Starting phenix.real_space_refine on Fri May 30 09:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fff_31567/05_2025/7fff_31567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fff_31567/05_2025/7fff_31567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fff_31567/05_2025/7fff_31567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fff_31567/05_2025/7fff_31567.map" model { file = "/net/cci-nas-00/data/ceres_data/7fff_31567/05_2025/7fff_31567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fff_31567/05_2025/7fff_31567.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 268 5.16 5 C 21736 2.51 5 N 5880 2.21 5 O 6468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 34356 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "E" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "R" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "M" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.73, per 1000 atoms: 0.55 Number of scatterers: 34356 At special positions: 0 Unit cell: (209.88, 158.4, 217.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 268 16.00 O 6468 8.00 N 5880 7.00 C 21736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=65, symmetry=0 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 42 " distance=2.03 Simple disulfide: pdb=" SG CYS H 37 " - pdb=" SG CYS H 55 " distance=1.25 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 64 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J-981 " - pdb=" SG CYS J-877 " distance=2.03 Simple disulfide: pdb=" SG CYS J-978 " - pdb=" SG CYS J-973 " distance=2.03 Simple disulfide: pdb=" SG CYS J-910 " - pdb=" SG CYS J-896 " distance=2.02 Simple disulfide: pdb=" SG CYS J-849 " - pdb=" SG CYS J-734 " distance=2.03 Simple disulfide: pdb=" SG CYS J-800 " - pdb=" SG CYS J-774 " distance=2.03 Simple disulfide: pdb=" SG CYS J-798 " - pdb=" SG CYS J-780 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 55 " distance=2.00 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 42 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 55 " distance=1.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 64 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 42 " distance=2.03 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 55 " distance=1.09 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 64 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 4.1 seconds 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8264 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 95 sheets defined 16.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 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: 12.87 Time building geometry restraints manager: 8.65 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 70.390 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.190 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:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.997 35309 Z= 0.541 Angle : 1.050 61.625 48098 Z= 0.567 Chirality : 0.068 2.015 5316 Planarity : 0.008 0.102 6196 Dihedral : 9.593 88.037 12788 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.22 % Rotamer: Outliers : 0.40 % Allowed : 2.52 % Favored : 97.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.11), residues: 4408 helix: -2.14 (0.17), residues: 548 sheet: -1.70 (0.13), residues: 1429 loop : -2.51 (0.10), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP J-764 HIS 0.011 0.002 HIS N 28 PHE 0.032 0.004 PHE Q 328 TYR 0.039 0.003 TYR C 308 ARG 0.015 0.001 ARG Q 21 Details of bonding type rmsd hydrogen bonds : bond 0.20784 ( 1017) hydrogen bonds : angle 8.33862 ( 2625) SS BOND : bond 0.20374 ( 65) SS BOND : angle 8.28552 ( 130) covalent geometry : bond 0.00745 (35244) covalent geometry : angle 0.95904 (47968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 801 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 159 ASN cc_start: 0.4531 (t0) cc_final: 0.4241 (t160) REVERT: K 193 HIS cc_start: 0.6886 (p-80) cc_final: 0.6531 (p90) REVERT: K 215 THR cc_start: 0.6433 (p) cc_final: 0.6000 (p) REVERT: K 270 GLU cc_start: 0.6727 (tt0) cc_final: 0.6342 (pm20) REVERT: S 256 VAL cc_start: 0.5820 (m) cc_final: 0.5526 (m) REVERT: S 261 LYS cc_start: 0.6548 (mmtt) cc_final: 0.6270 (mtmm) REVERT: S 266 LYS cc_start: 0.6495 (tttm) cc_final: 0.5909 (tmtp) REVERT: G 212 ASP cc_start: 0.7539 (t0) cc_final: 0.7314 (p0) REVERT: B 29 ILE cc_start: 0.7555 (mt) cc_final: 0.7203 (mm) REVERT: B 369 ILE cc_start: 0.8473 (tt) cc_final: 0.8267 (tt) REVERT: T 23 TYR cc_start: 0.6250 (t80) cc_final: 0.5677 (t80) REVERT: Q 112 MET cc_start: 0.8772 (ttm) cc_final: 0.8383 (ttm) REVERT: A 148 PHE cc_start: 0.8275 (m-10) cc_final: 0.8072 (m-80) REVERT: R 360 TYR cc_start: 0.8474 (t80) cc_final: 0.8181 (t80) REVERT: N 9 TYR cc_start: 0.8366 (m-80) cc_final: 0.8107 (m-80) REVERT: N 42 ASP cc_start: 0.7649 (m-30) cc_final: 0.7348 (m-30) REVERT: N 112 MET cc_start: 0.9013 (ttm) cc_final: 0.8793 (ttp) REVERT: N 365 MET cc_start: 0.7668 (ttt) cc_final: 0.7355 (pmt) REVERT: O 115 LEU cc_start: 0.8481 (tm) cc_final: 0.8263 (mm) REVERT: O 442 ASN cc_start: 0.6350 (OUTLIER) cc_final: 0.6017 (t0) outliers start: 15 outliers final: 4 residues processed: 809 average time/residue: 1.5119 time to fit residues: 1463.6698 Evaluate side-chains 416 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 411 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 7.9990 chunk 330 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 HIS G 264 ASN G 394 HIS G 396 GLN H 27 ASN H 30 ASN J-848 GLN ** J-775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-744 HIS J-647 HIS J-639 HIS B 10 GLN B 43 ASN B 235 GLN B 360 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN D 27 ASN D 30 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 ASN Q 212 ASN Q 225 GLN Q 232 GLN Q 239 ASN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS F 203 HIS C 130 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN C 442 ASN E 27 ASN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN R 347 ASN R 361 HIS R 405 ASN M 27 ASN M 30 ASN N 7 ASN N 52 GLN N 96 HIS ** N 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 353 HIS ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS O 392 GLN O 394 HIS O 442 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.177606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121789 restraints weight = 46380.027| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.54 r_work: 0.3238 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35309 Z= 0.178 Angle : 0.666 11.221 48098 Z= 0.348 Chirality : 0.046 0.208 5316 Planarity : 0.006 0.089 6196 Dihedral : 6.458 160.296 4819 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 3.48 % Allowed : 11.08 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.12), residues: 4408 helix: -0.23 (0.22), residues: 562 sheet: -1.11 (0.13), residues: 1443 loop : -1.87 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP J-764 HIS 0.007 0.001 HIS Q 305 PHE 0.021 0.002 PHE A 189 TYR 0.024 0.002 TYR O 308 ARG 0.007 0.001 ARG Q 67 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 1017) hydrogen bonds : angle 5.79037 ( 2625) SS BOND : bond 0.00341 ( 65) SS BOND : angle 1.47046 ( 130) covalent geometry : bond 0.00423 (35244) covalent geometry : angle 0.66216 (47968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 465 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.5821 (ptt) cc_final: 0.4639 (tpp) REVERT: K 151 MET cc_start: 0.8149 (mmp) cc_final: 0.7611 (mmp) REVERT: K 153 VAL cc_start: 0.8928 (t) cc_final: 0.8664 (p) REVERT: K 193 HIS cc_start: 0.7909 (p-80) cc_final: 0.7488 (p90) REVERT: K 208 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: K 215 THR cc_start: 0.8653 (p) cc_final: 0.8163 (p) REVERT: K 257 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8083 (ptp) REVERT: K 270 GLU cc_start: 0.8248 (tt0) cc_final: 0.7611 (pm20) REVERT: S 131 MET cc_start: 0.6904 (mmm) cc_final: 0.6667 (mmm) REVERT: S 135 LYS cc_start: 0.7024 (mptt) cc_final: 0.6769 (mmtp) REVERT: S 169 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7095 (mtmt) REVERT: S 199 TYR cc_start: 0.6247 (m-10) cc_final: 0.5857 (m-80) REVERT: S 223 LYS cc_start: 0.8440 (tttt) cc_final: 0.8124 (tptt) REVERT: S 251 THR cc_start: 0.7412 (p) cc_final: 0.7022 (t) REVERT: G 10 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: G 52 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8638 (tttp) REVERT: G 319 LYS cc_start: 0.7731 (ttpm) cc_final: 0.7464 (ttpt) REVERT: G 361 ILE cc_start: 0.8031 (mt) cc_final: 0.7729 (tt) REVERT: H 57 ASP cc_start: 0.7420 (p0) cc_final: 0.7155 (p0) REVERT: J -775 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: J -687 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7830 (mm-30) REVERT: J -609 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6855 (ttm170) REVERT: B 97 ASP cc_start: 0.7967 (m-30) cc_final: 0.7691 (m-30) REVERT: B 207 THR cc_start: 0.8292 (m) cc_final: 0.8022 (t) REVERT: B 433 MET cc_start: 0.5692 (pp-130) cc_final: 0.5107 (ptp) REVERT: D 41 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.8094 (ttt-90) REVERT: D 58 LYS cc_start: 0.8409 (mppt) cc_final: 0.8144 (mppt) REVERT: T 23 TYR cc_start: 0.5923 (t80) cc_final: 0.5051 (t80) REVERT: Q 130 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8772 (pttp) REVERT: Q 137 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: Q 144 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8185 (mt-10) REVERT: Q 213 LYS cc_start: 0.7436 (mttt) cc_final: 0.6876 (mmtp) REVERT: A 118 MET cc_start: 0.6165 (pmt) cc_final: 0.5592 (pmt) REVERT: A 207 VAL cc_start: 0.8163 (m) cc_final: 0.7961 (p) REVERT: F 131 MET cc_start: 0.7849 (mmp) cc_final: 0.7617 (mmm) REVERT: F 266 LYS cc_start: 0.8367 (tttt) cc_final: 0.8140 (tptm) REVERT: C 61 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8151 (ttmt) REVERT: C 73 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7487 (mtt-85) REVERT: C 140 HIS cc_start: 0.7818 (m90) cc_final: 0.7164 (m90) REVERT: C 160 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7708 (ttmt) REVERT: C 300 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: C 324 LYS cc_start: 0.6845 (mtmt) cc_final: 0.6515 (mtmm) REVERT: E 36 MET cc_start: 0.8279 (tpp) cc_final: 0.8004 (tpp) REVERT: R 8 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: R 79 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7590 (tp) REVERT: R 342 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7374 (mp0) REVERT: R 360 TYR cc_start: 0.8759 (t80) cc_final: 0.8384 (t80) REVERT: R 377 ILE cc_start: 0.7540 (mt) cc_final: 0.7306 (mm) REVERT: N 5 LEU cc_start: 0.6157 (mp) cc_final: 0.5837 (pp) REVERT: N 66 MET cc_start: 0.9334 (ttt) cc_final: 0.9037 (ttt) REVERT: N 365 MET cc_start: 0.8739 (ttt) cc_final: 0.7659 (pmt) REVERT: O 2 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: O 73 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7115 (mtp180) REVERT: O 175 ARG cc_start: 0.8349 (ttt-90) cc_final: 0.8011 (ttp-110) outliers start: 131 outliers final: 41 residues processed: 535 average time/residue: 1.3784 time to fit residues: 892.4537 Evaluate side-chains 429 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 373 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -775 GLN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 293 optimal weight: 9.9990 chunk 261 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 302 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 307 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 360 ASN C 394 HIS C 396 GLN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN O 130 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.179026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125180 restraints weight = 46117.946| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.33 r_work: 0.3253 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35309 Z= 0.162 Angle : 0.630 12.457 48098 Z= 0.326 Chirality : 0.046 0.379 5316 Planarity : 0.005 0.077 6196 Dihedral : 5.671 72.924 4814 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 3.48 % Allowed : 13.15 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.12), residues: 4408 helix: 0.50 (0.23), residues: 569 sheet: -0.77 (0.13), residues: 1436 loop : -1.58 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP J-764 HIS 0.006 0.001 HIS Q 305 PHE 0.017 0.002 PHE R 6 TYR 0.024 0.002 TYR O 308 ARG 0.004 0.001 ARG Q 21 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 1017) hydrogen bonds : angle 5.32956 ( 2625) SS BOND : bond 0.00361 ( 65) SS BOND : angle 1.39072 ( 130) covalent geometry : bond 0.00390 (35244) covalent geometry : angle 0.62697 (47968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 410 time to evaluate : 3.644 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: 0.5975 (ptt) cc_final: 0.4724 (tpp) REVERT: K 151 MET cc_start: 0.8277 (mmp) cc_final: 0.7667 (mmp) REVERT: K 153 VAL cc_start: 0.8944 (t) cc_final: 0.8598 (p) REVERT: K 193 HIS cc_start: 0.7969 (p-80) cc_final: 0.7598 (p90) REVERT: K 208 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: K 226 SER cc_start: 0.8332 (t) cc_final: 0.7658 (m) REVERT: K 257 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8247 (ptp) REVERT: K 270 GLU cc_start: 0.8231 (tt0) cc_final: 0.7662 (pm20) REVERT: S 120 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6322 (mpt) REVERT: S 131 MET cc_start: 0.6986 (mmm) cc_final: 0.6739 (mmm) REVERT: S 172 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8116 (tmmt) REVERT: S 199 TYR cc_start: 0.6331 (m-10) cc_final: 0.5857 (m-80) REVERT: S 223 LYS cc_start: 0.8498 (tttt) cc_final: 0.8191 (tptt) REVERT: S 251 THR cc_start: 0.7602 (p) cc_final: 0.7317 (t) REVERT: S 257 MET cc_start: 0.7642 (ptp) cc_final: 0.7380 (mpp) REVERT: S 266 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7803 (tmtp) REVERT: G 99 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: G 319 LYS cc_start: 0.7793 (ttpm) cc_final: 0.7483 (ttpt) REVERT: H 57 ASP cc_start: 0.7369 (p0) cc_final: 0.7048 (p0) REVERT: J -687 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: J -609 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6794 (ttm170) REVERT: B 282 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6483 (tp) REVERT: B 433 MET cc_start: 0.5780 (pp-130) cc_final: 0.5155 (ptm) REVERT: T 23 TYR cc_start: 0.6221 (t80) cc_final: 0.5114 (t80) REVERT: Q 130 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8788 (pttp) REVERT: Q 137 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: Q 144 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8203 (mt-10) REVERT: Q 159 GLN cc_start: 0.8340 (tt0) cc_final: 0.7930 (tp40) REVERT: Q 211 ILE cc_start: 0.8108 (tt) cc_final: 0.7793 (tp) REVERT: Q 213 LYS cc_start: 0.7705 (mttt) cc_final: 0.7204 (mmtp) REVERT: A 118 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5462 (pmt) REVERT: A 146 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4820 (ptpt) REVERT: A 184 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6354 (mpt) REVERT: F 131 MET cc_start: 0.7914 (mmp) cc_final: 0.7700 (mmm) REVERT: F 190 LYS cc_start: 0.8272 (mtmt) cc_final: 0.8034 (mmmt) REVERT: F 195 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6079 (pttm) REVERT: F 257 MET cc_start: 0.5935 (OUTLIER) cc_final: 0.5619 (ptm) REVERT: C 115 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8286 (tp) REVERT: C 139 GLU cc_start: 0.7697 (pp20) cc_final: 0.7434 (pp20) REVERT: C 140 HIS cc_start: 0.7427 (m90) cc_final: 0.6957 (m90) REVERT: C 364 GLU cc_start: 0.8150 (tp30) cc_final: 0.7609 (tp30) REVERT: C 377 LYS cc_start: 0.7295 (ttmm) cc_final: 0.6888 (tttm) REVERT: E 38 SER cc_start: 0.8929 (t) cc_final: 0.8515 (m) REVERT: R 8 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: R 197 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7289 (pt) REVERT: R 323 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: R 360 TYR cc_start: 0.8794 (t80) cc_final: 0.8456 (t80) REVERT: R 377 ILE cc_start: 0.7787 (mt) cc_final: 0.7559 (mm) REVERT: R 402 LEU cc_start: 0.7418 (mt) cc_final: 0.7184 (mp) REVERT: N 66 MET cc_start: 0.9356 (ttt) cc_final: 0.9045 (ttt) REVERT: N 167 MET cc_start: 0.8229 (mpt) cc_final: 0.8023 (mpt) REVERT: N 201 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7062 (tm-30) REVERT: N 365 MET cc_start: 0.8661 (ttt) cc_final: 0.7604 (pmt) REVERT: O 2 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: O 175 ARG cc_start: 0.8274 (ttt-90) cc_final: 0.7836 (ttp-110) outliers start: 131 outliers final: 50 residues processed: 495 average time/residue: 1.3058 time to fit residues: 786.7285 Evaluate side-chains 434 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 363 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 120 MET Chi-restraints excluded: chain S residue 126 LYS Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 266 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 50 optimal weight: 0.5980 chunk 151 optimal weight: 0.0040 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 403 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 2.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 203 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS R 256 HIS O 130 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.173907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119989 restraints weight = 46232.003| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.26 r_work: 0.3180 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35309 Z= 0.203 Angle : 0.650 10.449 48098 Z= 0.335 Chirality : 0.047 0.451 5316 Planarity : 0.005 0.092 6196 Dihedral : 5.660 75.817 4814 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 4.25 % Allowed : 13.50 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4408 helix: 0.88 (0.23), residues: 569 sheet: -0.63 (0.13), residues: 1463 loop : -1.44 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP J-764 HIS 0.007 0.001 HIS N 41 PHE 0.016 0.002 PHE N 328 TYR 0.027 0.002 TYR O 308 ARG 0.006 0.001 ARG Q 103 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 1017) hydrogen bonds : angle 5.18424 ( 2625) SS BOND : bond 0.00335 ( 65) SS BOND : angle 1.39706 ( 130) covalent geometry : bond 0.00501 (35244) covalent geometry : angle 0.64643 (47968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 386 time to evaluate : 3.675 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 151 MET cc_start: 0.8287 (mmp) cc_final: 0.7608 (mmp) REVERT: K 153 VAL cc_start: 0.8957 (t) cc_final: 0.8610 (p) REVERT: K 223 LYS cc_start: 0.8772 (tppt) cc_final: 0.8544 (tppt) REVERT: K 226 SER cc_start: 0.8499 (t) cc_final: 0.7814 (m) REVERT: K 257 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8027 (ptp) REVERT: K 270 GLU cc_start: 0.8090 (tt0) cc_final: 0.7494 (pm20) REVERT: S 131 MET cc_start: 0.6990 (mmm) cc_final: 0.6753 (mmm) REVERT: S 135 LYS cc_start: 0.7223 (mmtp) cc_final: 0.6722 (mptt) REVERT: S 169 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7119 (mtmt) REVERT: S 172 LYS cc_start: 0.8534 (tmmm) cc_final: 0.8304 (tmmt) REVERT: S 251 THR cc_start: 0.7831 (p) cc_final: 0.7591 (t) REVERT: S 257 MET cc_start: 0.7469 (ptp) cc_final: 0.7262 (mpp) REVERT: S 266 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7851 (tmtp) REVERT: G 2 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: G 10 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: G 52 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8603 (tttp) REVERT: G 99 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: G 293 THR cc_start: 0.8282 (m) cc_final: 0.7942 (t) REVERT: G 370 CYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7266 (m) REVERT: H 57 ASP cc_start: 0.7377 (p0) cc_final: 0.7115 (p0) REVERT: J -768 GLN cc_start: 0.8541 (mt0) cc_final: 0.8012 (tt0) REVERT: J -687 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7741 (mm-30) REVERT: J -609 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6688 (ttm170) REVERT: B 10 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: B 97 ASP cc_start: 0.8072 (m-30) cc_final: 0.7748 (p0) REVERT: B 282 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6642 (tp) REVERT: T 23 TYR cc_start: 0.5901 (t80) cc_final: 0.5179 (t80) REVERT: Q 4 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: Q 130 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8805 (mtmm) REVERT: Q 137 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: Q 144 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8188 (mt-10) REVERT: Q 159 GLN cc_start: 0.8437 (tt0) cc_final: 0.7926 (tp40) REVERT: Q 167 MET cc_start: 0.7911 (mmt) cc_final: 0.6923 (mmt) REVERT: Q 213 LYS cc_start: 0.7901 (mttt) cc_final: 0.7337 (mmtp) REVERT: A 118 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5582 (pmm) REVERT: A 146 LYS cc_start: 0.5030 (OUTLIER) cc_final: 0.4736 (ptpt) REVERT: A 184 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6416 (mpt) REVERT: F 195 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6129 (pttm) REVERT: F 257 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5586 (ptm) REVERT: C 140 HIS cc_start: 0.7329 (m90) cc_final: 0.6890 (m90) REVERT: C 160 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7716 (ttmt) REVERT: C 327 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8109 (tttp) REVERT: C 364 GLU cc_start: 0.8277 (tp30) cc_final: 0.7682 (tp30) REVERT: C 375 THR cc_start: 0.8630 (m) cc_final: 0.8407 (t) REVERT: E 38 SER cc_start: 0.8911 (t) cc_final: 0.8534 (m) REVERT: R 6 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7015 (t80) REVERT: R 8 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: R 60 ASN cc_start: 0.7097 (m110) cc_final: 0.6739 (m110) REVERT: R 323 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: R 360 TYR cc_start: 0.8734 (t80) cc_final: 0.8347 (t80) REVERT: L 44 ASP cc_start: 0.7159 (t0) cc_final: 0.6905 (m-30) REVERT: N 20 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.7916 (mt) REVERT: N 66 MET cc_start: 0.9384 (ttt) cc_final: 0.9172 (ttt) REVERT: N 160 ASN cc_start: 0.7340 (t0) cc_final: 0.6929 (t0) REVERT: N 201 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7116 (tm-30) REVERT: N 365 MET cc_start: 0.8741 (ttt) cc_final: 0.7603 (pmt) REVERT: O 2 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: O 175 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8159 (ttp-110) outliers start: 160 outliers final: 81 residues processed: 500 average time/residue: 1.2481 time to fit residues: 762.4140 Evaluate side-chains 458 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 351 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 126 LYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 266 LYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -833 MET Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 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 327 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 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 374 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 404 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 387 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 204 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J-920 HIS J-919 GLN J-767 ASN J-642 HIS B 386 HIS ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN O 157 ASN O 360 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117862 restraints weight = 46280.298| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.38 r_work: 0.3163 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 35309 Z= 0.225 Angle : 0.660 9.825 48098 Z= 0.340 Chirality : 0.047 0.495 5316 Planarity : 0.005 0.093 6196 Dihedral : 5.682 78.294 4814 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 4.70 % Allowed : 13.71 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 4408 helix: 1.38 (0.24), residues: 541 sheet: -0.57 (0.14), residues: 1380 loop : -1.34 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP J-764 HIS 0.008 0.002 HIS N 41 PHE 0.017 0.002 PHE N 328 TYR 0.027 0.002 TYR O 308 ARG 0.008 0.001 ARG Q 88 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1017) hydrogen bonds : angle 5.13770 ( 2625) SS BOND : bond 0.00332 ( 65) SS BOND : angle 1.36976 ( 130) covalent geometry : bond 0.00555 (35244) covalent geometry : angle 0.65727 (47968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 366 time to evaluate : 3.699 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: 0.5744 (OUTLIER) cc_final: 0.5490 (ppp) REVERT: K 151 MET cc_start: 0.8222 (mmp) cc_final: 0.7567 (mmp) REVERT: K 153 VAL cc_start: 0.8996 (t) cc_final: 0.8668 (p) REVERT: K 223 LYS cc_start: 0.8850 (tppt) cc_final: 0.8619 (tppt) REVERT: K 226 SER cc_start: 0.8711 (t) cc_final: 0.7882 (m) REVERT: K 257 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7961 (ptp) REVERT: K 270 GLU cc_start: 0.8041 (tt0) cc_final: 0.7505 (pm20) REVERT: S 131 MET cc_start: 0.6953 (mmm) cc_final: 0.6522 (mmm) REVERT: S 135 LYS cc_start: 0.7144 (mmtp) cc_final: 0.6569 (mptt) REVERT: S 169 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7101 (mtmt) REVERT: S 172 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8145 (tmmt) REVERT: G 6 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8069 (t) REVERT: G 10 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: G 52 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8541 (tttp) REVERT: G 99 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: G 293 THR cc_start: 0.8300 (m) cc_final: 0.7959 (t) REVERT: G 366 ARG cc_start: 0.8442 (ttp80) cc_final: 0.7570 (ttp80) REVERT: G 370 CYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7492 (m) REVERT: H 57 ASP cc_start: 0.7420 (p0) cc_final: 0.7156 (p0) REVERT: J -768 GLN cc_start: 0.8559 (mt0) cc_final: 0.8121 (tt0) REVERT: J -687 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: J -609 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6714 (ttm170) REVERT: J -588 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6927 (mp) REVERT: B 10 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: B 97 ASP cc_start: 0.8101 (m-30) cc_final: 0.7797 (p0) REVERT: B 282 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6464 (tp) REVERT: B 305 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5813 (mt-10) REVERT: B 341 GLU cc_start: 0.8221 (pm20) cc_final: 0.7754 (pm20) REVERT: D 41 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7718 (ttt-90) REVERT: T 23 TYR cc_start: 0.5946 (t80) cc_final: 0.5416 (t80) REVERT: Q 4 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: Q 130 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8829 (mtmm) REVERT: Q 137 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: Q 144 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8187 (mt-10) REVERT: Q 159 GLN cc_start: 0.8427 (tt0) cc_final: 0.7930 (tp40) REVERT: Q 213 LYS cc_start: 0.7871 (mttt) cc_final: 0.7360 (mmtp) REVERT: A 118 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6018 (pmm) REVERT: A 184 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6308 (mpt) REVERT: F 195 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6201 (pttm) REVERT: F 257 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5597 (ptm) REVERT: C 72 TYR cc_start: 0.8591 (m-80) cc_final: 0.8221 (m-80) REVERT: C 140 HIS cc_start: 0.7362 (m90) cc_final: 0.6810 (m90) REVERT: C 160 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7537 (tttm) REVERT: C 206 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8269 (tpt170) REVERT: C 281 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8879 (t70) REVERT: C 289 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7264 (mtm110) REVERT: C 364 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: E 38 SER cc_start: 0.8976 (t) cc_final: 0.8647 (m) REVERT: R 6 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7054 (t80) REVERT: R 8 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: R 60 ASN cc_start: 0.7013 (m110) cc_final: 0.6746 (m-40) REVERT: R 111 THR cc_start: 0.8408 (m) cc_final: 0.7969 (m) REVERT: R 323 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: R 360 TYR cc_start: 0.8731 (t80) cc_final: 0.8361 (t80) REVERT: R 398 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7043 (m) REVERT: N 66 MET cc_start: 0.9420 (ttp) cc_final: 0.9149 (ttt) REVERT: N 160 ASN cc_start: 0.7162 (t0) cc_final: 0.6835 (t0) REVERT: N 187 THR cc_start: 0.8154 (m) cc_final: 0.7675 (p) REVERT: N 365 MET cc_start: 0.8740 (ttt) cc_final: 0.7601 (pmt) REVERT: O 2 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: O 18 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8539 (pp) REVERT: O 175 ARG cc_start: 0.8546 (ttt-90) cc_final: 0.8232 (ttp-110) outliers start: 177 outliers final: 94 residues processed: 484 average time/residue: 1.3324 time to fit residues: 792.8697 Evaluate side-chains 464 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 338 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 126 LYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -631 LEU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain J residue -588 LEU Chi-restraints excluded: chain B residue 10 GLN Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain R residue 368 ILE Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 398 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 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 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 104 optimal weight: 0.6980 chunk 310 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 331 optimal weight: 1.9990 chunk 424 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 chunk 431 optimal weight: 3.9990 chunk 386 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 ASN J-919 GLN J-767 ASN Q 60 ASN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 203 HIS R 159 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.173967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119520 restraints weight = 46275.034| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.29 r_work: 0.3191 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35309 Z= 0.149 Angle : 0.612 10.471 48098 Z= 0.314 Chirality : 0.046 0.478 5316 Planarity : 0.005 0.068 6196 Dihedral : 5.485 78.577 4814 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 4.04 % Allowed : 14.77 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4408 helix: 1.50 (0.24), residues: 541 sheet: -0.43 (0.14), residues: 1362 loop : -1.25 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP J-764 HIS 0.005 0.001 HIS O 386 PHE 0.018 0.001 PHE R 217 TYR 0.026 0.001 TYR R 363 ARG 0.007 0.000 ARG Q 88 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 1017) hydrogen bonds : angle 4.99790 ( 2625) SS BOND : bond 0.00278 ( 65) SS BOND : angle 1.32437 ( 130) covalent geometry : bond 0.00357 (35244) covalent geometry : angle 0.60904 (47968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 368 time to evaluate : 4.120 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 132 LEU cc_start: 0.8546 (tp) cc_final: 0.8202 (mt) REVERT: K 151 MET cc_start: 0.8068 (mmp) cc_final: 0.7578 (mmp) REVERT: K 153 VAL cc_start: 0.8964 (t) cc_final: 0.8635 (p) REVERT: K 226 SER cc_start: 0.8713 (t) cc_final: 0.7963 (m) REVERT: K 270 GLU cc_start: 0.7960 (tt0) cc_final: 0.7425 (pm20) REVERT: S 131 MET cc_start: 0.6917 (mmm) cc_final: 0.6618 (mmm) REVERT: S 135 LYS cc_start: 0.7205 (mmtp) cc_final: 0.6656 (mptt) REVERT: S 169 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7090 (mtmt) REVERT: S 172 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8237 (tmmt) REVERT: G 52 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8527 (tttp) REVERT: G 99 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: G 293 THR cc_start: 0.8196 (m) cc_final: 0.7969 (t) REVERT: G 366 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7526 (ttp80) REVERT: G 370 CYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7258 (m) REVERT: H 57 ASP cc_start: 0.7377 (p0) cc_final: 0.7136 (p0) REVERT: J -768 GLN cc_start: 0.8548 (mt0) cc_final: 0.8077 (tt0) REVERT: J -687 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: J -609 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6733 (ttm170) REVERT: J -588 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6844 (mp) REVERT: B 7 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7925 (ttp) REVERT: B 9 SER cc_start: 0.8600 (t) cc_final: 0.8261 (p) REVERT: B 151 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6455 (pm20) REVERT: B 166 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7874 (tp) REVERT: B 282 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6514 (tp) REVERT: B 305 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.5653 (mt-10) REVERT: B 341 GLU cc_start: 0.8199 (pm20) cc_final: 0.7704 (pm20) REVERT: D 41 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.8008 (ttt-90) REVERT: T 23 TYR cc_start: 0.5950 (t80) cc_final: 0.5417 (t80) REVERT: Q 4 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: Q 130 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8762 (mtmm) REVERT: Q 137 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: Q 144 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8239 (mt-10) REVERT: Q 159 GLN cc_start: 0.8405 (tt0) cc_final: 0.7975 (tp40) REVERT: Q 213 LYS cc_start: 0.7792 (mttt) cc_final: 0.7293 (mmtp) REVERT: A 118 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6050 (pmm) REVERT: A 184 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6309 (mpt) REVERT: F 169 LYS cc_start: 0.7122 (tptp) cc_final: 0.6841 (tppt) REVERT: C 72 TYR cc_start: 0.8558 (m-80) cc_final: 0.8174 (m-80) REVERT: C 97 ASP cc_start: 0.7465 (m-30) cc_final: 0.7149 (p0) REVERT: C 140 HIS cc_start: 0.7340 (m90) cc_final: 0.7074 (m90) REVERT: C 281 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8849 (t70) REVERT: C 289 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7225 (mtm110) REVERT: C 364 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: C 396 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: E 38 SER cc_start: 0.8943 (t) cc_final: 0.8631 (m) REVERT: R 6 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7205 (t80) REVERT: R 8 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: R 60 ASN cc_start: 0.7026 (m110) cc_final: 0.6753 (m-40) REVERT: R 164 TYR cc_start: 0.8256 (m-80) cc_final: 0.8003 (m-80) REVERT: R 323 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: R 360 TYR cc_start: 0.8698 (t80) cc_final: 0.8296 (t80) REVERT: R 397 LEU cc_start: 0.7184 (mt) cc_final: 0.6858 (mp) REVERT: N 20 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8147 (mp) REVERT: N 66 MET cc_start: 0.9373 (ttp) cc_final: 0.9067 (ttt) REVERT: N 160 ASN cc_start: 0.7912 (t0) cc_final: 0.7515 (t0) REVERT: N 365 MET cc_start: 0.8737 (ttt) cc_final: 0.7615 (pmt) REVERT: O 2 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: O 73 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7099 (mtp180) REVERT: O 175 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8205 (ttp-110) outliers start: 152 outliers final: 79 residues processed: 468 average time/residue: 1.3053 time to fit residues: 744.2120 Evaluate side-chains 450 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 344 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain 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 169 LYS Chi-restraints excluded: chain S residue 172 LYS Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain 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 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 151 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain T residue 33 MET Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 143 VAL 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 179 GLN Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain R residue 398 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 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 73 ARG Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 263 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 20 optimal weight: 30.0000 chunk 307 optimal weight: 10.0000 chunk 312 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 421 optimal weight: 0.0070 chunk 85 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 399 optimal weight: 0.8980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 396 GLN Q 60 ASN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN R 353 HIS R 358 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121460 restraints weight = 46422.404| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.32 r_work: 0.3225 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35309 Z= 0.106 Angle : 0.580 10.805 48098 Z= 0.297 Chirality : 0.044 0.474 5316 Planarity : 0.005 0.069 6196 Dihedral : 5.193 78.290 4811 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 3.19 % Allowed : 15.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4408 helix: 1.56 (0.24), residues: 555 sheet: -0.25 (0.14), residues: 1351 loop : -1.20 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP J-764 HIS 0.004 0.001 HIS C 140 PHE 0.023 0.001 PHE R 217 TYR 0.022 0.001 TYR O 308 ARG 0.007 0.000 ARG Q 88 Details of bonding type rmsd hydrogen bonds : bond 0.02795 ( 1017) hydrogen bonds : angle 4.85297 ( 2625) SS BOND : bond 0.00206 ( 65) SS BOND : angle 1.14787 ( 130) covalent geometry : bond 0.00244 (35244) covalent geometry : angle 0.57737 (47968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 370 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 151 MET cc_start: 0.8050 (mmp) cc_final: 0.7521 (mmp) REVERT: K 153 VAL cc_start: 0.8878 (t) cc_final: 0.8533 (p) REVERT: K 226 SER cc_start: 0.8570 (t) cc_final: 0.7759 (m) REVERT: S 131 MET cc_start: 0.6911 (mmm) cc_final: 0.6612 (mmm) REVERT: S 135 LYS cc_start: 0.7195 (mmtp) cc_final: 0.6642 (mptt) REVERT: S 169 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7095 (mtmt) REVERT: S 172 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8235 (tmmt) REVERT: G 99 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: G 293 THR cc_start: 0.8102 (m) cc_final: 0.7880 (t) REVERT: G 366 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7537 (ttp80) REVERT: H 57 ASP cc_start: 0.7410 (p0) cc_final: 0.7115 (p0) REVERT: J -984 MET cc_start: 0.8860 (mtp) cc_final: 0.8533 (mtm) REVERT: J -799 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8609 (tm-30) REVERT: J -768 GLN cc_start: 0.8498 (mt0) cc_final: 0.8022 (tt0) REVERT: J -687 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: J -609 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6680 (ttm170) REVERT: B 29 ILE cc_start: 0.7603 (mt) cc_final: 0.7265 (mm) REVERT: B 212 ASP cc_start: 0.7261 (p0) cc_final: 0.6989 (t0) REVERT: B 305 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5688 (mt-10) REVERT: B 364 GLU cc_start: 0.7650 (pt0) cc_final: 0.7203 (pp20) REVERT: D 41 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7992 (ttt-90) REVERT: T 23 TYR cc_start: 0.5878 (t80) cc_final: 0.5353 (t80) REVERT: Q 4 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: Q 137 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: Q 159 GLN cc_start: 0.8354 (tt0) cc_final: 0.8008 (tp40) REVERT: Q 213 LYS cc_start: 0.7646 (mttt) cc_final: 0.7120 (mmtp) REVERT: A 118 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6469 (pmm) REVERT: A 120 MET cc_start: 0.5922 (pmm) cc_final: 0.5566 (pmm) REVERT: C 72 TYR cc_start: 0.8541 (m-80) cc_final: 0.8161 (m-80) REVERT: C 97 ASP cc_start: 0.7478 (m-30) cc_final: 0.7144 (p0) REVERT: C 140 HIS cc_start: 0.7492 (m90) cc_final: 0.7140 (m170) REVERT: C 160 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7528 (mttm) REVERT: C 281 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8842 (t70) REVERT: C 289 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7733 (ttp80) REVERT: C 364 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: R 8 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: R 60 ASN cc_start: 0.7078 (m110) cc_final: 0.6814 (m-40) REVERT: R 70 MET cc_start: 0.8526 (tpt) cc_final: 0.8233 (mmm) REVERT: R 164 TYR cc_start: 0.8221 (m-80) cc_final: 0.7939 (m-80) REVERT: R 197 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7091 (pt) REVERT: R 216 GLN cc_start: 0.7723 (tt0) cc_final: 0.7506 (tm-30) REVERT: R 360 TYR cc_start: 0.8745 (t80) cc_final: 0.8400 (t80) REVERT: R 397 LEU cc_start: 0.7167 (mt) cc_final: 0.6810 (mp) REVERT: N 66 MET cc_start: 0.9385 (ttp) cc_final: 0.9101 (ttt) REVERT: N 160 ASN cc_start: 0.7895 (t0) cc_final: 0.7493 (t0) REVERT: N 365 MET cc_start: 0.8737 (ttt) cc_final: 0.7636 (pmt) REVERT: O 2 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: O 18 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8510 (pp) REVERT: O 175 ARG cc_start: 0.8477 (ttt-90) cc_final: 0.8193 (ttp-110) outliers start: 120 outliers final: 69 residues processed: 446 average time/residue: 1.3232 time to fit residues: 723.6148 Evaluate side-chains 422 residues out of total 3764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 338 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain 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 169 LYS Chi-restraints excluded: chain S residue 172 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 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 -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain T residue 33 MET Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 140 THR Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 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 8 GLU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN 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 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.9535 > 50: distance: 95 - 100: 34.829 distance: 101 - 102: 47.956 distance: 101 - 104: 55.717 distance: 102 - 103: 29.317 distance: 102 - 105: 47.160 distance: 105 - 106: 36.663 distance: 106 - 107: 57.370 distance: 106 - 109: 51.636 distance: 107 - 108: 40.593 distance: 107 - 114: 26.166 distance: 110 - 111: 38.238 distance: 111 - 112: 32.324 distance: 111 - 113: 27.796 distance: 114 - 115: 53.967 distance: 115 - 116: 33.240 distance: 115 - 118: 52.734 distance: 116 - 117: 47.591 distance: 116 - 123: 40.872 distance: 118 - 119: 47.790 distance: 119 - 120: 38.676 distance: 120 - 121: 41.766 distance: 120 - 122: 30.794 distance: 123 - 124: 40.705 distance: 124 - 125: 40.297 distance: 124 - 127: 57.205 distance: 125 - 126: 68.996 distance: 127 - 128: 56.031 distance: 127 - 129: 57.895 distance: 130 - 131: 40.747 distance: 131 - 132: 40.955 distance: 131 - 134: 46.846 distance: 132 - 133: 54.947 distance: 132 - 135: 50.933 distance: 135 - 136: 32.764 distance: 135 - 141: 40.718 distance: 136 - 137: 40.297 distance: 136 - 139: 56.453 distance: 137 - 138: 39.868 distance: 137 - 142: 40.724 distance: 140 - 141: 51.058 distance: 142 - 143: 40.148 distance: 143 - 144: 39.393 distance: 144 - 145: 57.321 distance: 144 - 146: 11.686 distance: 146 - 147: 41.548 distance: 147 - 148: 39.005 distance: 147 - 150: 38.632 distance: 148 - 149: 40.516 distance: 150 - 151: 41.307 distance: 151 - 152: 8.473 distance: 151 - 153: 40.980 distance: 154 - 155: 40.411 distance: 154 - 160: 47.031 distance: 155 - 156: 40.090 distance: 155 - 158: 51.893 distance: 156 - 157: 56.222 distance: 158 - 159: 34.429 distance: 159 - 160: 39.814 distance: 161 - 162: 41.084 distance: 163 - 171: 35.677 distance: 165 - 166: 45.915 distance: 166 - 167: 43.874 distance: 166 - 168: 46.438 distance: 168 - 170: 61.419 distance: 169 - 170: 15.248