc_start: 0.8793 (tppt) cc_final: 0.8552 (tppt) REVERT: K 226 SER cc_start: 0.8497 (t) cc_final: 0.7636 (m) REVERT: K 257 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7996 (ptp) REVERT: K 270 GLU cc_start: 0.8097 (tt0) cc_final: 0.7507 (pm20) REVERT: S 120 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5912 (mpt) REVERT: S 131 MET cc_start: 0.6974 (mmm) cc_final: 0.6764 (mmm) REVERT: S 169 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7111 (mtmt) REVERT: S 251 THR cc_start: 0.7842 (p) cc_final: 0.7604 (t) REVERT: S 257 MET cc_start: 0.7526 (ptp) cc_final: 0.7324 (ptp) REVERT: G 10 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: G 99 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: G 293 THR cc_start: 0.8286 (m) cc_final: 0.7943 (t) REVERT: H 57 ASP cc_start: 0.7263 (p0) cc_final: 0.7027 (p0) REVERT: J -768 GLN cc_start: 0.8550 (mt0) cc_final: 0.8023 (tt0) REVERT: J -687 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: J -609 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6674 (ttm170) REVERT: J -588 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6778 (mp) REVERT: B 10 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 97 ASP cc_start: 0.8019 (m-30) cc_final: 0.7718 (p0) REVERT: B 282 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6755 (tp) REVERT: T 23 TYR cc_start: 0.5970 (t80) cc_final: 0.5349 (t80) REVERT: Q 4 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: Q 74 ILE cc_start: 0.8830 (mt) cc_final: 0.8546 (mp) REVERT: Q 130 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8798 (mtmm) REVERT: Q 137 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: Q 144 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8159 (mt-10) REVERT: Q 159 GLN cc_start: 0.8409 (tt0) cc_final: 0.7924 (tp40) REVERT: Q 213 LYS cc_start: 0.7922 (mttt) cc_final: 0.7365 (mmtp) REVERT: A 118 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5521 (pmm) REVERT: A 146 LYS cc_start: 0.4865 (OUTLIER) cc_final: 0.4496 (ptpt) REVERT: A 184 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6424 (mpt) REVERT: F 176 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5911 (tm-30) REVERT: F 190 LYS cc_start: 0.8304 (mtmt) cc_final: 0.8103 (mmmt) REVERT: F 195 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6162 (pttm) REVERT: F 257 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5585 (ptm) REVERT: C 140 HIS cc_start: 0.7338 (m90) cc_final: 0.6942 (m90) REVERT: C 160 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7692 (ttmt) REVERT: C 364 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: C 375 THR cc_start: 0.8627 (m) cc_final: 0.8410 (t) REVERT: C 377 LYS cc_start: 0.7314 (ttpt) cc_final: 0.7095 (tttm) REVERT: E 38 SER cc_start: 0.8875 (t) cc_final: 0.8520 (m) REVERT: R 6 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7035 (t80) REVERT: R 8 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: R 60 ASN cc_start: 0.7077 (m110) cc_final: 0.6762 (m110) REVERT: R 323 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: R 360 TYR cc_start: 0.8744 (t80) cc_final: 0.8353 (t80) REVERT: R 402 LEU cc_start: 0.7338 (mt) cc_final: 0.7063 (mp) REVERT: M 36 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8674 (ttt) REVERT: N 66 MET cc_start: 0.9384 (ttt) cc_final: 0.9175 (ttt) REVERT: N 160 ASN cc_start: 0.7358 (t0) cc_final: 0.6865 (t0) REVERT: N 201 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7092 (tm-30) REVERT: N 365 MET cc_start: 0.8706 (ttt) cc_final: 0.7559 (pmt) REVERT: O 2 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: O 18 ILE cc_start: 0.9009 (pt) cc_final: 0.8781 (pp) REVERT: O 175 ARG cc_start: 0.8522 (ttt-90) cc_final: 0.8168 (ttp-110) outliers start: 165 outliers final: 78 residues processed: 491 average time/residue: 0.5477 time to fit residues: 328.6708 Evaluate side-chains 452 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 348 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL 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 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 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 371 THR 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 J residue -588 LEU 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 282 ILE 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 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 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 221 THR Chi-restraints excluded: chain Q residue 233 ASN 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 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 176 GLU 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 364 GLU 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 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 36 MET Chi-restraints excluded: chain M residue 52 LEU 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 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 80 VAL Chi-restraints excluded: chain O residue 82 THR 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 126 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 287 optimal weight: 7.9990 chunk 415 optimal weight: 0.6980 chunk 397 optimal weight: 2.9990 chunk 398 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-767 ASN J-642 HIS Q 60 ASN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS O 130 GLN O 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121712 restraints weight = 46363.944| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.41 r_work: 0.3220 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35309 Z= 0.109 Angle : 0.583 9.878 48098 Z= 0.300 Chirality : 0.044 0.466 5316 Planarity : 0.005 0.069 6196 Dihedral : 5.345 75.921 4814 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 3.37 % Allowed : 14.72 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 4408 helix: 1.35 (0.24), residues: 545 sheet: -0.53 (0.13), residues: 1460 loop : -1.30 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 88 TYR 0.024 0.001 TYR O 308 PHE 0.017 0.001 PHE A 148 TRP 0.051 0.001 TRP J-764 HIS 0.004 0.001 HIS J-832 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (35244) covalent geometry : angle 0.58093 / 0.30 (47968) SS BOND : bond 0.00226 / 0.15 ( 65) SS BOND : angle 1.04612 / 0.64 ( 130) hydrogen bonds : bond 0.02902 / 1.88 ( 1017) hydrogen bonds : angle 5.01597 / 3.42 ( 2625) *********************** 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 511 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 384 time to evaluate : 1.242 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: 0.6106 (ptt) cc_final: 0.5885 (ppp) REVERT: K 151 MET cc_start: 0.8140 (mmp) cc_final: 0.7603 (mmp) REVERT: K 153 VAL cc_start: 0.8879 (t) cc_final: 0.8513 (p) REVERT: K 223 LYS cc_start: 0.8768 (tppt) cc_final: 0.8513 (tppt) REVERT: K 226 SER cc_start: 0.8486 (t) cc_final: 0.7618 (m) REVERT: K 270 GLU cc_start: 0.8032 (tt0) cc_final: 0.7492 (pm20) REVERT: S 120 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5846 (mpt) REVERT: S 135 LYS cc_start: 0.6761 (mptt) cc_final: 0.6432 (mmtp) REVERT: S 251 THR cc_start: 0.7848 (p) cc_final: 0.7620 (t) REVERT: G 293 THR cc_start: 0.8146 (m) cc_final: 0.7915 (t) REVERT: G 361 ILE cc_start: 0.7844 (mt) cc_final: 0.7566 (tt) REVERT: G 370 CYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7336 (m) REVERT: H 57 ASP cc_start: 0.7268 (p0) cc_final: 0.7031 (p0) REVERT: J -768 GLN cc_start: 0.8463 (mt0) cc_final: 0.7939 (tt0) REVERT: J -709 ASN cc_start: 0.8765 (p0) cc_final: 0.8557 (p0) REVERT: J -687 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: J -609 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6731 (ttm170) REVERT: B 7 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7937 (ttp) REVERT: B 10 GLN cc_start: 0.8309 (tt0) cc_final: 0.8048 (tt0) REVERT: B 97 ASP cc_start: 0.8158 (m-30) cc_final: 0.7858 (p0) REVERT: B 99 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: B 282 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6537 (tp) REVERT: B 433 MET cc_start: 0.5901 (ppp) cc_final: 0.5053 (ptm) REVERT: T 23 TYR cc_start: 0.5732 (t80) cc_final: 0.5021 (t80) REVERT: Q 4 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: Q 74 ILE cc_start: 0.8772 (mt) cc_final: 0.8448 (mp) REVERT: Q 130 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8769 (mtmm) REVERT: Q 137 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: Q 159 GLN cc_start: 0.8375 (tt0) cc_final: 0.7988 (tp40) REVERT: Q 213 LYS cc_start: 0.7706 (mttt) cc_final: 0.7216 (mmtp) REVERT: A 118 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6056 (pmm) REVERT: A 184 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6248 (mpt) REVERT: F 176 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: C 72 TYR cc_start: 0.8546 (m-80) cc_final: 0.8168 (m-80) REVERT: C 140 HIS cc_start: 0.7358 (m90) cc_final: 0.6774 (m90) REVERT: C 160 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7664 (ttmt) REVERT: C 281 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8856 (t70) REVERT: C 327 LYS cc_start: 0.8548 (ptmm) cc_final: 0.8149 (tttp) REVERT: C 364 GLU cc_start: 0.8149 (tp30) cc_final: 0.7699 (tp30) REVERT: E 38 SER cc_start: 0.8931 (t) cc_final: 0.8619 (m) REVERT: R 6 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7102 (t80) REVERT: R 8 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: R 60 ASN cc_start: 0.7099 (m110) cc_final: 0.6741 (m110) REVERT: R 70 MET cc_start: 0.8536 (tpt) cc_final: 0.8262 (mmm) REVERT: R 111 THR cc_start: 0.8431 (m) cc_final: 0.7979 (m) REVERT: R 197 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7152 (pt) REVERT: R 216 GLN cc_start: 0.7793 (tt0) cc_final: 0.7491 (tm-30) REVERT: R 323 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: R 360 TYR cc_start: 0.8725 (t80) cc_final: 0.8383 (t80) REVERT: R 398 THR cc_start: 0.7327 (m) cc_final: 0.7088 (m) REVERT: R 402 LEU cc_start: 0.7298 (mt) cc_final: 0.7033 (mp) REVERT: M 36 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8569 (ttt) REVERT: N 66 MET cc_start: 0.9316 (ttt) cc_final: 0.8994 (ttt) REVERT: N 160 ASN cc_start: 0.7990 (t0) cc_final: 0.7355 (t0) REVERT: N 365 MET cc_start: 0.8730 (ttt) cc_final: 0.7588 (pmt) REVERT: O 2 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: O 175 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8176 (ttp-110) outliers start: 127 outliers final: 56 residues processed: 468 average time/residue: 0.5912 time to fit residues: 336.7810 Evaluate side-chains 422 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 346 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 120 MET 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 168 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS 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 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER 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 186 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 233 ASN 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 F residue 119 VAL Chi-restraints excluded: chain F residue 176 GLU 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 179 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 370 CYS 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 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 36 MET Chi-restraints excluded: chain M residue 52 LEU 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 42 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 176 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 381 optimal weight: 0.7980 chunk 417 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 316 optimal weight: 0.0020 chunk 116 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-767 ASN B 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.177069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.123054 restraints weight = 46209.315| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.24 r_work: 0.3242 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35309 Z= 0.103 Angle : 0.578 10.305 48098 Z= 0.296 Chirality : 0.044 0.497 5316 Planarity : 0.004 0.067 6196 Dihedral : 5.104 76.720 4811 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 3.03 % Allowed : 15.62 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4408 helix: 1.63 (0.24), residues: 542 sheet: -0.31 (0.14), residues: 1400 loop : -1.19 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 88 TYR 0.022 0.001 TYR O 308 PHE 0.021 0.001 PHE R 217 TRP 0.055 0.001 TRP J-764 HIS 0.004 0.001 HIS R 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (35244) covalent geometry : angle 0.57545 / 0.29 (47968) SS BOND : bond 0.00205 / 0.14 ( 65) SS BOND : angle 1.20171 / 0.73 ( 130) hydrogen bonds : bond 0.02750 / 1.78 ( 1017) hydrogen bonds : angle 4.87709 / 3.32 ( 2625) *********************** 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 485 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 371 time to evaluate : 1.153 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: K 118 MET cc_start: 0.6144 (ptt) cc_final: 0.5910 (ppp) REVERT: K 126 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6953 (ptpt) REVERT: K 132 LEU cc_start: 0.8473 (tp) cc_final: 0.8149 (mt) REVERT: K 151 MET cc_start: 0.8030 (mmp) cc_final: 0.7574 (mmp) REVERT: K 153 VAL cc_start: 0.8802 (t) cc_final: 0.8321 (p) REVERT: K 223 LYS cc_start: 0.8682 (tppt) cc_final: 0.8477 (tppt) REVERT: K 226 SER cc_start: 0.8470 (t) cc_final: 0.7658 (m) REVERT: K 257 MET cc_start: 0.8428 (ptt) cc_final: 0.8012 (ptp) REVERT: K 270 GLU cc_start: 0.8020 (tt0) cc_final: 0.7441 (pm20) REVERT: S 120 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6436 (mpt) REVERT: S 131 MET cc_start: 0.6902 (mmm) cc_final: 0.5423 (mpt) REVERT: S 251 THR cc_start: 0.7649 (p) cc_final: 0.7436 (t) REVERT: G 293 THR cc_start: 0.8053 (m) cc_final: 0.7837 (t) REVERT: G 319 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7270 (tptp) REVERT: G 361 ILE cc_start: 0.7776 (mt) cc_final: 0.7507 (tt) REVERT: G 366 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8041 (ttp80) REVERT: G 370 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7350 (m) REVERT: H 57 ASP cc_start: 0.7203 (p0) cc_final: 0.6943 (p0) REVERT: J -833 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8065 (ptm) REVERT: J -799 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8583 (tm-30) REVERT: J -768 GLN cc_start: 0.8470 (mt0) cc_final: 0.7991 (tt0) REVERT: J -687 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: J -609 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6661 (ttm170) REVERT: B 10 GLN cc_start: 0.8278 (tt0) cc_final: 0.8015 (tt0) REVERT: B 29 ILE cc_start: 0.7558 (mt) cc_final: 0.7212 (mm) REVERT: B 97 ASP cc_start: 0.8094 (m-30) cc_final: 0.7765 (p0) REVERT: B 99 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: B 364 GLU cc_start: 0.7575 (pt0) cc_final: 0.7049 (pp20) REVERT: T 23 TYR cc_start: 0.5810 (t80) cc_final: 0.5120 (t80) REVERT: Q 4 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: Q 130 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8771 (mtmm) REVERT: Q 137 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: Q 159 GLN cc_start: 0.8351 (tt0) cc_final: 0.8005 (tp40) REVERT: Q 167 MET cc_start: 0.7998 (mmt) cc_final: 0.7123 (mmt) REVERT: Q 213 LYS cc_start: 0.7581 (mttt) cc_final: 0.7062 (mmtp) REVERT: A 118 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6341 (pmm) REVERT: A 120 MET cc_start: 0.5956 (pmm) cc_final: 0.5556 (pmm) REVERT: A 184 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6251 (mpt) REVERT: A 265 VAL cc_start: 0.7511 (t) cc_final: 0.7142 (p) REVERT: F 190 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8313 (mtmt) REVERT: C 72 TYR cc_start: 0.8566 (m-80) cc_final: 0.8238 (m-80) REVERT: C 73 ARG cc_start: 0.7588 (mtp180) cc_final: 0.7370 (mtt-85) REVERT: C 140 HIS cc_start: 0.7402 (m90) cc_final: 0.7006 (m90) REVERT: C 281 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8840 (t70) REVERT: C 289 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7475 (mtm110) REVERT: C 364 GLU cc_start: 0.8145 (tp30) cc_final: 0.7590 (tp30) REVERT: R 6 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.7023 (t80) REVERT: R 8 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: R 60 ASN cc_start: 0.7044 (m110) cc_final: 0.6708 (m110) REVERT: R 197 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7122 (pt) REVERT: R 216 GLN cc_start: 0.7687 (tt0) cc_final: 0.7480 (tm-30) REVERT: R 323 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: R 360 TYR cc_start: 0.8747 (t80) cc_final: 0.8457 (t80) REVERT: R 398 THR cc_start: 0.7304 (m) cc_final: 0.7068 (m) REVERT: R 402 LEU cc_start: 0.7233 (mt) cc_final: 0.6956 (mp) REVERT: M 36 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8659 (ttt) REVERT: N 66 MET cc_start: 0.9304 (ttp) cc_final: 0.9005 (ttt) REVERT: N 160 ASN cc_start: 0.7764 (t0) cc_final: 0.7276 (t0) REVERT: N 365 MET cc_start: 0.8666 (ttt) cc_final: 0.7599 (pmt) REVERT: O 2 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8312 (mm-30) REVERT: O 175 ARG cc_start: 0.8490 (ttt-90) cc_final: 0.8147 (ttp-110) outliers start: 114 outliers final: 56 residues processed: 444 average time/residue: 0.5590 time to fit residues: 303.2882 Evaluate side-chains 420 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 345 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS 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 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -833 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 B residue 99 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain Q residue 4 GLU 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 194 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN 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 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 119 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 234 THR Chi-restraints excluded: chain C residue 281 ASP 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 291 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 52 LEU 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 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 327 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 57 optimal weight: 1.9990 chunk 356 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 391 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 396 optimal weight: 0.0170 chunk 295 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-920 HIS J-919 GLN J-848 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN R 232 GLN R 353 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121166 restraints weight = 46330.487| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.35 r_work: 0.3219 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35309 Z= 0.128 Angle : 0.589 10.370 48098 Z= 0.301 Chirality : 0.045 0.481 5316 Planarity : 0.005 0.067 6196 Dihedral : 5.118 78.340 4811 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 3.00 % Allowed : 15.99 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4408 helix: 1.75 (0.24), residues: 541 sheet: -0.21 (0.14), residues: 1298 loop : -1.14 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 120 TYR 0.022 0.001 TYR O 308 PHE 0.024 0.001 PHE R 217 TRP 0.032 0.001 TRP J-764 HIS 0.005 0.001 HIS R 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (35244) covalent geometry : angle 0.58693 / 0.30 (47968) SS BOND : bond 0.00223 / 0.15 ( 65) SS BOND : angle 1.20116 / 0.74 ( 130) hydrogen bonds : bond 0.02819 / 1.83 ( 1017) hydrogen bonds : angle 4.81109 / 3.28 ( 2625) *********************** 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 485 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 372 time to evaluate : 1.351 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: K 118 MET cc_start: 0.6108 (ptt) cc_final: 0.5786 (ppp) REVERT: K 126 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7038 (ptpt) REVERT: K 151 MET cc_start: 0.8019 (mmp) cc_final: 0.7642 (mmp) REVERT: K 153 VAL cc_start: 0.8825 (t) cc_final: 0.8428 (p) REVERT: K 226 SER cc_start: 0.8612 (t) cc_final: 0.7751 (m) REVERT: K 270 GLU cc_start: 0.7999 (tt0) cc_final: 0.7469 (pm20) REVERT: S 120 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6579 (mpt) REVERT: S 131 MET cc_start: 0.6960 (mmm) cc_final: 0.6753 (mmm) REVERT: S 251 THR cc_start: 0.7782 (p) cc_final: 0.7562 (t) REVERT: G 293 THR cc_start: 0.8086 (m) cc_final: 0.7858 (t) REVERT: G 361 ILE cc_start: 0.7880 (mt) cc_final: 0.7581 (tt) REVERT: G 370 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7322 (m) REVERT: H 57 ASP cc_start: 0.7194 (p0) cc_final: 0.6939 (p0) REVERT: I 33 MET cc_start: 0.5508 (ttp) cc_final: 0.4748 (ttm) REVERT: J -979 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8277 (tpt-90) REVERT: J -799 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8507 (tm-30) REVERT: J -768 GLN cc_start: 0.8490 (mt0) cc_final: 0.8034 (tt0) REVERT: J -687 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: J -609 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6688 (ttm170) REVERT: B 7 MET cc_start: 0.8393 (ttp) cc_final: 0.8045 (ptt) REVERT: B 10 GLN cc_start: 0.8264 (tt0) cc_final: 0.8044 (tt0) REVERT: B 29 ILE cc_start: 0.7618 (mt) cc_final: 0.7290 (mm) REVERT: B 97 ASP cc_start: 0.8096 (m-30) cc_final: 0.7774 (p0) REVERT: B 99 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: B 282 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6381 (tp) REVERT: B 305 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5662 (mt-10) REVERT: T 23 TYR cc_start: 0.5980 (t80) cc_final: 0.5397 (t80) REVERT: Q 4 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: Q 137 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: Q 159 GLN cc_start: 0.8348 (tt0) cc_final: 0.8010 (tp40) REVERT: Q 213 LYS cc_start: 0.7695 (mttt) cc_final: 0.7195 (mmtp) REVERT: A 118 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6444 (pmm) REVERT: A 120 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5746 (pmm) REVERT: A 184 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6308 (mpt) REVERT: C 72 TYR cc_start: 0.8545 (m-80) cc_final: 0.8142 (m-80) REVERT: C 73 ARG cc_start: 0.7619 (mtp180) cc_final: 0.7375 (mtt-85) REVERT: C 140 HIS cc_start: 0.7331 (m90) cc_final: 0.6944 (m90) REVERT: C 160 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7484 (mttm) REVERT: C 281 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8846 (t70) REVERT: C 289 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7255 (mtm110) REVERT: C 327 LYS cc_start: 0.8559 (ptmm) cc_final: 0.8018 (tttp) REVERT: C 411 THR cc_start: 0.7855 (m) cc_final: 0.7415 (p) REVERT: R 8 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: R 70 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8267 (mmm) REVERT: R 197 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7147 (pt) REVERT: R 232 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: R 323 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: R 360 TYR cc_start: 0.8753 (t80) cc_final: 0.8453 (t80) REVERT: R 397 LEU cc_start: 0.7052 (mt) cc_final: 0.6715 (mp) REVERT: R 402 LEU cc_start: 0.7253 (mt) cc_final: 0.6953 (mp) REVERT: N 20 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8160 (mp) REVERT: N 66 MET cc_start: 0.9347 (ttp) cc_final: 0.9070 (ttt) REVERT: N 160 ASN cc_start: 0.7947 (t0) cc_final: 0.7198 (t0) REVERT: N 187 THR cc_start: 0.8061 (m) cc_final: 0.7605 (p) REVERT: N 365 MET cc_start: 0.8642 (ttt) cc_final: 0.7587 (pmt) REVERT: O 2 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: O 18 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8507 (pp) REVERT: O 175 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8141 (ttp-110) outliers start: 113 outliers final: 64 residues processed: 443 average time/residue: 0.5879 time to fit residues: 319.1856 Evaluate side-chains 437 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 350 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 120 MET 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 256 VAL Chi-restraints excluded: chain G residue 63 CYS 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 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain J residue -979 ARG 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 -709 ASN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 99 GLU 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 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 148 GLU 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 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 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 A residue 257 MET 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 234 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 70 MET 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 232 GLN 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 20 ILE 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 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 213 LEU 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 373 optimal weight: 10.0000 chunk 245 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 415 optimal weight: 3.9990 chunk 277 optimal weight: 0.0670 chunk 427 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 64 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 414 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-919 GLN J-709 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 HIS Q 233 ASN A 159 ASN C 396 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.176893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122836 restraints weight = 46411.961| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.27 r_work: 0.3247 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35309 Z= 0.102 Angle : 0.571 11.932 48098 Z= 0.291 Chirality : 0.044 0.470 5316 Planarity : 0.004 0.069 6196 Dihedral : 4.974 77.970 4811 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 2.60 % Allowed : 16.76 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4408 helix: 1.59 (0.24), residues: 560 sheet: -0.07 (0.15), residues: 1270 loop : -1.08 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 88 TYR 0.020 0.001 TYR O 308 PHE 0.027 0.001 PHE R 217 TRP 0.048 0.001 TRP J-764 HIS 0.006 0.001 HIS R 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (35244) covalent geometry : angle 0.56926 / 0.29 (47968) SS BOND : bond 0.00180 / 0.12 ( 65) SS BOND : angle 1.01587 / 0.63 ( 130) hydrogen bonds : bond 0.02665 / 1.72 ( 1017) hydrogen bonds : angle 4.72645 / 3.21 ( 2625) *********************** 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 465 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 367 time to evaluate : 1.231 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: 0.6120 (ptt) cc_final: 0.5794 (ppp) REVERT: K 126 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7045 (ptpt) REVERT: K 132 LEU cc_start: 0.8467 (tp) cc_final: 0.8227 (mt) REVERT: K 151 MET cc_start: 0.7934 (mmp) cc_final: 0.7557 (mmp) REVERT: K 153 VAL cc_start: 0.8722 (t) cc_final: 0.8276 (p) REVERT: K 208 GLN cc_start: 0.7544 (pm20) cc_final: 0.6914 (pm20) REVERT: K 226 SER cc_start: 0.8478 (t) cc_final: 0.7635 (m) REVERT: K 257 MET cc_start: 0.8440 (ptt) cc_final: 0.8017 (ptp) REVERT: K 270 GLU cc_start: 0.7966 (tt0) cc_final: 0.7455 (pm20) REVERT: S 120 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6583 (mpt) REVERT: S 131 MET cc_start: 0.7007 (mmm) cc_final: 0.6758 (mmm) REVERT: S 251 THR cc_start: 0.7590 (p) cc_final: 0.7381 (t) REVERT: G 99 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: G 293 THR cc_start: 0.8114 (m) cc_final: 0.7883 (t) REVERT: G 361 ILE cc_start: 0.7755 (mt) cc_final: 0.7470 (tt) REVERT: G 370 CYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7173 (m) REVERT: H 57 ASP cc_start: 0.7161 (p0) cc_final: 0.6913 (p0) REVERT: I 33 MET cc_start: 0.5564 (ttp) cc_final: 0.5212 (ttt) REVERT: J -979 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8209 (tpt-90) REVERT: J -833 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.8004 (ptm) REVERT: J -799 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8492 (tm-30) REVERT: J -783 PHE cc_start: 0.8461 (m-80) cc_final: 0.8260 (m-80) REVERT: J -768 GLN cc_start: 0.8479 (mt0) cc_final: 0.7957 (tt0) REVERT: J -609 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6645 (ttm170) REVERT: B 7 MET cc_start: 0.8325 (ttp) cc_final: 0.8063 (ptt) REVERT: B 10 GLN cc_start: 0.8257 (tt0) cc_final: 0.8042 (tt0) REVERT: B 97 ASP cc_start: 0.8102 (m-30) cc_final: 0.7766 (p0) REVERT: B 99 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: B 282 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6391 (tp) REVERT: B 305 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5742 (mt-10) REVERT: D 57 ASP cc_start: 0.7938 (t70) cc_final: 0.7659 (t0) REVERT: T 23 TYR cc_start: 0.5766 (t80) cc_final: 0.5246 (t80) REVERT: Q 137 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: Q 159 GLN cc_start: 0.8368 (tt0) cc_final: 0.8021 (tp40) REVERT: Q 213 LYS cc_start: 0.7552 (mttt) cc_final: 0.7015 (mmtp) REVERT: A 118 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6562 (pmm) REVERT: A 120 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5781 (pmm) REVERT: A 151 MET cc_start: 0.7289 (mtt) cc_final: 0.7089 (mtt) REVERT: A 184 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6299 (mpt) REVERT: F 190 LYS cc_start: 0.8624 (mmpt) cc_final: 0.8348 (mppt) REVERT: F 257 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5553 (pmm) REVERT: C 72 TYR cc_start: 0.8567 (m-80) cc_final: 0.8189 (m-80) REVERT: C 73 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7350 (mtt-85) REVERT: C 97 ASP cc_start: 0.7476 (m-30) cc_final: 0.7125 (p0) REVERT: C 140 HIS cc_start: 0.7331 (m90) cc_final: 0.6956 (m90) REVERT: C 160 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7488 (mttm) REVERT: C 281 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8845 (t70) REVERT: C 289 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7744 (ttp80) REVERT: C 364 GLU cc_start: 0.8023 (tp30) cc_final: 0.7607 (tp30) REVERT: C 379 ASP cc_start: 0.7288 (m-30) cc_final: 0.7074 (m-30) REVERT: C 411 THR cc_start: 0.7896 (m) cc_final: 0.7443 (p) REVERT: R 8 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: R 323 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: R 360 TYR cc_start: 0.8734 (t80) cc_final: 0.8490 (t80) REVERT: R 397 LEU cc_start: 0.7023 (mt) cc_final: 0.6657 (mp) REVERT: R 402 LEU cc_start: 0.7203 (mt) cc_final: 0.6896 (mp) REVERT: N 20 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8115 (mt) REVERT: N 66 MET cc_start: 0.9335 (ttp) cc_final: 0.9064 (ttt) REVERT: N 365 MET cc_start: 0.8645 (ttt) cc_final: 0.7587 (pmt) REVERT: O 2 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: O 18 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8452 (pp) REVERT: O 175 ARG cc_start: 0.8473 (ttt-90) cc_final: 0.8168 (ttp-110) outliers start: 98 outliers final: 60 residues processed: 435 average time/residue: 0.6081 time to fit residues: 322.8036 Evaluate side-chains 436 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 355 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain S residue 120 MET 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 257 MET 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 213 LEU 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 62 LYS Chi-restraints excluded: chain J residue -979 ARG Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -833 MET Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 ASP 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 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 148 GLU Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 221 THR 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 121 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 256 VAL Chi-restraints excluded: chain F residue 257 MET 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 402 VAL Chi-restraints excluded: chain C residue 433 MET 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 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 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 20 ILE 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 O residue 2 GLU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 346 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 310 optimal weight: 0.9990 chunk 380 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 367 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 376 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 ASN A 159 ASN C 222 GLN R 232 GLN R 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.176576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122558 restraints weight = 46260.134| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.25 r_work: 0.3241 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3951 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= 0.114 Angle : 0.581 11.660 48098 Z= 0.295 Chirality : 0.044 0.463 5316 Planarity : 0.004 0.070 6196 Dihedral : 4.949 77.985 4811 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 2.44 % Allowed : 17.35 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4408 helix: 1.63 (0.24), residues: 560 sheet: -0.01 (0.15), residues: 1264 loop : -1.07 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 88 TYR 0.027 0.001 TYR G 122 PHE 0.021 0.001 PHE R 217 TRP 0.035 0.001 TRP J-764 HIS 0.006 0.001 HIS R 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (35244) covalent geometry : angle 0.57951 / 0.29 (47968) SS BOND : bond 0.00197 / 0.13 ( 65) SS BOND : angle 1.04746 / 0.65 ( 130) hydrogen bonds : bond 0.02722 / 1.76 ( 1017) hydrogen bonds : angle 4.70449 / 3.20 ( 2625) *********************** REFINEMENT MACRO_CYCLE 9 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 462 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 370 time to evaluate : 1.241 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: 0.6123 (ptt) cc_final: 0.5801 (ppp) REVERT: K 126 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7088 (ptpt) REVERT: K 132 LEU cc_start: 0.8441 (tp) cc_final: 0.8199 (mt) REVERT: K 151 MET cc_start: 0.7945 (mmp) cc_final: 0.7579 (mmp) REVERT: K 215 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8352 (t) REVERT: K 226 SER cc_start: 0.8523 (t) cc_final: 0.7698 (m) REVERT: K 270 GLU cc_start: 0.8000 (tt0) cc_final: 0.7479 (pm20) REVERT: S 120 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6737 (mpt) REVERT: S 131 MET cc_start: 0.7032 (mmm) cc_final: 0.6806 (mmm) REVERT: G 99 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: G 293 THR cc_start: 0.8136 (m) cc_final: 0.7899 (t) REVERT: G 361 ILE cc_start: 0.7795 (mt) cc_final: 0.7508 (tt) REVERT: G 370 CYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7245 (m) REVERT: H 57 ASP cc_start: 0.7176 (p0) cc_final: 0.6930 (p0) REVERT: I 33 MET cc_start: 0.5514 (ttp) cc_final: 0.5186 (ttt) REVERT: J -979 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8192 (tpt-90) REVERT: J -799 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8483 (tm-30) REVERT: J -768 GLN cc_start: 0.8474 (mt0) cc_final: 0.7980 (tt0) REVERT: J -609 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6665 (ttm170) REVERT: B 7 MET cc_start: 0.8261 (ttp) cc_final: 0.8009 (ptt) REVERT: B 88 MET cc_start: 0.8552 (mtt) cc_final: 0.8329 (mtm) REVERT: B 99 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: B 282 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6410 (tp) REVERT: B 305 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5696 (mt-10) REVERT: D 57 ASP cc_start: 0.7952 (t70) cc_final: 0.7679 (t0) REVERT: T 23 TYR cc_start: 0.5752 (t80) cc_final: 0.5481 (t80) REVERT: Q 4 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: Q 108 ASP cc_start: 0.8639 (p0) cc_final: 0.8392 (p0) REVERT: Q 137 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: Q 159 GLN cc_start: 0.8365 (tt0) cc_final: 0.8024 (tp40) REVERT: Q 213 LYS cc_start: 0.7555 (mttt) cc_final: 0.7027 (mmtp) REVERT: A 118 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6436 (pmm) REVERT: A 120 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5809 (pmm) REVERT: A 151 MET cc_start: 0.7316 (mtt) cc_final: 0.7101 (mtt) REVERT: A 261 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7129 (pttt) REVERT: F 190 LYS cc_start: 0.8631 (mmpt) cc_final: 0.8381 (mppt) REVERT: F 257 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5625 (pmm) REVERT: C 72 TYR cc_start: 0.8560 (m-80) cc_final: 0.8177 (m-80) REVERT: C 73 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7345 (mtt-85) REVERT: C 97 ASP cc_start: 0.7499 (m-30) cc_final: 0.7147 (p0) REVERT: C 140 HIS cc_start: 0.7327 (m90) cc_final: 0.6938 (m90) REVERT: C 160 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7358 (mttm) REVERT: C 281 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8829 (t70) REVERT: C 289 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7620 (ttp80) REVERT: C 327 LYS cc_start: 0.8550 (ptmm) cc_final: 0.8014 (tttp) REVERT: C 364 GLU cc_start: 0.7991 (tp30) cc_final: 0.7562 (tp30) REVERT: C 379 ASP cc_start: 0.7276 (m-30) cc_final: 0.7062 (m-30) REVERT: C 411 THR cc_start: 0.7887 (m) cc_final: 0.7442 (p) REVERT: R 8 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: R 70 MET cc_start: 0.8502 (tpt) cc_final: 0.8230 (mmm) REVERT: R 111 THR cc_start: 0.8403 (m) cc_final: 0.7920 (m) REVERT: R 197 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7108 (pt) REVERT: R 323 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: R 354 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7758 (mt-10) REVERT: R 360 TYR cc_start: 0.8736 (t80) cc_final: 0.8490 (t80) REVERT: R 397 LEU cc_start: 0.6842 (mt) cc_final: 0.6458 (mp) REVERT: R 402 LEU cc_start: 0.7249 (mt) cc_final: 0.6938 (mp) REVERT: N 34 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8801 (mm-30) REVERT: N 66 MET cc_start: 0.9357 (ttp) cc_final: 0.9048 (ttt) REVERT: N 187 THR cc_start: 0.8022 (m) cc_final: 0.7602 (p) REVERT: N 365 MET cc_start: 0.8632 (ttt) cc_final: 0.7593 (pmt) REVERT: O 2 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8246 (mm-30) REVERT: O 175 ARG cc_start: 0.8503 (ttt-90) cc_final: 0.8206 (ttp-110) outliers start: 92 outliers final: 59 residues processed: 432 average time/residue: 0.5893 time to fit residues: 310.5121 Evaluate side-chains 428 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 349 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 257 MET 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 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 62 LYS Chi-restraints excluded: chain J residue -979 ARG Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 ASP 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 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 148 GLU 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 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 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 F residue 257 MET 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 402 VAL Chi-restraints excluded: chain C residue 433 MET 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 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 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 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 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 213 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 230 optimal weight: 8.9990 chunk 418 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 387 optimal weight: 0.9990 chunk 278 optimal weight: 0.0570 chunk 241 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 396 GLN Q 132 ASN Q 233 ASN C 222 GLN R 232 GLN O 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.178088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124634 restraints weight = 46523.743| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.62 r_work: 0.3259 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35309 Z= 0.097 Angle : 0.567 12.976 48098 Z= 0.288 Chirality : 0.044 0.441 5316 Planarity : 0.004 0.073 6196 Dihedral : 4.806 78.218 4811 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 2.21 % Allowed : 17.75 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4408 helix: 1.68 (0.24), residues: 560 sheet: 0.09 (0.15), residues: 1252 loop : -1.01 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 120 TYR 0.021 0.001 TYR J-637 PHE 0.018 0.001 PHE C 95 TRP 0.060 0.001 TRP J-764 HIS 0.007 0.001 HIS Q 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (35244) covalent geometry : angle 0.56530 / 0.29 (47968) SS BOND : bond 0.00171 / 0.12 ( 65) SS BOND : angle 0.94265 / 0.59 ( 130) hydrogen bonds : bond 0.02571 / 1.66 ( 1017) hydrogen bonds : angle 4.63032 / 3.14 ( 2625) ********************** REFINEMENT MACRO_CYCLE 10 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 462 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 379 time to evaluate : 1.386 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: 0.6113 (ptt) cc_final: 0.5808 (ppp) REVERT: K 131 MET cc_start: 0.8221 (mmt) cc_final: 0.7827 (mmm) REVERT: K 132 LEU cc_start: 0.8482 (tp) cc_final: 0.8174 (mt) REVERT: K 151 MET cc_start: 0.7941 (mmp) cc_final: 0.7576 (mmp) REVERT: K 208 GLN cc_start: 0.7898 (pm20) cc_final: 0.7622 (pm20) REVERT: K 215 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8377 (t) REVERT: K 226 SER cc_start: 0.8471 (t) cc_final: 0.7629 (m) REVERT: K 270 GLU cc_start: 0.8053 (tt0) cc_final: 0.7578 (pm20) REVERT: S 131 MET cc_start: 0.7055 (mmm) cc_final: 0.6796 (mmm) REVERT: G 99 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: G 361 ILE cc_start: 0.7776 (mt) cc_final: 0.7512 (tt) REVERT: G 370 CYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7165 (m) REVERT: H 57 ASP cc_start: 0.7147 (p0) cc_final: 0.6900 (p0) REVERT: I 33 MET cc_start: 0.5335 (ttp) cc_final: 0.5012 (ttt) REVERT: J -979 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8101 (tpt-90) REVERT: J -833 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7817 (ptt) REVERT: J -799 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8476 (tm-30) REVERT: J -768 GLN cc_start: 0.8491 (mt0) cc_final: 0.8043 (tt0) REVERT: J -609 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6652 (ttm170) REVERT: B 7 MET cc_start: 0.8289 (ttp) cc_final: 0.8077 (ptt) REVERT: B 27 LEU cc_start: 0.7475 (tp) cc_final: 0.7216 (tm) REVERT: B 99 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: B 282 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6419 (tp) REVERT: B 305 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5695 (mt-10) REVERT: D 57 ASP cc_start: 0.7930 (t70) cc_final: 0.7669 (t0) REVERT: Q 4 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: Q 108 ASP cc_start: 0.8621 (p0) cc_final: 0.8403 (p0) REVERT: Q 148 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: Q 159 GLN cc_start: 0.8376 (tt0) cc_final: 0.8064 (tp40) REVERT: Q 167 MET cc_start: 0.8133 (mtt) cc_final: 0.7933 (mtt) REVERT: Q 213 LYS cc_start: 0.7520 (mttt) cc_final: 0.7018 (mmtp) REVERT: Q 313 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8500 (mp0) REVERT: A 118 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6449 (pmm) REVERT: A 120 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5829 (pmm) REVERT: A 131 MET cc_start: 0.7699 (tpt) cc_final: 0.7458 (tpt) REVERT: A 261 LYS cc_start: 0.7465 (mmtt) cc_final: 0.7129 (pttt) REVERT: A 265 VAL cc_start: 0.7587 (t) cc_final: 0.7148 (p) REVERT: F 184 MET cc_start: 0.7286 (ptp) cc_final: 0.6736 (pmm) REVERT: F 257 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5686 (pmm) REVERT: C 72 TYR cc_start: 0.8496 (m-80) cc_final: 0.8184 (m-80) REVERT: C 97 ASP cc_start: 0.7505 (m-30) cc_final: 0.7163 (p0) REVERT: C 140 HIS cc_start: 0.7211 (m90) cc_final: 0.6957 (m90) REVERT: C 160 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7454 (mttm) REVERT: C 281 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8851 (t70) REVERT: C 289 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7650 (ttp80) REVERT: C 327 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8149 (tttp) REVERT: C 364 GLU cc_start: 0.8052 (tp30) cc_final: 0.7711 (tp30) REVERT: C 366 ARG cc_start: 0.8706 (ttp-170) cc_final: 0.8298 (ttp-170) REVERT: C 379 ASP cc_start: 0.7287 (m-30) cc_final: 0.7053 (m-30) REVERT: C 411 THR cc_start: 0.7974 (m) cc_final: 0.7536 (p) REVERT: R 8 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: R 70 MET cc_start: 0.8507 (tpt) cc_final: 0.8303 (mmm) REVERT: R 164 TYR cc_start: 0.8162 (m-80) cc_final: 0.7916 (m-80) REVERT: R 354 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7881 (mt-10) REVERT: R 402 LEU cc_start: 0.7279 (mt) cc_final: 0.6965 (mp) REVERT: N 20 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8236 (mt) REVERT: N 187 THR cc_start: 0.8143 (m) cc_final: 0.7664 (p) REVERT: N 365 MET cc_start: 0.8641 (ttt) cc_final: 0.7606 (pmt) REVERT: O 2 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8420 (mm-30) REVERT: O 175 ARG cc_start: 0.8539 (ttt-90) cc_final: 0.8252 (ttp-110) REVERT: O 327 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8311 (mttm) REVERT: O 409 TRP cc_start: 0.8670 (m100) cc_final: 0.8341 (m100) outliers start: 83 outliers final: 48 residues processed: 441 average time/residue: 0.5973 time to fit residues: 322.0635 Evaluate side-chains 430 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 363 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 211 ASN 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 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 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 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -979 ARG Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -833 MET Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU 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 148 GLU 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 A residue 118 MET Chi-restraints excluded: chain A residue 120 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 F residue 257 MET Chi-restraints excluded: chain F residue 263 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 402 VAL Chi-restraints excluded: chain C residue 433 MET 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 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE 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 O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 327 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 71 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 385 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 338 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 331 optimal weight: 0.0970 chunk 403 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** N 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.177934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124586 restraints weight = 46165.017| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.14 r_work: 0.3246 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35309 Z= 0.110 Angle : 0.572 12.231 48098 Z= 0.290 Chirality : 0.044 0.444 5316 Planarity : 0.004 0.072 6196 Dihedral : 4.822 78.919 4811 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 2.13 % Allowed : 17.88 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4408 helix: 1.69 (0.24), residues: 560 sheet: 0.09 (0.15), residues: 1259 loop : -0.98 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 120 TYR 0.028 0.001 TYR G 122 PHE 0.018 0.001 PHE C 95 TRP 0.051 0.001 TRP J-764 HIS 0.008 0.001 HIS R 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (35244) covalent geometry : angle 0.57048 / 0.29 (47968) SS BOND : bond 0.00186 / 0.12 ( 65) SS BOND : angle 0.98427 / 0.62 ( 130) hydrogen bonds : bond 0.02657 / 1.72 ( 1017) hydrogen bonds : angle 4.62985 / 3.15 ( 2625) =============================================================================== Job complete usr+sys time: 15607.35 seconds wall clock time: 265 minutes 39.65 seconds (15939.65 seconds total)