Starting phenix.real_space_refine on Fri Mar 6 18:29:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fff_31567/03_2026/7fff_31567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fff_31567/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fff_31567/03_2026/7fff_31567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fff_31567/03_2026/7fff_31567.map" model { file = "/net/cci-nas-00/data/ceres_data/7fff_31567/03_2026/7fff_31567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fff_31567/03_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 7.53, per 1000 atoms: 0.22 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 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: 7.65 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11020 1.34 - 1.46: 8594 1.46 - 1.59: 15277 1.59 - 1.72: 1 1.72 - 1.84: 352 Bond restraints: 35244 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.089 1.08e-02 8.57e+03 6.74e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.310 -0.076 1.21e-02 6.83e+03 3.90e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.89e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.065 1.22e-02 6.72e+03 2.81e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.505 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 35239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.48: 47918 7.48 - 14.97: 46 14.97 - 22.45: 3 22.45 - 29.93: 0 29.93 - 37.42: 1 Bond angle restraints: 47968 Sorted by residual: angle pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" C PRO R 409 " ideal model delta sigma weight residual 112.47 149.89 -37.42 2.06e+00 2.36e-01 3.30e+02 angle pdb=" N PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta sigma weight residual 110.49 132.06 -21.57 1.69e+00 3.50e-01 1.63e+02 angle pdb=" N LYS D 58 " pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 111.39 123.03 -11.64 1.38e+00 5.25e-01 7.12e+01 angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.32 -15.88 1.93e+00 2.68e-01 6.77e+01 angle pdb=" N LYS H 58 " pdb=" CA LYS H 58 " pdb=" C LYS H 58 " ideal model delta sigma weight residual 111.54 120.31 -8.77 1.36e+00 5.41e-01 4.16e+01 ... (remaining 47963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 20397 17.61 - 35.22: 671 35.22 - 52.82: 141 52.82 - 70.43: 30 70.43 - 88.04: 8 Dihedral angle restraints: 21247 sinusoidal: 8347 harmonic: 12900 Sorted by residual: dihedral pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual 115.10 155.01 -39.91 0 2.50e+00 1.60e-01 2.55e+02 dihedral pdb=" C PRO R 409 " pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual -120.70 -155.06 34.36 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta harmonic sigma weight residual 122.80 157.11 -34.31 0 2.50e+00 1.60e-01 1.88e+02 ... (remaining 21244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 5310 0.403 - 0.806: 4 0.806 - 1.209: 0 1.209 - 1.612: 1 1.612 - 2.015: 1 Chirality restraints: 5316 Sorted by residual: chirality pdb=" CA PRO R 409 " pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CB PRO R 409 " both_signs ideal model delta sigma weight residual False 2.72 0.70 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA PHE R 410 " pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CB PHE R 410 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.63e+01 chirality pdb=" CA LYS D 58 " pdb=" N LYS D 58 " pdb=" C LYS D 58 " pdb=" CB LYS D 58 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 5313 not shown) Planarity restraints: 6196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 265 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J-764 " 0.039 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP J-764 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J-764 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP J-764 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J-764 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J-764 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J-764 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP J-764 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J-764 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J-764 " 0.018 2.00e-02 2.50e+03 ... (remaining 6193 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 146 2.52 - 3.11: 23006 3.11 - 3.71: 49451 3.71 - 4.30: 70655 4.30 - 4.90: 120782 Nonbonded interactions: 264040 Sorted by model distance: nonbonded pdb=" OH TYR K 173 " pdb=" NE2 GLN O 439 " model vdw 1.924 3.120 nonbonded pdb=" NZ LYS K 156 " pdb=" OE2 GLU A 133 " model vdw 2.002 3.120 nonbonded pdb=" OG SER J-823 " pdb=" OD1 ASP D 57 " model vdw 2.091 3.040 nonbonded pdb=" O ASN O 442 " pdb=" ND2 ASN O 442 " model vdw 2.111 3.120 nonbonded pdb=" O HIS G 441 " pdb=" OXT ASN G 442 " model vdw 2.236 3.040 ... (remaining 264035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.300 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.997 35309 Z= 0.541 Angle : 1.050 61.625 48098 Z= 0.567 Chirality : 0.068 2.015 5316 Planarity : 0.008 0.102 6196 Dihedral : 9.593 88.037 12788 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.22 % Rotamer: Outliers : 0.40 % Allowed : 2.52 % Favored : 97.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.12 % Rama-Z 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 covalent geometry : bond 0.00745 (35244) covalent geometry : angle 0.95904 (47968) SS BOND : bond 0.20374 ( 65) SS BOND : angle 8.28552 ( 130) hydrogen bonds : bond 0.20784 ( 1017) hydrogen bonds : angle 8.33862 ( 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 : 1.265 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: K 159 ASN cc_start: 0.4531 (t0) cc_final: 0.4239 (t160) REVERT: K 193 HIS cc_start: 0.6886 (p-80) cc_final: 0.6532 (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: 0.5525 (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: 0.8180 (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: 0.7014 time to fit residues: 671.1846 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 : 1.176 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 HIS G 264 ASN G 394 HIS G 396 GLN H 27 ASN 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** F 203 HIS ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN C 442 ASN E 27 ASN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 347 ASN R 361 HIS R 405 ASN M 27 ASN M 30 ASN N 7 ASN N 52 GLN N 96 HIS O 3 HIS ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS O 392 GLN O 394 HIS O 442 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.175130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119489 restraints weight = 46549.854| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.46 r_work: 0.3191 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 35309 Z= 0.253 Angle : 0.724 11.573 48098 Z= 0.377 Chirality : 0.049 0.211 5316 Planarity : 0.006 0.094 6196 Dihedral : 6.657 161.219 4819 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.49 % Favored : 94.40 % Rotamer: Outliers : 3.83 % Allowed : 10.92 % Favored : 85.26 % 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: -2.11 (0.12), residues: 4408 helix: -0.22 (0.22), residues: 562 sheet: -1.12 (0.13), residues: 1449 loop : -1.88 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 46 TYR 0.028 0.002 TYR O 308 PHE 0.020 0.002 PHE A 189 TRP 0.055 0.002 TRP J-764 HIS 0.010 0.002 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00619 (35244) covalent geometry : angle 0.71957 (47968) SS BOND : bond 0.00501 ( 65) SS BOND : angle 1.64210 ( 130) hydrogen bonds : bond 0.04105 ( 1017) hydrogen bonds : angle 5.82852 ( 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 581 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 437 time to evaluate : 1.203 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: 0.5899 (ptt) cc_final: 0.4787 (tpp) REVERT: K 151 MET cc_start: 0.8049 (mmp) cc_final: 0.7482 (mmp) REVERT: K 153 VAL cc_start: 0.8954 (t) cc_final: 0.8688 (p) REVERT: K 193 HIS cc_start: 0.7948 (p-80) cc_final: 0.7552 (p90) REVERT: K 208 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6295 (pm20) REVERT: K 215 THR cc_start: 0.8689 (p) cc_final: 0.8119 (p) REVERT: K 270 GLU cc_start: 0.8292 (tt0) cc_final: 0.7689 (pm20) REVERT: S 120 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6270 (mpt) REVERT: S 131 MET cc_start: 0.6963 (mmm) cc_final: 0.6722 (mmm) REVERT: S 135 LYS cc_start: 0.7058 (mptt) cc_final: 0.6788 (mmtp) REVERT: S 169 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7111 (mtmt) REVERT: S 199 TYR cc_start: 0.6329 (m-10) cc_final: 0.5930 (m-80) REVERT: S 223 LYS cc_start: 0.8472 (tttt) cc_final: 0.8168 (tptt) REVERT: S 251 THR cc_start: 0.7556 (p) cc_final: 0.7201 (t) REVERT: G 10 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: G 99 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: J -775 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: J -687 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: J -609 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6851 (ttm170) REVERT: B 97 ASP cc_start: 0.8021 (m-30) cc_final: 0.7755 (m-30) REVERT: B 433 MET cc_start: 0.5743 (pp-130) cc_final: 0.5109 (ptp) REVERT: D 41 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.8115 (ttt-90) REVERT: Q 113 GLU cc_start: 0.8315 (pt0) cc_final: 0.8102 (pt0) REVERT: Q 130 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8847 (pttp) REVERT: Q 137 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: Q 144 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8170 (mt-10) REVERT: Q 213 LYS cc_start: 0.7586 (mttt) cc_final: 0.7102 (mmtp) REVERT: A 207 VAL cc_start: 0.8153 (m) cc_final: 0.7942 (p) REVERT: F 176 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5720 (tm-30) REVERT: F 190 LYS cc_start: 0.8230 (mtmt) cc_final: 0.8003 (mmmt) REVERT: C 140 HIS cc_start: 0.7892 (m90) cc_final: 0.7467 (m90) REVERT: C 160 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7761 (ttmt) REVERT: C 300 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: E 36 MET cc_start: 0.8260 (tpp) cc_final: 0.7947 (tpp) REVERT: R 8 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: R 79 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7666 (tp) REVERT: R 275 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8430 (mtm) REVERT: R 323 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: R 342 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7522 (mp0) REVERT: R 360 TYR cc_start: 0.8802 (t80) cc_final: 0.8393 (t80) REVERT: R 377 ILE cc_start: 0.7581 (mt) cc_final: 0.7343 (mm) REVERT: R 402 LEU cc_start: 0.7385 (mt) cc_final: 0.7105 (mp) REVERT: N 66 MET cc_start: 0.9349 (ttt) cc_final: 0.9012 (ttt) REVERT: N 365 MET cc_start: 0.8789 (ttt) cc_final: 0.7618 (pmt) REVERT: O 2 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8580 (mm-30) REVERT: O 175 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.8105 (ttp-110) outliers start: 144 outliers final: 47 residues processed: 518 average time/residue: 0.6580 time to fit residues: 409.3074 Evaluate side-chains 430 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 366 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 208 GLN 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 207 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -775 GLN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 412 SER 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 221 THR Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain F residue 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 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 275 MET Chi-restraints excluded: chain R residue 323 GLU 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 Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 427 optimal weight: 0.8980 chunk 154 optimal weight: 0.0010 chunk 236 optimal weight: 20.0000 chunk 409 optimal weight: 3.9990 chunk 379 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 412 optimal weight: 0.8980 chunk 407 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 394 HIS ** 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 152 GLN N 353 HIS O 130 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126775 restraints weight = 46291.983| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.70 r_work: 0.3277 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35309 Z= 0.117 Angle : 0.599 10.575 48098 Z= 0.311 Chirality : 0.045 0.390 5316 Planarity : 0.005 0.077 6196 Dihedral : 5.513 72.230 4811 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.13 % Allowed : 13.23 % Favored : 83.63 % 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: -1.53 (0.12), residues: 4408 helix: 0.53 (0.23), residues: 569 sheet: -0.76 (0.13), residues: 1444 loop : -1.57 (0.12), residues: 2395 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 0.023 0.001 PHE R 6 TRP 0.045 0.001 TRP J-764 HIS 0.005 0.001 HIS R 96 Details of bonding type rmsd covalent geometry : bond 0.00266 (35244) covalent geometry : angle 0.59626 (47968) SS BOND : bond 0.00290 ( 65) SS BOND : angle 1.30616 ( 130) hydrogen bonds : bond 0.03216 ( 1017) hydrogen bonds : angle 5.35269 ( 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: 118 poor density : 423 time to evaluate : 1.261 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: 0.8224 (mmp) cc_final: 0.7546 (mmp) REVERT: K 153 VAL cc_start: 0.8924 (t) cc_final: 0.8631 (p) REVERT: K 193 HIS cc_start: 0.7960 (p-80) cc_final: 0.7590 (p90) REVERT: K 208 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: K 215 THR cc_start: 0.8764 (p) cc_final: 0.8288 (p) REVERT: K 270 GLU cc_start: 0.8255 (tt0) cc_final: 0.7659 (pm20) REVERT: S 120 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5756 (mpt) REVERT: S 131 MET cc_start: 0.6995 (mmm) cc_final: 0.6775 (mmm) REVERT: S 135 LYS cc_start: 0.7017 (mptt) cc_final: 0.6815 (mmtp) REVERT: S 199 TYR cc_start: 0.6383 (m-10) cc_final: 0.5899 (m-80) REVERT: S 223 LYS cc_start: 0.8494 (tttt) cc_final: 0.8191 (tptt) REVERT: S 251 THR cc_start: 0.7577 (p) cc_final: 0.7236 (t) REVERT: S 257 MET cc_start: 0.7754 (ptp) cc_final: 0.7456 (mpp) REVERT: H 57 ASP cc_start: 0.7260 (p0) cc_final: 0.6919 (p0) REVERT: J -775 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: J -687 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: J -609 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6811 (ttm170) REVERT: B 282 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6587 (tp) REVERT: B 433 MET cc_start: 0.5755 (pp-130) cc_final: 0.5142 (ptm) REVERT: T 23 TYR cc_start: 0.6217 (t80) cc_final: 0.5142 (t80) REVERT: Q 74 ILE cc_start: 0.8618 (mt) cc_final: 0.8290 (mp) REVERT: Q 113 GLU cc_start: 0.8335 (pt0) cc_final: 0.8135 (pt0) REVERT: Q 120 ARG cc_start: 0.8360 (ttm170) cc_final: 0.8127 (ttm170) REVERT: Q 130 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8756 (pttp) REVERT: Q 144 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8226 (mt-10) REVERT: Q 159 GLN cc_start: 0.8343 (tt0) cc_final: 0.8014 (tp40) REVERT: Q 211 ILE cc_start: 0.8107 (tt) cc_final: 0.7819 (tp) REVERT: Q 213 LYS cc_start: 0.7561 (mttt) cc_final: 0.7063 (mmtp) REVERT: A 118 MET cc_start: 0.6428 (pmt) cc_final: 0.5446 (pmm) REVERT: F 169 LYS cc_start: 0.6890 (tmtt) cc_final: 0.6666 (tppp) REVERT: F 176 GLU cc_start: 0.6046 (tp30) cc_final: 0.5439 (tm-30) REVERT: F 190 LYS cc_start: 0.8275 (mtmt) cc_final: 0.8050 (mmmt) REVERT: F 192 THR cc_start: 0.7990 (t) cc_final: 0.7763 (m) REVERT: F 195 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.6043 (pttm) REVERT: F 257 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5695 (ptm) REVERT: C 73 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7515 (mtt-85) REVERT: C 115 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8305 (tp) REVERT: C 140 HIS cc_start: 0.7383 (m90) cc_final: 0.6917 (m90) REVERT: C 364 GLU cc_start: 0.8177 (tp30) cc_final: 0.7606 (tp30) REVERT: C 377 LYS cc_start: 0.7272 (ttmm) cc_final: 0.6892 (tttm) REVERT: E 38 SER cc_start: 0.8942 (t) cc_final: 0.8498 (m) REVERT: P 6 MET cc_start: 0.4441 (tpp) cc_final: 0.4176 (ttp) REVERT: R 8 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: R 79 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7689 (tp) REVERT: R 197 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7290 (pt) REVERT: R 360 TYR cc_start: 0.8834 (t80) cc_final: 0.8506 (t80) REVERT: R 377 ILE cc_start: 0.7793 (mt) cc_final: 0.7555 (mm) REVERT: R 402 LEU cc_start: 0.7452 (mt) cc_final: 0.7195 (mp) REVERT: N 66 MET cc_start: 0.9210 (ttt) cc_final: 0.8961 (ttt) REVERT: N 201 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7080 (tm-30) REVERT: N 365 MET cc_start: 0.8802 (ttt) cc_final: 0.7701 (pmt) REVERT: O 2 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: O 175 ARG cc_start: 0.8267 (ttt-90) cc_final: 0.7860 (ttp-110) outliers start: 118 outliers final: 38 residues processed: 503 average time/residue: 0.6395 time to fit residues: 388.5502 Evaluate side-chains 416 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 364 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 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 174 ASP 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 112 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain A residue 120 MET 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 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain 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 305 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 370 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 396 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 203 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS J-832 HIS J-642 HIS B 386 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 288 HIS Q 361 HIS C 394 HIS R 358 HIS N 358 HIS O 130 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117299 restraints weight = 46150.501| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.36 r_work: 0.3158 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 35309 Z= 0.244 Angle : 0.687 9.852 48098 Z= 0.354 Chirality : 0.048 0.444 5316 Planarity : 0.006 0.108 6196 Dihedral : 5.782 76.357 4811 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 4.46 % Allowed : 13.42 % Favored : 82.12 % 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: -1.35 (0.12), residues: 4408 helix: 0.82 (0.23), residues: 569 sheet: -0.70 (0.13), residues: 1489 loop : -1.46 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 298 TYR 0.026 0.002 TYR O 308 PHE 0.018 0.002 PHE Q 6 TRP 0.060 0.002 TRP J-764 HIS 0.009 0.002 HIS R 156 Details of bonding type rmsd covalent geometry : bond 0.00600 (35244) covalent geometry : angle 0.68353 (47968) SS BOND : bond 0.00552 ( 65) SS BOND : angle 1.56590 ( 130) hydrogen bonds : bond 0.03568 ( 1017) hydrogen bonds : angle 5.23616 ( 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 547 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 379 time to evaluate : 1.409 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: 0.5677 (ptt) cc_final: 0.5434 (ppp) REVERT: K 151 MET cc_start: 0.8298 (mmp) cc_final: 0.7580 (mmp) REVERT: K 153 VAL cc_start: 0.8990 (t) cc_final: 0.8645 (p) REVERT: K 176 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8231 (mt-10) REVERT: K 208 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: K 215 THR cc_start: 0.8729 (p) cc_final: 0.8520 (p) REVERT: K 223 LYS cc_start: 0.8788 (tppt) cc_final: 0.8499 (tppt) REVERT: K 231 LEU cc_start: 0.8820 (mt) cc_final: 0.8611 (mm) REVERT: K 257 MET cc_start: 0.8720 (ptp) cc_final: 0.8444 (mpp) REVERT: K 270 GLU cc_start: 0.8112 (tt0) cc_final: 0.7537 (pm20) REVERT: S 120 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5927 (mpt) REVERT: S 131 MET cc_start: 0.7000 (mmm) cc_final: 0.6774 (mmm) REVERT: S 169 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7130 (mtmt) REVERT: S 251 THR cc_start: 0.7908 (p) cc_final: 0.7668 (t) REVERT: S 257 MET cc_start: 0.7636 (ptp) cc_final: 0.7194 (mpp) REVERT: G 10 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: G 99 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: G 241 GLU cc_start: 0.8438 (tp30) cc_final: 0.8230 (tp30) REVERT: G 293 THR cc_start: 0.8290 (m) cc_final: 0.7953 (t) REVERT: G 319 LYS cc_start: 0.7780 (ttpm) cc_final: 0.7445 (ttpt) REVERT: H 57 ASP cc_start: 0.7361 (p0) cc_final: 0.7117 (p0) REVERT: J -768 GLN cc_start: 0.8549 (mt0) cc_final: 0.8081 (tt0) REVERT: J -687 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: J -609 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6701 (ttm170) REVERT: J -588 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6893 (mp) REVERT: B 7 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7913 (ttp) REVERT: B 97 ASP cc_start: 0.8140 (m-30) cc_final: 0.7817 (p0) REVERT: B 282 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6733 (tp) REVERT: B 305 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6591 (mt-10) REVERT: B 433 MET cc_start: 0.5707 (pp-130) cc_final: 0.5499 (ppp) REVERT: T 23 TYR cc_start: 0.5837 (t80) cc_final: 0.5196 (t80) REVERT: Q 4 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: Q 74 ILE cc_start: 0.8844 (mt) cc_final: 0.8575 (mp) REVERT: Q 88 ARG cc_start: 0.8668 (mtt90) cc_final: 0.8279 (mtt-85) REVERT: Q 113 GLU cc_start: 0.8436 (pt0) cc_final: 0.8224 (pt0) REVERT: Q 130 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8806 (mtmm) REVERT: Q 137 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: Q 144 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8167 (mt-10) REVERT: Q 159 GLN cc_start: 0.8426 (tt0) cc_final: 0.7912 (tp40) REVERT: Q 213 LYS cc_start: 0.7918 (mttt) cc_final: 0.7344 (mmtp) REVERT: A 184 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6427 (mpt) REVERT: F 176 GLU cc_start: 0.6656 (tp30) cc_final: 0.5953 (tm-30) REVERT: F 195 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6208 (pttm) REVERT: F 257 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5561 (ptm) REVERT: C 140 HIS cc_start: 0.7379 (m90) cc_final: 0.6912 (m90) REVERT: C 160 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7499 (tttm) REVERT: C 364 GLU cc_start: 0.8234 (tp30) cc_final: 0.7630 (tp30) REVERT: C 366 ARG cc_start: 0.8671 (ttp-170) cc_final: 0.8467 (ttp-170) REVERT: C 375 THR cc_start: 0.8590 (m) cc_final: 0.8371 (t) REVERT: E 38 SER cc_start: 0.8965 (t) cc_final: 0.8596 (m) REVERT: R 6 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6924 (t80) REVERT: R 60 ASN cc_start: 0.7020 (m110) cc_final: 0.6646 (m110) REVERT: R 323 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: R 360 TYR cc_start: 0.8739 (t80) cc_final: 0.8337 (t80) REVERT: R 402 LEU cc_start: 0.7366 (mt) cc_final: 0.7126 (mp) REVERT: N 20 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8021 (mt) REVERT: N 66 MET cc_start: 0.9367 (ttt) cc_final: 0.9121 (ttt) REVERT: N 160 ASN cc_start: 0.7354 (t0) cc_final: 0.6865 (t0) REVERT: N 365 MET cc_start: 0.8729 (ttt) cc_final: 0.7570 (pmt) REVERT: O 2 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8677 (mm-30) REVERT: O 18 ILE cc_start: 0.9072 (pt) cc_final: 0.8869 (pp) REVERT: O 175 ARG cc_start: 0.8543 (ttt-90) cc_final: 0.8202 (ttp-110) outliers start: 168 outliers final: 80 residues processed: 493 average time/residue: 0.6074 time to fit residues: 364.0897 Evaluate side-chains 447 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 346 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 211 ASN 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 220 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR 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 -826 VAL 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 7 MET Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 GLU 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 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 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR 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 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 319 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 88 ARG Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 115 LEU 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: 0.9990 chunk 300 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 287 optimal weight: 9.9990 chunk 415 optimal weight: 0.9980 chunk 397 optimal weight: 5.9990 chunk 398 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 ASN J-767 ASN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS O 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.174153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119455 restraints weight = 46270.687| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.35 r_work: 0.3195 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35309 Z= 0.143 Angle : 0.606 9.394 48098 Z= 0.311 Chirality : 0.045 0.462 5316 Planarity : 0.005 0.070 6196 Dihedral : 5.490 77.284 4811 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 3.37 % Allowed : 14.77 % Favored : 81.85 % 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: -1.15 (0.13), residues: 4408 helix: 1.09 (0.23), residues: 569 sheet: -0.59 (0.14), residues: 1387 loop : -1.33 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 289 TYR 0.025 0.001 TYR O 308 PHE 0.017 0.001 PHE A 148 TRP 0.050 0.001 TRP J-764 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00344 (35244) covalent geometry : angle 0.60367 (47968) SS BOND : bond 0.00226 ( 65) SS BOND : angle 1.14616 ( 130) hydrogen bonds : bond 0.03067 ( 1017) hydrogen bonds : angle 5.07859 ( 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 490 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 363 time to evaluate : 1.542 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: 0.6165 (ptt) cc_final: 0.5936 (ppp) REVERT: K 151 MET cc_start: 0.8226 (mmp) cc_final: 0.7612 (mmp) REVERT: K 153 VAL cc_start: 0.8953 (t) cc_final: 0.8591 (p) REVERT: K 176 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8204 (mt-10) REVERT: K 215 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8412 (p) REVERT: K 223 LYS cc_start: 0.8860 (tppt) cc_final: 0.8589 (tppt) REVERT: K 226 SER cc_start: 0.8500 (t) cc_final: 0.7653 (m) REVERT: K 270 GLU cc_start: 0.7996 (tt0) cc_final: 0.7449 (pm20) REVERT: S 120 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5960 (mpt) REVERT: S 251 THR cc_start: 0.7936 (p) cc_final: 0.7712 (t) REVERT: G 293 THR cc_start: 0.8193 (m) cc_final: 0.7970 (t) REVERT: G 300 GLU cc_start: 0.6064 (pm20) cc_final: 0.5857 (pm20) REVERT: G 319 LYS cc_start: 0.7762 (ttpm) cc_final: 0.7157 (ttmt) REVERT: G 370 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7249 (m) REVERT: H 57 ASP cc_start: 0.7355 (p0) cc_final: 0.7088 (p0) REVERT: J -768 GLN cc_start: 0.8538 (mt0) cc_final: 0.8023 (tt0) REVERT: J -687 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: J -609 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6695 (ttm170) REVERT: J -588 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6946 (mp) REVERT: B 7 MET cc_start: 0.8170 (ttp) cc_final: 0.7929 (ttp) REVERT: B 10 GLN cc_start: 0.8306 (tt0) cc_final: 0.8034 (tt0) REVERT: B 97 ASP cc_start: 0.8059 (m-30) cc_final: 0.7780 (p0) REVERT: B 282 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6585 (tp) REVERT: B 305 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: T 23 TYR cc_start: 0.5941 (t80) cc_final: 0.5317 (t80) REVERT: Q 4 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: Q 74 ILE cc_start: 0.8814 (mt) cc_final: 0.8505 (mp) REVERT: Q 130 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8796 (mtmm) REVERT: Q 144 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8240 (mt-10) REVERT: Q 159 GLN cc_start: 0.8375 (tt0) cc_final: 0.7961 (tp40) REVERT: Q 213 LYS cc_start: 0.7744 (mttt) cc_final: 0.7232 (mmtp) REVERT: A 118 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.5826 (pmm) REVERT: A 184 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6272 (mpt) REVERT: F 169 LYS cc_start: 0.6981 (tmtt) cc_final: 0.6733 (tppp) REVERT: F 190 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8177 (mtmt) REVERT: C 72 TYR cc_start: 0.8549 (m-80) cc_final: 0.8161 (m-80) REVERT: C 140 HIS cc_start: 0.7383 (m90) cc_final: 0.6954 (m90) REVERT: C 160 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7421 (tttm) REVERT: C 281 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8875 (t70) REVERT: C 364 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: E 38 SER cc_start: 0.8938 (t) cc_final: 0.8627 (m) REVERT: P 6 MET cc_start: 0.4543 (tpp) cc_final: 0.4242 (ttp) REVERT: R 6 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7131 (t80) REVERT: R 60 ASN cc_start: 0.7006 (m110) cc_final: 0.6720 (m-40) REVERT: R 111 THR cc_start: 0.8428 (m) cc_final: 0.7983 (m) REVERT: R 323 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: R 354 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7820 (mt-10) REVERT: R 360 TYR cc_start: 0.8757 (t80) cc_final: 0.8396 (t80) REVERT: R 402 LEU cc_start: 0.7341 (mt) cc_final: 0.7091 (mp) REVERT: N 66 MET cc_start: 0.9342 (ttt) cc_final: 0.9043 (ttt) REVERT: N 160 ASN cc_start: 0.7362 (t0) cc_final: 0.6890 (t0) REVERT: N 365 MET cc_start: 0.8707 (ttt) cc_final: 0.7545 (pmt) REVERT: O 2 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: O 175 ARG cc_start: 0.8457 (ttt-90) cc_final: 0.8147 (ttp-110) outliers start: 127 outliers final: 65 residues processed: 452 average time/residue: 0.6142 time to fit residues: 337.2724 Evaluate side-chains 423 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 341 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 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 213 LEU 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 -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 14 SER 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 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 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 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 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain 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 166 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 281 ASP 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 6 PHE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain 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 167 SER Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 300 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: 10.0000 chunk 128 optimal weight: 7.9990 chunk 381 optimal weight: 0.9980 chunk 417 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 288 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 316 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-767 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121461 restraints weight = 46158.111| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.31 r_work: 0.3219 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35309 Z= 0.110 Angle : 0.582 9.849 48098 Z= 0.299 Chirality : 0.044 0.474 5316 Planarity : 0.005 0.068 6196 Dihedral : 5.254 77.253 4811 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % Rotamer: Outliers : 3.24 % Allowed : 15.28 % Favored : 81.48 % 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: -0.94 (0.13), residues: 4408 helix: 1.55 (0.24), residues: 541 sheet: -0.45 (0.14), residues: 1384 loop : -1.23 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 88 TYR 0.023 0.001 TYR O 308 PHE 0.019 0.001 PHE R 217 TRP 0.052 0.001 TRP J-764 HIS 0.004 0.001 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.00249 (35244) covalent geometry : angle 0.57943 (47968) SS BOND : bond 0.00193 ( 65) SS BOND : angle 1.13046 ( 130) hydrogen bonds : bond 0.02851 ( 1017) hydrogen bonds : angle 4.92940 ( 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 493 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 371 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: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6176 (ptt) cc_final: 0.5961 (ppp) REVERT: K 132 LEU cc_start: 0.8498 (tp) cc_final: 0.8175 (mt) REVERT: K 151 MET cc_start: 0.8133 (mmp) cc_final: 0.7615 (mmp) REVERT: K 153 VAL cc_start: 0.8916 (t) cc_final: 0.8537 (p) REVERT: K 176 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8086 (mt-10) REVERT: K 223 LYS cc_start: 0.8825 (tppt) cc_final: 0.8564 (tppt) REVERT: K 226 SER cc_start: 0.8544 (t) cc_final: 0.7788 (m) REVERT: K 257 MET cc_start: 0.8648 (ptp) cc_final: 0.8433 (mpp) REVERT: K 270 GLU cc_start: 0.7982 (tt0) cc_final: 0.7438 (pm20) REVERT: S 120 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6160 (mpt) REVERT: S 131 MET cc_start: 0.7054 (mmm) cc_final: 0.5772 (mpt) REVERT: S 135 LYS cc_start: 0.7181 (mmtp) cc_final: 0.6624 (mptt) REVERT: S 251 THR cc_start: 0.7842 (p) cc_final: 0.7626 (t) REVERT: G 293 THR cc_start: 0.8109 (m) cc_final: 0.7897 (t) REVERT: G 319 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7124 (ttmt) REVERT: G 361 ILE cc_start: 0.7800 (mt) cc_final: 0.7527 (tt) REVERT: H 57 ASP cc_start: 0.7273 (p0) cc_final: 0.7035 (p0) REVERT: J -799 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8497 (tm-30) REVERT: J -768 GLN cc_start: 0.8507 (mt0) cc_final: 0.8014 (tt0) REVERT: J -709 ASN cc_start: 0.8745 (p0) cc_final: 0.8510 (p0) REVERT: J -687 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: J -609 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6683 (ttm170) REVERT: B 7 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7984 (ttp) REVERT: B 10 GLN cc_start: 0.8299 (tt0) cc_final: 0.8022 (tt0) REVERT: B 166 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 207 THR cc_start: 0.8496 (m) cc_final: 0.8219 (t) REVERT: B 305 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6501 (mt-10) REVERT: B 433 MET cc_start: 0.6170 (pp-130) cc_final: 0.5416 (ptm) REVERT: T 23 TYR cc_start: 0.5983 (t80) cc_final: 0.5364 (t80) REVERT: Q 4 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: Q 74 ILE cc_start: 0.8773 (mt) cc_final: 0.8462 (mp) REVERT: Q 130 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8773 (mtmm) REVERT: Q 159 GLN cc_start: 0.8385 (tt0) cc_final: 0.7978 (tp40) REVERT: Q 213 LYS cc_start: 0.7656 (mttt) cc_final: 0.7154 (mmtp) REVERT: A 118 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6133 (pmm) REVERT: A 120 MET cc_start: 0.6139 (pmm) cc_final: 0.5719 (pmm) REVERT: A 184 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6271 (mpt) REVERT: F 169 LYS cc_start: 0.7040 (tmtt) cc_final: 0.6812 (tppp) REVERT: C 72 TYR cc_start: 0.8543 (m-80) cc_final: 0.8141 (m-80) REVERT: C 140 HIS cc_start: 0.7382 (m90) cc_final: 0.6862 (m90) REVERT: C 281 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8871 (t70) REVERT: C 364 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: E 38 SER cc_start: 0.8932 (t) cc_final: 0.8652 (m) REVERT: R 6 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7183 (t80) REVERT: R 60 ASN cc_start: 0.7040 (m110) cc_final: 0.6770 (m-40) REVERT: R 88 ARG cc_start: 0.6211 (mmt180) cc_final: 0.5995 (mmm160) REVERT: R 197 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7179 (pt) REVERT: R 360 TYR cc_start: 0.8775 (t80) cc_final: 0.8465 (t80) REVERT: R 402 LEU cc_start: 0.7302 (mt) cc_final: 0.7000 (mp) REVERT: N 66 MET cc_start: 0.9324 (ttp) cc_final: 0.8992 (ttt) REVERT: N 160 ASN cc_start: 0.7993 (t0) cc_final: 0.7243 (t0) REVERT: N 365 MET cc_start: 0.8744 (ttt) cc_final: 0.7627 (pmt) REVERT: O 2 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: O 175 ARG cc_start: 0.8546 (ttt-90) cc_final: 0.8234 (ttp-110) outliers start: 122 outliers final: 64 residues processed: 448 average time/residue: 0.6053 time to fit residues: 329.5310 Evaluate side-chains 422 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 342 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 213 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -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 7 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 130 LYS 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 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 234 THR Chi-restraints excluded: chain C residue 281 ASP 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 6 PHE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 57 optimal weight: 0.9990 chunk 356 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 391 optimal weight: 0.7980 chunk 91 optimal weight: 0.0370 chunk 12 optimal weight: 0.0770 chunk 396 optimal weight: 3.9990 chunk 295 optimal weight: 0.3980 chunk 243 optimal weight: 20.0000 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-642 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN R 353 HIS O 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123699 restraints weight = 46446.558| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.44 r_work: 0.3257 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3808 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= 0.093 Angle : 0.565 10.573 48098 Z= 0.288 Chirality : 0.044 0.487 5316 Planarity : 0.004 0.069 6196 Dihedral : 5.005 76.555 4811 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.71 % Allowed : 16.42 % Favored : 80.87 % 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: -0.75 (0.13), residues: 4408 helix: 1.50 (0.24), residues: 560 sheet: -0.24 (0.14), residues: 1356 loop : -1.13 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 88 TYR 0.021 0.001 TYR O 308 PHE 0.027 0.001 PHE R 217 TRP 0.036 0.001 TRP J-764 HIS 0.005 0.000 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.00204 (35244) covalent geometry : angle 0.56356 (47968) SS BOND : bond 0.00190 ( 65) SS BOND : angle 0.99841 ( 130) hydrogen bonds : bond 0.02605 ( 1017) hydrogen bonds : angle 4.76775 ( 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 491 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 389 time to evaluate : 1.417 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: 0.6109 (ptt) cc_final: 0.5789 (ppp) REVERT: K 151 MET cc_start: 0.8124 (mmp) cc_final: 0.7623 (mmp) REVERT: K 153 VAL cc_start: 0.8796 (t) cc_final: 0.8361 (p) REVERT: K 176 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8078 (mt-10) REVERT: K 215 THR cc_start: 0.8444 (p) cc_final: 0.8217 (t) REVERT: K 223 LYS cc_start: 0.8767 (tppt) cc_final: 0.8516 (tppt) REVERT: K 226 SER cc_start: 0.8534 (t) cc_final: 0.7814 (m) REVERT: S 120 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6600 (mpt) REVERT: S 131 MET cc_start: 0.7073 (mmm) cc_final: 0.5859 (mpt) REVERT: S 135 LYS cc_start: 0.7183 (mmtp) cc_final: 0.6590 (mptt) REVERT: S 251 THR cc_start: 0.7795 (p) cc_final: 0.7577 (t) REVERT: G 293 THR cc_start: 0.8031 (m) cc_final: 0.7811 (t) REVERT: G 366 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8253 (ttp80) REVERT: H 57 ASP cc_start: 0.7241 (p0) cc_final: 0.6969 (p0) REVERT: J -799 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8589 (tm-30) REVERT: J -783 PHE cc_start: 0.8504 (m-80) cc_final: 0.8291 (m-80) REVERT: J -768 GLN cc_start: 0.8499 (mt0) cc_final: 0.8050 (tt0) REVERT: J -609 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6711 (ttm170) REVERT: B 10 GLN cc_start: 0.8257 (tt0) cc_final: 0.8038 (tt0) REVERT: B 29 ILE cc_start: 0.7691 (mt) cc_final: 0.7364 (mm) REVERT: B 166 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7637 (tp) REVERT: B 282 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6452 (tp) REVERT: B 433 MET cc_start: 0.6143 (pp-130) cc_final: 0.5455 (ptm) REVERT: T 23 TYR cc_start: 0.5974 (t80) cc_final: 0.5363 (t80) REVERT: Q 4 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: Q 159 GLN cc_start: 0.8341 (tt0) cc_final: 0.8020 (tp40) REVERT: Q 213 LYS cc_start: 0.7581 (mttt) cc_final: 0.7079 (mmtp) REVERT: Q 313 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8419 (mp0) REVERT: A 118 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6373 (pmm) REVERT: A 120 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5782 (pmm) REVERT: A 184 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6339 (mpt) REVERT: A 261 LYS cc_start: 0.7612 (mmtt) cc_final: 0.7238 (pttt) REVERT: A 265 VAL cc_start: 0.7577 (t) cc_final: 0.7214 (p) REVERT: F 169 LYS cc_start: 0.7063 (tmtt) cc_final: 0.6849 (tppp) REVERT: F 190 LYS cc_start: 0.8597 (mmpt) cc_final: 0.8357 (mppt) REVERT: C 72 TYR cc_start: 0.8566 (m-80) cc_final: 0.8241 (m-80) REVERT: C 73 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7324 (mtt-85) REVERT: C 140 HIS cc_start: 0.7352 (m90) cc_final: 0.7049 (m90) REVERT: C 160 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7515 (mttm) REVERT: C 281 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8832 (t70) REVERT: C 327 LYS cc_start: 0.8571 (ptmm) cc_final: 0.8190 (tttp) REVERT: C 364 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: C 379 ASP cc_start: 0.7294 (m-30) cc_final: 0.7078 (m-30) REVERT: R 3 GLU cc_start: 0.7529 (tp30) cc_final: 0.7204 (tp30) REVERT: R 197 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7149 (pt) REVERT: R 360 TYR cc_start: 0.8757 (t80) cc_final: 0.8510 (t80) REVERT: R 397 LEU cc_start: 0.7078 (mt) cc_final: 0.6724 (mp) REVERT: R 402 LEU cc_start: 0.7291 (mt) cc_final: 0.7054 (mp) REVERT: N 66 MET cc_start: 0.9325 (ttp) cc_final: 0.9065 (ttt) REVERT: N 160 ASN cc_start: 0.7773 (t0) cc_final: 0.7136 (t0) REVERT: N 365 MET cc_start: 0.8635 (ttt) cc_final: 0.7578 (pmt) REVERT: O 2 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: O 18 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8427 (pp) REVERT: O 175 ARG cc_start: 0.8464 (ttt-90) cc_final: 0.8153 (ttp-110) outliers start: 102 outliers final: 53 residues processed: 451 average time/residue: 0.6332 time to fit residues: 346.2810 Evaluate side-chains 408 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 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 -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 112 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 407 TRP 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 221 THR Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 343 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 F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain R residue 69 ASP 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 307 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 400 TYR 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 213 LEU Chi-restraints excluded: chain O residue 305 GLU 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: 7.9990 chunk 20 optimal weight: 0.8980 chunk 415 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 427 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 414 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 208 GLN J-920 HIS J-919 GLN J-848 GLN J-642 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 HIS Q 233 ASN O 43 ASN O 130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120533 restraints weight = 46351.915| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.22 r_work: 0.3213 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35309 Z= 0.143 Angle : 0.596 10.955 48098 Z= 0.304 Chirality : 0.045 0.484 5316 Planarity : 0.005 0.067 6196 Dihedral : 5.106 78.042 4811 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 2.60 % Allowed : 17.08 % Favored : 80.31 % 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: -0.71 (0.13), residues: 4408 helix: 1.54 (0.24), residues: 559 sheet: -0.21 (0.14), residues: 1372 loop : -1.11 (0.12), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 88 TYR 0.022 0.001 TYR J-637 PHE 0.026 0.001 PHE R 217 TRP 0.030 0.001 TRP J-764 HIS 0.006 0.001 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.00346 (35244) covalent geometry : angle 0.59393 (47968) SS BOND : bond 0.00231 ( 65) SS BOND : angle 1.08176 ( 130) hydrogen bonds : bond 0.02852 ( 1017) hydrogen bonds : angle 4.77259 ( 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 457 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 359 time to evaluate : 1.179 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: 0.6320 (ptt) cc_final: 0.5929 (ppp) REVERT: K 132 LEU cc_start: 0.8494 (tp) cc_final: 0.8246 (mt) REVERT: K 151 MET cc_start: 0.8154 (mmp) cc_final: 0.7666 (mmp) REVERT: K 153 VAL cc_start: 0.8811 (t) cc_final: 0.8379 (p) REVERT: K 176 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8207 (mt-10) REVERT: K 223 LYS cc_start: 0.8789 (tppt) cc_final: 0.8531 (tppt) REVERT: K 226 SER cc_start: 0.8628 (t) cc_final: 0.7841 (m) REVERT: K 257 MET cc_start: 0.8699 (ptp) cc_final: 0.8487 (mpp) REVERT: K 270 GLU cc_start: 0.8037 (tt0) cc_final: 0.7501 (pm20) REVERT: S 120 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6700 (mpt) REVERT: S 131 MET cc_start: 0.7050 (mmm) cc_final: 0.6770 (mmm) REVERT: S 135 LYS cc_start: 0.7200 (mmtp) cc_final: 0.6657 (mptt) REVERT: G 99 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: G 293 THR cc_start: 0.8083 (m) cc_final: 0.7856 (t) REVERT: G 300 GLU cc_start: 0.8222 (tp30) cc_final: 0.7991 (pm20) REVERT: G 361 ILE cc_start: 0.7874 (mt) cc_final: 0.7599 (tt) REVERT: G 366 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8243 (ttp80) REVERT: H 57 ASP cc_start: 0.7308 (p0) cc_final: 0.7043 (p0) REVERT: J -799 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8542 (tm-30) REVERT: J -768 GLN cc_start: 0.8501 (mt0) cc_final: 0.8041 (tt0) REVERT: J -687 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7994 (mt-10) REVERT: J -635 MET cc_start: 0.6385 (pmt) cc_final: 0.6141 (pmt) REVERT: J -609 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6722 (ttm170) REVERT: B 7 MET cc_start: 0.8392 (ttp) cc_final: 0.8066 (ptt) REVERT: B 27 LEU cc_start: 0.7549 (tp) cc_final: 0.7290 (tm) REVERT: B 166 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7653 (tp) REVERT: B 282 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6458 (tp) REVERT: D 57 ASP cc_start: 0.8004 (t70) cc_final: 0.7725 (t0) REVERT: T 23 TYR cc_start: 0.5978 (t80) cc_final: 0.5422 (t80) REVERT: Q 4 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: Q 159 GLN cc_start: 0.8371 (tt0) cc_final: 0.8031 (tp40) REVERT: Q 213 LYS cc_start: 0.7745 (mttt) cc_final: 0.7351 (mmtp) REVERT: Q 313 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8461 (mp0) REVERT: A 118 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6389 (pmm) REVERT: A 120 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5688 (pmm) REVERT: F 151 MET cc_start: 0.7468 (mpm) cc_final: 0.7247 (mpp) REVERT: F 184 MET cc_start: 0.7202 (ptp) cc_final: 0.6705 (pmm) REVERT: C 72 TYR cc_start: 0.8560 (m-80) cc_final: 0.8157 (m-80) REVERT: C 140 HIS cc_start: 0.7314 (m90) cc_final: 0.6979 (m90) REVERT: C 160 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7609 (mttm) REVERT: C 281 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8843 (t70) REVERT: C 289 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7281 (mtm110) REVERT: C 364 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: C 366 ARG cc_start: 0.8650 (ttp-170) cc_final: 0.8450 (ttp-170) REVERT: C 411 THR cc_start: 0.7968 (m) cc_final: 0.7505 (p) REVERT: R 3 GLU cc_start: 0.7555 (tp30) cc_final: 0.7271 (tp30) REVERT: R 164 TYR cc_start: 0.8241 (m-80) cc_final: 0.7966 (m-80) REVERT: R 197 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7185 (pt) REVERT: R 360 TYR cc_start: 0.8759 (t80) cc_final: 0.8501 (t80) REVERT: R 397 LEU cc_start: 0.7080 (mt) cc_final: 0.6704 (mp) REVERT: R 402 LEU cc_start: 0.7292 (mt) cc_final: 0.6982 (mp) REVERT: N 66 MET cc_start: 0.9377 (ttp) cc_final: 0.9113 (ttt) REVERT: N 160 ASN cc_start: 0.7976 (t0) cc_final: 0.7209 (t0) REVERT: N 187 THR cc_start: 0.8056 (m) cc_final: 0.7607 (p) REVERT: N 365 MET cc_start: 0.8708 (ttt) cc_final: 0.7631 (pmt) REVERT: O 2 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: O 18 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8583 (pp) REVERT: O 175 ARG cc_start: 0.8466 (ttt-90) cc_final: 0.8166 (ttp-110) outliers start: 98 outliers final: 62 residues processed: 426 average time/residue: 0.5842 time to fit residues: 304.1971 Evaluate side-chains 416 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 341 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 272 CYS 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 215 THR 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 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 62 LYS 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 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 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 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 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 207 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET 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 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 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 18 ILE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 310 optimal weight: 0.8980 chunk 380 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 367 optimal weight: 0.7980 chunk 132 optimal weight: 0.2980 chunk 226 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 376 optimal weight: 0.8980 chunk 228 optimal weight: 20.0000 chunk 124 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J-919 GLN J-642 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 ASN A 159 ASN R 159 GLN O 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.177044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123602 restraints weight = 46379.736| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.26 r_work: 0.3249 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 35309 Z= 0.098 Angle : 0.573 13.237 48098 Z= 0.292 Chirality : 0.044 0.475 5316 Planarity : 0.004 0.070 6196 Dihedral : 4.938 78.174 4811 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 2.05 % Allowed : 17.91 % 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: -0.57 (0.13), residues: 4408 helix: 1.61 (0.24), residues: 559 sheet: -0.09 (0.15), residues: 1334 loop : -1.00 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 88 TYR 0.021 0.001 TYR J-637 PHE 0.020 0.001 PHE R 217 TRP 0.051 0.001 TRP J-764 HIS 0.007 0.001 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.00221 (35244) covalent geometry : angle 0.57163 (47968) SS BOND : bond 0.00182 ( 65) SS BOND : angle 0.93450 ( 130) hydrogen bonds : bond 0.02608 ( 1017) hydrogen bonds : angle 4.67528 ( 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 444 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 367 time to evaluate : 1.372 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: 0.6134 (ptt) cc_final: 0.5811 (ppp) REVERT: K 132 LEU cc_start: 0.8480 (tp) cc_final: 0.8200 (mt) REVERT: K 151 MET cc_start: 0.8147 (mmp) cc_final: 0.7632 (mmp) REVERT: K 153 VAL cc_start: 0.8778 (t) cc_final: 0.8331 (p) REVERT: K 176 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8181 (mt-10) REVERT: K 223 LYS cc_start: 0.8773 (tppt) cc_final: 0.8555 (tppt) REVERT: K 226 SER cc_start: 0.8588 (t) cc_final: 0.7842 (m) REVERT: K 270 GLU cc_start: 0.8005 (tt0) cc_final: 0.7488 (pm20) REVERT: S 120 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6790 (mpt) REVERT: S 131 MET cc_start: 0.7059 (mmm) cc_final: 0.6800 (mmm) REVERT: S 135 LYS cc_start: 0.7173 (mmtp) cc_final: 0.6633 (mptt) REVERT: G 99 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: G 293 THR cc_start: 0.8104 (m) cc_final: 0.7875 (t) REVERT: G 300 GLU cc_start: 0.8316 (tp30) cc_final: 0.8043 (tp30) REVERT: G 361 ILE cc_start: 0.7717 (mt) cc_final: 0.7413 (tt) REVERT: G 366 ARG cc_start: 0.8556 (ttp80) cc_final: 0.8325 (ttp80) REVERT: H 57 ASP cc_start: 0.7283 (p0) cc_final: 0.7020 (p0) REVERT: J -799 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8531 (tm-30) REVERT: J -768 GLN cc_start: 0.8488 (mt0) cc_final: 0.7975 (tt0) REVERT: J -635 MET cc_start: 0.6299 (pmt) cc_final: 0.6038 (pmt) REVERT: J -609 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6637 (ttm170) REVERT: B 7 MET cc_start: 0.8269 (ttp) cc_final: 0.8036 (ptt) REVERT: B 10 GLN cc_start: 0.8248 (tt0) cc_final: 0.8013 (tm-30) REVERT: B 166 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7628 (tp) REVERT: B 282 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6389 (tp) REVERT: B 433 MET cc_start: 0.5731 (ppp) cc_final: 0.4958 (ptm) REVERT: D 57 ASP cc_start: 0.7972 (t70) cc_final: 0.7687 (t0) REVERT: Q 4 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: Q 108 ASP cc_start: 0.8658 (p0) cc_final: 0.8429 (p0) REVERT: Q 159 GLN cc_start: 0.8388 (tt0) cc_final: 0.8042 (tp40) REVERT: Q 213 LYS cc_start: 0.7613 (mttt) cc_final: 0.7072 (mmtp) REVERT: Q 313 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8462 (mp0) REVERT: A 118 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6220 (pmm) REVERT: A 120 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5740 (pmm) REVERT: A 202 TRP cc_start: 0.7524 (t60) cc_final: 0.7321 (t60) REVERT: F 184 MET cc_start: 0.7198 (ptp) cc_final: 0.6656 (pmm) REVERT: F 190 LYS cc_start: 0.8528 (mmpt) cc_final: 0.8228 (mppt) REVERT: C 72 TYR cc_start: 0.8551 (m-80) cc_final: 0.8224 (m-80) REVERT: C 73 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7334 (mtt-85) REVERT: C 160 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7422 (mttm) REVERT: C 281 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8852 (t70) REVERT: C 289 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7402 (mtm110) REVERT: C 327 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8189 (tttp) REVERT: C 364 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7823 (tp30) REVERT: C 366 ARG cc_start: 0.8710 (ttp-170) cc_final: 0.8490 (ttp-170) REVERT: C 370 CYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7832 (m) REVERT: C 411 THR cc_start: 0.7932 (m) cc_final: 0.7497 (p) REVERT: R 3 GLU cc_start: 0.7460 (tp30) cc_final: 0.7217 (tp30) REVERT: R 6 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7243 (t80) REVERT: R 164 TYR cc_start: 0.8175 (m-80) cc_final: 0.7918 (m-80) REVERT: R 197 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7049 (pt) REVERT: R 360 TYR cc_start: 0.8732 (t80) cc_final: 0.8471 (t80) REVERT: R 402 LEU cc_start: 0.7146 (mt) cc_final: 0.6902 (mp) REVERT: N 66 MET cc_start: 0.9344 (ttp) cc_final: 0.9097 (ttt) REVERT: N 160 ASN cc_start: 0.7954 (t0) cc_final: 0.7200 (t0) REVERT: N 365 MET cc_start: 0.8626 (ttt) cc_final: 0.7580 (pmt) REVERT: O 2 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8388 (mm-30) REVERT: O 175 ARG cc_start: 0.8490 (ttt-90) cc_final: 0.8200 (ttp-110) REVERT: O 409 TRP cc_start: 0.8646 (m100) cc_final: 0.8307 (m100) outliers start: 77 outliers final: 44 residues processed: 421 average time/residue: 0.6103 time to fit residues: 312.1984 Evaluate side-chains 399 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 341 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 272 CYS 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 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 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 -609 ARG Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 166 LEU 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 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 194 THR 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 F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 119 VAL 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 307 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 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 213 LEU 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: 4.9990 chunk 418 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 387 optimal weight: 0.6980 chunk 278 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 194 optimal weight: 0.0040 overall best weight: 2.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN J-642 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119141 restraints weight = 46266.123| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.30 r_work: 0.3188 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35309 Z= 0.178 Angle : 0.634 12.715 48098 Z= 0.323 Chirality : 0.046 0.469 5316 Planarity : 0.005 0.069 6196 Dihedral : 5.189 80.025 4811 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 2.13 % Allowed : 17.91 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % 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: 1.83 (0.24), residues: 541 sheet: -0.16 (0.14), residues: 1363 loop : -1.03 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 120 TYR 0.027 0.002 TYR J-637 PHE 0.016 0.002 PHE K 128 TRP 0.049 0.002 TRP J-764 HIS 0.008 0.001 HIS Q 256 Details of bonding type rmsd covalent geometry : bond 0.00438 (35244) covalent geometry : angle 0.63247 (47968) SS BOND : bond 0.00252 ( 65) SS BOND : angle 1.15935 ( 130) hydrogen bonds : bond 0.03036 ( 1017) hydrogen bonds : angle 4.80451 ( 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 418 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 338 time to evaluate : 1.177 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: 0.6156 (ptt) cc_final: 0.5680 (ppp) REVERT: K 132 LEU cc_start: 0.8495 (tp) cc_final: 0.8234 (mt) REVERT: K 151 MET cc_start: 0.8260 (mmp) cc_final: 0.7692 (mmp) REVERT: K 153 VAL cc_start: 0.8915 (t) cc_final: 0.8422 (p) REVERT: K 176 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8311 (mt-10) REVERT: K 208 GLN cc_start: 0.7193 (pm20) cc_final: 0.6931 (pm20) REVERT: K 223 LYS cc_start: 0.8822 (tppt) cc_final: 0.8576 (tppt) REVERT: K 226 SER cc_start: 0.8671 (t) cc_final: 0.7892 (m) REVERT: K 270 GLU cc_start: 0.8056 (tt0) cc_final: 0.7556 (pm20) REVERT: S 131 MET cc_start: 0.7034 (mmm) cc_final: 0.6758 (mmm) REVERT: S 135 LYS cc_start: 0.7232 (mmtp) cc_final: 0.6694 (mptt) REVERT: S 169 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6925 (mtmt) REVERT: G 99 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: G 293 THR cc_start: 0.8118 (m) cc_final: 0.7884 (t) REVERT: G 366 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8227 (ttp80) REVERT: H 57 ASP cc_start: 0.7410 (p0) cc_final: 0.7152 (p0) REVERT: I 33 MET cc_start: 0.5322 (ttp) cc_final: 0.4916 (ttt) REVERT: J -799 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8490 (tm-30) REVERT: J -768 GLN cc_start: 0.8510 (mt0) cc_final: 0.8053 (tt0) REVERT: J -609 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6671 (ttm170) REVERT: B 7 MET cc_start: 0.8269 (ttp) cc_final: 0.8022 (ptt) REVERT: B 10 GLN cc_start: 0.8291 (tt0) cc_final: 0.8046 (tt0) REVERT: B 166 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7776 (tp) REVERT: B 282 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6438 (tp) REVERT: D 57 ASP cc_start: 0.8074 (t70) cc_final: 0.7826 (t0) REVERT: Q 4 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: Q 70 MET cc_start: 0.8911 (tpt) cc_final: 0.8638 (tpt) REVERT: Q 159 GLN cc_start: 0.8404 (tt0) cc_final: 0.8007 (tp40) REVERT: Q 213 LYS cc_start: 0.7873 (mttt) cc_final: 0.7352 (mmtp) REVERT: Q 251 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6767 (tp) REVERT: A 118 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6331 (pmm) REVERT: A 120 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5743 (pmm) REVERT: A 202 TRP cc_start: 0.7544 (t60) cc_final: 0.7248 (t60) REVERT: F 184 MET cc_start: 0.7230 (ptp) cc_final: 0.6671 (pmm) REVERT: F 190 LYS cc_start: 0.8558 (mmpt) cc_final: 0.8106 (mppt) REVERT: C 72 TYR cc_start: 0.8562 (m-80) cc_final: 0.8214 (m-80) REVERT: C 160 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7490 (mttm) REVERT: C 281 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8832 (t70) REVERT: C 289 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7304 (mtm110) REVERT: C 366 ARG cc_start: 0.8712 (ttp-170) cc_final: 0.8470 (ttp-170) REVERT: C 370 CYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7973 (m) REVERT: C 411 THR cc_start: 0.7995 (m) cc_final: 0.7555 (p) REVERT: R 3 GLU cc_start: 0.7509 (tp30) cc_final: 0.7214 (tp30) REVERT: R 164 TYR cc_start: 0.8067 (m-80) cc_final: 0.7776 (m-80) REVERT: R 197 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7252 (pt) REVERT: R 360 TYR cc_start: 0.8724 (t80) cc_final: 0.8450 (t80) REVERT: R 402 LEU cc_start: 0.7246 (mt) cc_final: 0.6932 (mp) REVERT: N 66 MET cc_start: 0.9380 (ttp) cc_final: 0.9058 (ttt) REVERT: N 160 ASN cc_start: 0.8010 (t0) cc_final: 0.7516 (t0) REVERT: N 187 THR cc_start: 0.8039 (m) cc_final: 0.7625 (p) REVERT: N 365 MET cc_start: 0.8719 (ttt) cc_final: 0.7631 (pmt) REVERT: O 2 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: O 175 ARG cc_start: 0.8511 (ttt-90) cc_final: 0.8223 (ttp-110) outliers start: 80 outliers final: 49 residues processed: 396 average time/residue: 0.6029 time to fit residues: 291.6834 Evaluate side-chains 392 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 330 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 166 LEU 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 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 251 LEU 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 F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL 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 233 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU 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 71 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 154 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 385 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 338 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 403 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J-840 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 396 GLN Q 233 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN R 232 GLN ** N 168 HIS ** 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 = 0.4101 r_free = 0.4101 target = 0.174513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119870 restraints weight = 46071.422| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.50 r_work: 0.3198 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35309 Z= 0.143 Angle : 0.612 12.740 48098 Z= 0.311 Chirality : 0.045 0.467 5316 Planarity : 0.005 0.071 6196 Dihedral : 5.154 80.057 4811 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 1.94 % Allowed : 18.17 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % 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: -0.63 (0.13), residues: 4408 helix: 1.61 (0.24), residues: 559 sheet: -0.16 (0.14), residues: 1367 loop : -1.05 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 120 TYR 0.024 0.001 TYR J-637 PHE 0.016 0.001 PHE A 148 TRP 0.058 0.001 TRP J-764 HIS 0.010 0.001 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.00346 (35244) covalent geometry : angle 0.60994 (47968) SS BOND : bond 0.00218 ( 65) SS BOND : angle 1.06864 ( 130) hydrogen bonds : bond 0.02908 ( 1017) hydrogen bonds : angle 4.76841 ( 2625) =============================================================================== Job complete usr+sys time: 16086.38 seconds wall clock time: 273 minutes 4.49 seconds (16384.49 seconds total)