Starting phenix.real_space_refine on Fri Aug 9 04:32:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/08_2024/7ffl_31568_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/08_2024/7ffl_31568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/08_2024/7ffl_31568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/08_2024/7ffl_31568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/08_2024/7ffl_31568_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/08_2024/7ffl_31568_neut.cif" } resolution = 3.1 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 201 5.16 5 C 16302 2.51 5 N 4410 2.21 5 O 4851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 161": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J ARG 419": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q ARG 281": "NH1" <-> "NH2" Residue "Q ARG 419": "NH1" <-> "NH2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 103": "NH1" <-> "NH2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "R ARG 407": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25767 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "E" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "R" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.42, per 1000 atoms: 0.56 Number of scatterers: 25767 At special positions: 0 Unit cell: (158.4, 199.32, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 201 16.00 O 4851 8.00 N 4410 7.00 C 16302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 55 " distance=2.00 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 42 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 55 " distance=1.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 64 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 42 " distance=2.03 Simple disulfide: pdb=" SG CYS H 37 " - pdb=" SG CYS H 55 " distance=1.25 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 64 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 266 " distance=2.03 Simple disulfide: pdb=" SG CYS J 200 " - pdb=" SG CYS J 226 " distance=2.03 Simple disulfide: pdb=" SG CYS J 202 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 9.33 Conformation dependent library (CDL) restraints added in 4.9 seconds 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 69 sheets defined 16.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.094A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.858A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.238A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.542A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 404 through 438 removed outlier: 4.834A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.730A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.662A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 404 through 439 removed outlier: 3.665A pdb=" N LEU C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.902A pdb=" N SER E 59 " --> pdb=" O PHE E 56 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP E 60 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS E 62 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.743A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.648A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.566A pdb=" N ARG F 185 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 289 through 293 removed outlier: 3.586A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.758A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 55 through 62 removed outlier: 4.434A pdb=" N SER H 59 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP H 60 " --> pdb=" O ASP H 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.968A pdb=" N VAL I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.545A pdb=" N LYS I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 351 through 363 removed outlier: 3.785A pdb=" N VAL J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE J 356 " --> pdb=" O PRO J 352 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR J 357 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE J 368 " --> pdb=" O PRO J 364 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU J 369 " --> pdb=" O MET J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 416 Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.593A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.207A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.532A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.774A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 8 through 12 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.736A pdb=" N ILE R 356 " --> pdb=" O PRO R 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE R 368 " --> pdb=" O PRO R 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 369 " --> pdb=" O MET R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 410 through 416 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.873A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.591A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.098A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.654A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.734A pdb=" N TYR A 139 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 143 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.098A pdb=" N ALA A 206 " --> pdb=" O PRO A 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 214 through 217 current: chain 'A' and resid 239 through 247 removed outlier: 7.859A pdb=" N ALA A 239 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 147 current: chain 'B' and resid 183 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.752A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 103 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 101 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.307A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.647A pdb=" N CYS B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 147 current: chain 'C' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 55 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.699A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.405A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC3, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AC4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC5, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.640A pdb=" N VAL F 143 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 190 through 191 current: chain 'F' and resid 205 through 209 removed outlier: 8.538A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 214 through 217 current: chain 'F' and resid 236 through 246 removed outlier: 5.774A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD1, first strand: chain 'G' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 27 through 31 current: chain 'G' and resid 119 through 137 removed outlier: 3.505A pdb=" N THR G 144 " --> pdb=" O LEU G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 141 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD2, first strand: chain 'G' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 55 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD4, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.337A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AD7, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AD8, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AE1, first strand: chain 'I' and resid 6 through 8 removed outlier: 3.616A pdb=" N PHE I 14 " --> pdb=" O CYS I 7 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AE3, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.587A pdb=" N GLN J 48 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL J 36 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG J 46 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J 65 " --> pdb=" O GLY J 54 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.504A pdb=" N ILE J 110 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 147 through 149 Processing sheet with id=AE6, first strand: chain 'J' and resid 152 through 154 Processing sheet with id=AE7, first strand: chain 'J' and resid 237 through 238 removed outlier: 3.534A pdb=" N VAL J 237 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY J 253 " --> pdb=" O MET J 167 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 179 through 181 Processing sheet with id=AE9, first strand: chain 'J' and resid 196 through 200 removed outlier: 3.983A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 275 through 279 Processing sheet with id=AF2, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AF3, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AF4, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.623A pdb=" N GLN Q 48 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR Q 65 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AF6, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AF7, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.785A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 179 through 181 removed outlier: 4.120A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AG1, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AG2, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AG3, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.795A pdb=" N GLN R 48 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL R 36 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG R 46 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AG5, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AG6, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.629A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.879A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.562A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AH1, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.655A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AH3, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AH4, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.496A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.156A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.516A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 10.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8253 1.34 - 1.46: 6441 1.46 - 1.59: 11475 1.59 - 1.71: 0 1.71 - 1.84: 264 Bond restraints: 26433 Sorted by residual: bond pdb=" CB VAL G 148 " pdb=" CG2 VAL G 148 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.75e+00 bond pdb=" CB VAL C 148 " pdb=" CG2 VAL C 148 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.56e+00 bond pdb=" CB VAL G 42 " pdb=" CG1 VAL G 42 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.54e+00 bond pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.83e+00 bond pdb=" C ASN G 264 " pdb=" N PRO G 265 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.74e+00 ... (remaining 26428 not shown) Histogram of bond angle deviations from ideal: 98.16 - 108.50: 2251 108.50 - 118.84: 19218 118.84 - 129.18: 14292 129.18 - 139.52: 214 139.52 - 149.86: 1 Bond angle restraints: 35976 Sorted by residual: angle pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" C PRO R 409 " ideal model delta sigma weight residual 112.47 149.86 -37.39 2.06e+00 2.36e-01 3.29e+02 angle pdb=" N PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta sigma weight residual 110.49 132.07 -21.58 1.69e+00 3.50e-01 1.63e+02 angle pdb=" N LYS D 58 " pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 111.39 123.04 -11.65 1.38e+00 5.25e-01 7.12e+01 angle pdb=" N LYS H 58 " pdb=" CA LYS H 58 " pdb=" C LYS H 58 " ideal model delta sigma weight residual 111.54 120.30 -8.76 1.36e+00 5.41e-01 4.15e+01 angle pdb=" N PHE H 56 " pdb=" CA PHE H 56 " pdb=" C PHE H 56 " ideal model delta sigma weight residual 109.96 100.78 9.18 1.50e+00 4.44e-01 3.75e+01 ... (remaining 35971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 14964 14.33 - 28.65: 732 28.65 - 42.98: 189 42.98 - 57.31: 31 57.31 - 71.64: 20 Dihedral angle restraints: 15936 sinusoidal: 6261 harmonic: 9675 Sorted by residual: dihedral pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual 115.10 155.02 -39.92 0 2.50e+00 1.60e-01 2.55e+02 dihedral pdb=" C PRO R 409 " pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual -120.70 -155.07 34.37 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta harmonic sigma weight residual 122.80 157.10 -34.30 0 2.50e+00 1.60e-01 1.88e+02 ... (remaining 15933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 3981 0.403 - 0.806: 4 0.806 - 1.209: 0 1.209 - 1.612: 1 1.612 - 2.014: 1 Chirality restraints: 3987 Sorted by residual: chirality pdb=" CA PRO R 409 " pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CB PRO R 409 " both_signs ideal model delta sigma weight residual False 2.72 0.70 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA PHE R 410 " pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CB PHE R 410 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.63e+01 chirality pdb=" CA LYS D 58 " pdb=" N LYS D 58 " pdb=" C LYS D 58 " pdb=" CB LYS D 58 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 3984 not shown) Planarity restraints: 4647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 265 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 236 " -0.039 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP J 236 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J 236 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP J 236 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 236 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J 236 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 236 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 236 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 236 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J 236 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 264 " 0.057 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO B 265 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " 0.049 5.00e-02 4.00e+02 ... (remaining 4644 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 376 2.65 - 3.22: 21300 3.22 - 3.78: 37781 3.78 - 4.34: 51412 4.34 - 4.90: 86899 Nonbonded interactions: 197768 Sorted by model distance: nonbonded pdb=" OD1 ASP D 57 " pdb=" OG SER J 177 " model vdw 2.092 3.040 nonbonded pdb=" O HIS G 441 " pdb=" OXT ASN G 442 " model vdw 2.236 3.040 nonbonded pdb=" O ALA C 401 " pdb=" OH TYR R 359 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU B 120 " pdb=" OH TYR B 122 " model vdw 2.269 3.040 nonbonded pdb=" O ALA B 401 " pdb=" OH TYR Q 359 " model vdw 2.272 3.040 ... (remaining 197763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 68.380 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 26433 Z= 0.499 Angle : 0.964 37.389 35976 Z= 0.532 Chirality : 0.071 2.014 3987 Planarity : 0.008 0.102 4647 Dihedral : 9.546 71.636 9591 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.65 % Favored : 93.19 % Rotamer: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.20 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % Rama-Z (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: -3.39 (0.12), residues: 3306 helix: -2.35 (0.18), residues: 435 sheet: -1.84 (0.16), residues: 909 loop : -2.50 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP J 236 HIS 0.010 0.002 HIS J 288 PHE 0.032 0.004 PHE Q 328 TYR 0.039 0.003 TYR C 308 ARG 0.015 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 649 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7298 (t) REVERT: A 200 TYR cc_start: 0.6210 (m-80) cc_final: 0.5619 (m-80) REVERT: A 267 TYR cc_start: 0.6714 (t80) cc_final: 0.6229 (t80) REVERT: B 55 MET cc_start: 0.8105 (mtm) cc_final: 0.7902 (mtm) REVERT: C 115 LEU cc_start: 0.8423 (tm) cc_final: 0.8192 (tp) REVERT: C 354 ILE cc_start: 0.8152 (pt) cc_final: 0.7800 (mt) REVERT: D 28 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7146 (mm-30) REVERT: E 43 ILE cc_start: 0.8924 (pt) cc_final: 0.8711 (pt) REVERT: F 193 HIS cc_start: 0.7965 (p-80) cc_final: 0.7571 (p-80) REVERT: J 356 ILE cc_start: 0.9038 (mt) cc_final: 0.8733 (mp) REVERT: J 390 CYS cc_start: 0.6584 (m) cc_final: 0.6128 (t) REVERT: R 21 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.6578 (mmm160) REVERT: S 184 MET cc_start: 0.6585 (ttm) cc_final: 0.6328 (ttm) REVERT: S 228 ARG cc_start: 0.3559 (mtt-85) cc_final: 0.3315 (mtp85) REVERT: S 256 VAL cc_start: 0.6193 (m) cc_final: 0.5901 (m) REVERT: S 266 LYS cc_start: 0.6712 (tttm) cc_final: 0.6208 (tptm) outliers start: 10 outliers final: 2 residues processed: 658 average time/residue: 0.4049 time to fit residues: 398.4620 Evaluate side-chains 351 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 348 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain G residue 263 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN B 43 ASN B 140 HIS B 218 ASN B 386 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 442 ASN C 235 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 394 HIS C 442 ASN D 27 ASN D 30 ASN E 30 ASN F 137 ASN F 203 HIS G 125 HIS G 264 ASN G 360 ASN G 394 HIS ** G 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN H 30 ASN J 256 HIS J 353 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS R 121 HIS R 152 GLN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 HIS R 405 ASN T 37 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26433 Z= 0.307 Angle : 0.675 9.891 35976 Z= 0.354 Chirality : 0.047 0.212 3987 Planarity : 0.006 0.095 4647 Dihedral : 6.162 73.430 3609 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 2.34 % Allowed : 7.97 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % 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: -2.26 (0.14), residues: 3306 helix: -0.52 (0.24), residues: 438 sheet: -1.29 (0.16), residues: 951 loop : -1.88 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP J 236 HIS 0.008 0.002 HIS B 140 PHE 0.021 0.002 PHE A 148 TYR 0.022 0.002 TYR C 308 ARG 0.006 0.001 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 375 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6600 (m-80) cc_final: 0.6199 (m-80) REVERT: B 160 LYS cc_start: 0.7653 (tppt) cc_final: 0.7431 (tppt) REVERT: C 115 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8367 (tp) REVERT: C 354 ILE cc_start: 0.8360 (pt) cc_final: 0.8025 (mt) REVERT: D 28 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7254 (mm-30) REVERT: J 342 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7185 (mm-30) REVERT: J 356 ILE cc_start: 0.9014 (mt) cc_final: 0.8775 (mp) REVERT: J 390 CYS cc_start: 0.6628 (m) cc_final: 0.6196 (t) REVERT: Q 360 TYR cc_start: 0.8063 (t80) cc_final: 0.7039 (t80) REVERT: R 88 ARG cc_start: 0.6276 (mmt180) cc_final: 0.5932 (mmt90) REVERT: R 216 GLN cc_start: 0.7912 (tp40) cc_final: 0.7565 (tp40) REVERT: S 184 MET cc_start: 0.6237 (ttm) cc_final: 0.5914 (ttt) REVERT: S 189 PHE cc_start: 0.4357 (m-80) cc_final: 0.4157 (m-10) REVERT: S 255 VAL cc_start: 0.3975 (m) cc_final: 0.3707 (m) REVERT: T 6 MET cc_start: 0.5393 (mpp) cc_final: 0.4506 (mmm) outliers start: 66 outliers final: 42 residues processed: 413 average time/residue: 0.3981 time to fit residues: 254.9273 Evaluate side-chains 358 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 315 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 chunk 321 optimal weight: 20.0000 chunk 264 optimal weight: 3.9990 chunk 295 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 386 HIS G 441 HIS J 358 HIS Q 91 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 26433 Z= 0.384 Angle : 0.680 10.217 35976 Z= 0.354 Chirality : 0.048 0.333 3987 Planarity : 0.006 0.137 4647 Dihedral : 6.086 76.039 3608 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 3.26 % Allowed : 10.31 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.06 % 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: -1.76 (0.14), residues: 3306 helix: 0.35 (0.26), residues: 438 sheet: -1.03 (0.15), residues: 1038 loop : -1.65 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 236 HIS 0.012 0.002 HIS C 230 PHE 0.023 0.002 PHE Q 259 TYR 0.022 0.002 TYR B 308 ARG 0.010 0.001 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 343 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6719 (m-80) cc_final: 0.6222 (m-80) REVERT: C 151 GLU cc_start: 0.7766 (pm20) cc_final: 0.7459 (pm20) REVERT: C 354 ILE cc_start: 0.8509 (pt) cc_final: 0.8182 (mt) REVERT: D 52 LEU cc_start: 0.8697 (mt) cc_final: 0.8473 (mt) REVERT: F 118 MET cc_start: 0.6439 (tmm) cc_final: 0.6116 (tmm) REVERT: J 342 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7189 (mm-30) REVERT: J 390 CYS cc_start: 0.6702 (m) cc_final: 0.6194 (t) REVERT: P 33 MET cc_start: 0.7334 (ttp) cc_final: 0.6846 (ptm) REVERT: Q 357 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7695 (p) REVERT: Q 360 TYR cc_start: 0.8138 (t80) cc_final: 0.7330 (t80) REVERT: R 88 ARG cc_start: 0.6337 (mmt180) cc_final: 0.5843 (mmt180) REVERT: S 184 MET cc_start: 0.5875 (ttm) cc_final: 0.5607 (ttt) outliers start: 92 outliers final: 63 residues processed: 404 average time/residue: 0.3792 time to fit residues: 238.6854 Evaluate side-chains 367 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 303 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain S residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 1.9990 chunk 223 optimal weight: 40.0000 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 316 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 125 HIS ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN C 360 ASN J 232 GLN Q 132 ASN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26433 Z= 0.201 Angle : 0.592 8.311 35976 Z= 0.307 Chirality : 0.045 0.249 3987 Planarity : 0.005 0.073 4647 Dihedral : 5.725 76.977 3608 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 2.34 % Allowed : 11.87 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -1.33 (0.14), residues: 3306 helix: 0.81 (0.26), residues: 438 sheet: -0.69 (0.16), residues: 996 loop : -1.42 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP J 236 HIS 0.005 0.001 HIS C 230 PHE 0.017 0.001 PHE A 189 TYR 0.017 0.001 TYR A 267 ARG 0.006 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 333 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6801 (mppt) cc_final: 0.6283 (ptpp) REVERT: A 200 TYR cc_start: 0.6892 (m-80) cc_final: 0.6434 (m-80) REVERT: A 209 TYR cc_start: 0.6374 (t80) cc_final: 0.6026 (t80) REVERT: C 97 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: C 354 ILE cc_start: 0.8494 (pt) cc_final: 0.8144 (mt) REVERT: F 254 SER cc_start: 0.7576 (p) cc_final: 0.7261 (m) REVERT: G 97 ASP cc_start: 0.7347 (p0) cc_final: 0.7045 (p0) REVERT: G 377 LYS cc_start: 0.8103 (tttm) cc_final: 0.7744 (ptpp) REVERT: J 342 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7062 (mm-30) REVERT: J 390 CYS cc_start: 0.6692 (m) cc_final: 0.6129 (t) REVERT: Q 360 TYR cc_start: 0.8161 (t80) cc_final: 0.7138 (t80) REVERT: R 88 ARG cc_start: 0.6339 (mmt180) cc_final: 0.5915 (mmt90) REVERT: S 184 MET cc_start: 0.5888 (ttm) cc_final: 0.5618 (ttt) REVERT: S 197 GLN cc_start: 0.6756 (pm20) cc_final: 0.6384 (tt0) outliers start: 66 outliers final: 46 residues processed: 374 average time/residue: 0.3751 time to fit residues: 219.2286 Evaluate side-chains 353 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 306 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 235 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 218 optimal weight: 0.3980 chunk 0 optimal weight: 50.0000 chunk 161 optimal weight: 2.9990 chunk 283 optimal weight: 40.0000 chunk 79 optimal weight: 0.0000 overall best weight: 3.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 81 GLN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26433 Z= 0.210 Angle : 0.583 9.736 35976 Z= 0.303 Chirality : 0.045 0.340 3987 Planarity : 0.005 0.080 4647 Dihedral : 5.563 77.237 3608 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 2.76 % Allowed : 12.40 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -1.11 (0.15), residues: 3306 helix: 0.98 (0.26), residues: 444 sheet: -0.53 (0.16), residues: 996 loop : -1.29 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP J 236 HIS 0.006 0.001 HIS C 230 PHE 0.018 0.001 PHE A 189 TYR 0.017 0.001 TYR C 308 ARG 0.005 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 327 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6688 (mppt) cc_final: 0.6153 (ptpp) REVERT: A 200 TYR cc_start: 0.6975 (m-80) cc_final: 0.6557 (m-80) REVERT: C 354 ILE cc_start: 0.8550 (pt) cc_final: 0.8197 (mt) REVERT: F 254 SER cc_start: 0.7610 (p) cc_final: 0.7278 (m) REVERT: G 377 LYS cc_start: 0.8133 (tttm) cc_final: 0.7728 (ptpp) REVERT: J 342 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7033 (mm-30) REVERT: J 390 CYS cc_start: 0.6730 (m) cc_final: 0.6127 (t) REVERT: Q 357 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7635 (p) REVERT: Q 360 TYR cc_start: 0.8087 (t80) cc_final: 0.7291 (t80) REVERT: R 88 ARG cc_start: 0.6336 (mmt180) cc_final: 0.5915 (mmt90) REVERT: S 184 MET cc_start: 0.6341 (ttm) cc_final: 0.5971 (ttt) REVERT: S 197 GLN cc_start: 0.6802 (pm20) cc_final: 0.6447 (tt0) REVERT: T 6 MET cc_start: 0.5585 (mpp) cc_final: 0.5244 (mpp) outliers start: 78 outliers final: 63 residues processed: 373 average time/residue: 0.3660 time to fit residues: 214.3185 Evaluate side-chains 366 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 302 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8455 > 50: distance: 48 - 139: 34.888 distance: 51 - 136: 34.812 distance: 62 - 124: 35.176 distance: 64 - 69: 32.551 distance: 65 - 121: 34.624 distance: 69 - 70: 45.496 distance: 70 - 71: 33.655 distance: 70 - 73: 25.898 distance: 71 - 72: 36.885 distance: 71 - 77: 45.063 distance: 73 - 74: 49.577 distance: 74 - 75: 36.633 distance: 74 - 76: 39.354 distance: 77 - 78: 41.330 distance: 78 - 79: 38.855 distance: 78 - 81: 39.443 distance: 79 - 80: 39.810 distance: 79 - 88: 25.000 distance: 81 - 82: 25.029 distance: 82 - 83: 47.986 distance: 83 - 84: 8.894 distance: 84 - 85: 8.503 distance: 85 - 86: 23.172 distance: 85 - 87: 10.237 distance: 88 - 89: 19.696 distance: 89 - 90: 44.085 distance: 89 - 92: 52.374 distance: 90 - 91: 39.601 distance: 90 - 93: 3.613 distance: 93 - 94: 50.188 distance: 94 - 95: 32.702 distance: 95 - 96: 44.976 distance: 95 - 97: 31.778 distance: 97 - 98: 26.455 distance: 98 - 99: 16.487 distance: 98 - 101: 20.871 distance: 99 - 100: 40.846 distance: 99 - 109: 39.015 distance: 101 - 102: 27.822 distance: 102 - 103: 19.154 distance: 102 - 104: 29.529 distance: 103 - 105: 22.708 distance: 104 - 106: 37.646 distance: 105 - 107: 45.051 distance: 106 - 107: 31.346 distance: 107 - 108: 10.917 distance: 109 - 110: 28.774 distance: 110 - 111: 57.860 distance: 110 - 113: 42.112 distance: 111 - 112: 23.725 distance: 111 - 114: 46.127 distance: 114 - 115: 30.818 distance: 114 - 120: 40.236 distance: 115 - 116: 22.227 distance: 115 - 118: 25.349 distance: 116 - 117: 34.607 distance: 116 - 121: 39.901 distance: 118 - 119: 39.673 distance: 121 - 122: 40.876 distance: 122 - 123: 19.830 distance: 123 - 124: 44.855 distance: 123 - 129: 60.120 distance: 125 - 126: 13.056 distance: 126 - 127: 25.165 distance: 126 - 128: 15.267 distance: 129 - 130: 59.829 distance: 129 - 135: 32.573 distance: 130 - 131: 36.153 distance: 130 - 133: 29.516 distance: 131 - 136: 39.713 distance: 133 - 134: 6.457 distance: 134 - 135: 18.692 distance: 137 - 138: 51.846 distance: 137 - 140: 61.713 distance: 138 - 139: 40.590 distance: 138 - 144: 32.311 distance: 140 - 141: 35.963 distance: 140 - 142: 36.327