Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 5 09:59:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/05_2023/6ue7_20749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/05_2023/6ue7_20749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/05_2023/6ue7_20749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/05_2023/6ue7_20749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/05_2023/6ue7_20749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/05_2023/6ue7_20749.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.014 sd= 0.361 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7378 2.51 5 N 1991 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 11701 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1559 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1621 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 17, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4109 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1632 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "G" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1556 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1003 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.52, per 1000 atoms: 0.56 Number of scatterers: 11701 At special positions: 0 Unit cell: (127.35, 181.346, 122.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2268 8.00 N 1991 7.00 C 7378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 46 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.05 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 311 " distance=2.05 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.03 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS D 15 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.04 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 263 " " NAG B 501 " - " ASN B 263 " " NAG B 502 " - " ASN B 459 " " NAG C 601 " - " ASN C 65 " " NAG C 605 " - " ASN C 168 " " NAG C 608 " - " ASN C 481 " " NAG C 609 " - " ASN C 403 " " NAG E 1 " - " ASN C 72 " " NAG H 1 " - " ASN C 451 " " NAG I 1 " - " ASN F 263 " " NAG J 1 " - " ASN D 49 " Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 34 sheets defined 10.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.715A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.201A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.815A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.991A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 362' Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.111A pdb=" N TYR B 395 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.179A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.953A pdb=" N SER C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 4.132A pdb=" N THR C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.649A pdb=" N ASP C 196 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 197' Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.715A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.555A pdb=" N GLU C 359 " --> pdb=" O ASN C 356 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.838A pdb=" N GLU C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.518A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'F' and resid 252 through 258 Processing helix chain 'F' and resid 311 through 317 removed outlier: 4.341A pdb=" N TRP F 315 " --> pdb=" O CYS F 311 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 395 removed outlier: 4.181A pdb=" N TYR F 395 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 425 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.505A pdb=" N LEU G 256 " --> pdb=" O ALA G 252 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 257 " --> pdb=" O LEU G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 252 through 257' Processing helix chain 'G' and resid 355 through 360 removed outlier: 3.821A pdb=" N LEU G 359 " --> pdb=" O PRO G 355 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 355 through 360' Processing helix chain 'G' and resid 421 through 427 removed outlier: 3.764A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.543A pdb=" N ASP A 297 " --> pdb=" O CYS A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.551A pdb=" N LEU A 338 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 336 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.921A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.921A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.410A pdb=" N ASN A 459 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL B 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER A 461 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N PHE D 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER B 461 " --> pdb=" O PHE D 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 249 removed outlier: 3.790A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 264 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.654A pdb=" N THR B 324 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 338 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.746A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.746A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.726A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG C 89 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS C 35 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER C 51 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'C' and resid 123 through 125 removed outlier: 7.177A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN C 199 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 150 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 135 Processing sheet with id=AB8, first strand: chain 'C' and resid 226 through 229 removed outlier: 3.618A pdb=" N GLY C 308 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 251 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS C 250 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN C 266 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 239 Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 344 removed outlier: 3.776A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 424 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS C 364 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 382 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP C 366 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 348 through 354 Processing sheet with id=AC3, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=AC4, first strand: chain 'C' and resid 486 through 487 removed outlier: 4.007A pdb=" N GLN C 486 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 479 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU C 536 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLN C 530 " --> pdb=" O TYR C 534 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 245 through 249 removed outlier: 3.761A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 268 " --> pdb=" O VAL F 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 279 through 280 removed outlier: 3.975A pdb=" N THR F 280 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU F 334 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.848A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 396 " --> pdb=" O ILE F 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.848A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AD1, first strand: chain 'G' and resid 458 through 463 removed outlier: 3.796A pdb=" N MET F 464 " --> pdb=" O VAL G 463 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS F 457 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE D 38 " --> pdb=" O HIS F 457 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN F 459 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE D 40 " --> pdb=" O ASN F 459 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER F 461 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 42 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL F 463 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER D 20 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL D 7 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 245 through 247 removed outlier: 3.811A pdb=" N SER G 247 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 304 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 295 " --> pdb=" O SER G 303 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.074A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.074A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR G 410 " --> pdb=" O GLU G 403 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD6, first strand: chain 'D' and resid 75 through 78 Processing sheet with id=AD7, first strand: chain 'D' and resid 111 through 116 removed outlier: 3.548A pdb=" N ALA D 112 " --> pdb=" O THR D 127 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 942 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: 3.87 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2144 1.32 - 1.45: 3329 1.45 - 1.58: 6419 1.58 - 1.71: 1 1.71 - 1.84: 73 Bond restraints: 11966 Sorted by residual: bond pdb=" C PRO F 309 " pdb=" O PRO F 309 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.10e-02 8.26e+03 1.20e+01 bond pdb=" C GLU B 403 " pdb=" N PRO B 404 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.33e-02 5.65e+03 9.51e+00 bond pdb=" N SER F 260 " pdb=" CA SER F 260 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 8.75e+00 bond pdb=" C LEU F 351 " pdb=" N LEU F 352 " ideal model delta sigma weight residual 1.331 1.270 0.061 2.07e-02 2.33e+03 8.70e+00 bond pdb=" C PRO F 314 " pdb=" O PRO F 314 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.26e-02 6.30e+03 8.63e+00 ... (remaining 11961 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.46: 478 106.46 - 113.38: 6722 113.38 - 120.29: 3995 120.29 - 127.21: 5025 127.21 - 134.12: 186 Bond angle restraints: 16406 Sorted by residual: angle pdb=" C VAL C 165 " pdb=" N ASN C 166 " pdb=" CA ASN C 166 " ideal model delta sigma weight residual 120.60 130.47 -9.87 1.53e+00 4.27e-01 4.16e+01 angle pdb=" C ASN C 329 " pdb=" N GLU C 330 " pdb=" CA GLU C 330 " ideal model delta sigma weight residual 121.54 132.30 -10.76 1.91e+00 2.74e-01 3.18e+01 angle pdb=" C LEU A 271 " pdb=" N ARG A 272 " pdb=" CA ARG A 272 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" CA MET A 464 " pdb=" CB MET A 464 " pdb=" CG MET A 464 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" N VAL C 264 " pdb=" CA VAL C 264 " pdb=" C VAL C 264 " ideal model delta sigma weight residual 112.12 108.69 3.43 8.40e-01 1.42e+00 1.67e+01 ... (remaining 16401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 6397 17.37 - 34.73: 522 34.73 - 52.10: 81 52.10 - 69.47: 15 69.47 - 86.83: 9 Dihedral angle restraints: 7024 sinusoidal: 2514 harmonic: 4510 Sorted by residual: dihedral pdb=" CB CYS D 72 " pdb=" SG CYS D 72 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.14 -82.14 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual -86.00 -162.76 76.76 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS C 468 " pdb=" SG CYS C 468 " pdb=" SG CYS F 311 " pdb=" CB CYS F 311 " ideal model delta sinusoidal sigma weight residual -86.00 -158.95 72.95 1 1.00e+01 1.00e-02 6.78e+01 ... (remaining 7021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1688 0.079 - 0.159: 276 0.159 - 0.238: 26 0.238 - 0.318: 4 0.318 - 0.397: 1 Chirality restraints: 1995 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.89e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 65 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1992 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.091 2.00e-02 2.50e+03 7.49e-02 7.02e+01 pdb=" C7 NAG I 1 " -0.023 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.067 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.121 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 259 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C GLY F 259 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY F 259 " 0.018 2.00e-02 2.50e+03 pdb=" N SER F 260 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 166 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 167 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " 0.037 5.00e-02 4.00e+02 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 101 2.62 - 3.19: 8771 3.19 - 3.76: 15578 3.76 - 4.33: 20774 4.33 - 4.90: 36789 Nonbonded interactions: 82013 Sorted by model distance: nonbonded pdb=" O3 NAG I 1 " pdb=" O7 NAG I 1 " model vdw 2.051 2.440 nonbonded pdb=" OG1 THR A 282 " pdb=" OG1 THR A 322 " model vdw 2.278 2.440 nonbonded pdb=" O GLY B 469 " pdb=" OG SER G 356 " model vdw 2.297 2.440 nonbonded pdb=" O SER F 284 " pdb=" OG SER F 284 " model vdw 2.308 2.440 nonbonded pdb=" OG SER C 256 " pdb=" O ASN C 260 " model vdw 2.316 2.440 ... (remaining 82008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 421 or (resid 422 and (name N \ or name CA or name C or name O or name CB )) or resid 423 through 425 or (resid \ 426 and (name N or name CA or name C or name O or name CB )) or resid 427 throug \ h 445 or (resid 446 and (name N or name CA or name C or name O or name CB )) or \ resid 447 through 449 or (resid 450 and (name N or name CA or name C or name O o \ r name CB )) or resid 451 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 34 \ 5 or (resid 346 and (name N or name CA or name C or name O or name CB )) or resi \ d 347 through 356 or (resid 357 and (name N or name CA or name C or name O or na \ me CB )) or resid 358 through 404 or (resid 405 through 406 and (name N or name \ CA or name C or name O or name CB )) or resid 407 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 451 through 453 or \ resid 456 through 464)) selection = (chain 'F' and (resid 242 through 310 or (resid 311 through 313 and (name N or n \ ame CA or name C or name O or name CB )) or resid 314 through 345 or (resid 346 \ and (name N or name CA or name C or name O or name CB )) or resid 347 through 35 \ 6 or (resid 357 and (name N or name CA or name C or name O or name CB )) or resi \ d 358 through 424 or (resid 425 through 426 and (name N or name CA or name C or \ name O or name CB )) or resid 427 through 449 or (resid 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 453 or resid 456 throu \ gh 464)) selection = (chain 'G' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 356 or (resid 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 445 or (resid \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 throug \ h 453 or resid 456 through 464)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 0.010 Extract box with map and model: 13.360 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 32.510 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.077 11966 Z= 0.463 Angle : 1.053 12.783 16406 Z= 0.576 Chirality : 0.060 0.397 1995 Planarity : 0.008 0.075 2095 Dihedral : 12.902 86.832 4039 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % 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: -3.16 (0.19), residues: 1551 helix: -4.14 (0.30), residues: 79 sheet: -1.03 (0.20), residues: 629 loop : -2.83 (0.18), residues: 843 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 257 average time/residue: 1.2645 time to fit residues: 351.1287 Evaluate side-chains 171 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0973 time to fit residues: 2.1629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN C 218 GLN C 412 GLN C 426 ASN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11966 Z= 0.234 Angle : 0.722 12.123 16406 Z= 0.361 Chirality : 0.044 0.214 1995 Planarity : 0.006 0.051 2095 Dihedral : 5.784 28.457 1659 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 4.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.41 (0.20), residues: 1551 helix: -2.59 (0.46), residues: 85 sheet: -0.50 (0.21), residues: 626 loop : -2.45 (0.19), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 16 residues processed: 201 average time/residue: 1.2881 time to fit residues: 280.9846 Evaluate side-chains 174 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 8 average time/residue: 0.2285 time to fit residues: 4.6590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN F 402 GLN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 11966 Z= 0.224 Angle : 0.673 10.238 16406 Z= 0.334 Chirality : 0.043 0.193 1995 Planarity : 0.005 0.044 2095 Dihedral : 5.366 32.533 1659 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 5.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.98 (0.21), residues: 1551 helix: -1.63 (0.52), residues: 84 sheet: -0.27 (0.21), residues: 632 loop : -2.20 (0.20), residues: 835 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 169 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 24 residues processed: 204 average time/residue: 1.2277 time to fit residues: 271.6549 Evaluate side-chains 179 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 9 average time/residue: 0.3980 time to fit residues: 6.3531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11966 Z= 0.198 Angle : 0.666 9.736 16406 Z= 0.330 Chirality : 0.043 0.186 1995 Planarity : 0.004 0.040 2095 Dihedral : 5.158 33.039 1659 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.75 (0.21), residues: 1551 helix: -1.29 (0.54), residues: 84 sheet: -0.13 (0.21), residues: 638 loop : -2.06 (0.21), residues: 829 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 1.289 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 31 residues processed: 194 average time/residue: 1.3281 time to fit residues: 277.6452 Evaluate side-chains 181 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 12 average time/residue: 0.5901 time to fit residues: 10.0980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11966 Z= 0.216 Angle : 0.674 12.822 16406 Z= 0.330 Chirality : 0.043 0.186 1995 Planarity : 0.004 0.045 2095 Dihedral : 5.001 29.474 1659 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 4.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.69 (0.21), residues: 1551 helix: -1.11 (0.54), residues: 90 sheet: -0.04 (0.21), residues: 634 loop : -2.07 (0.21), residues: 827 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 153 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 31 residues processed: 190 average time/residue: 1.2649 time to fit residues: 259.5139 Evaluate side-chains 175 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 12 average time/residue: 0.4264 time to fit residues: 8.0473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.0000 chunk 135 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11966 Z= 0.181 Angle : 0.656 10.408 16406 Z= 0.321 Chirality : 0.042 0.202 1995 Planarity : 0.004 0.041 2095 Dihedral : 4.772 26.323 1659 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 4.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.52 (0.21), residues: 1551 helix: -0.78 (0.55), residues: 84 sheet: 0.10 (0.21), residues: 619 loop : -1.97 (0.21), residues: 848 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 186 average time/residue: 1.4013 time to fit residues: 281.2663 Evaluate side-chains 177 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 9 average time/residue: 0.5528 time to fit residues: 7.7212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 52.2384 > 50: distance: 32 - 46: 6.927 distance: 42 - 46: 10.831 distance: 46 - 47: 7.867 distance: 47 - 48: 20.891 distance: 47 - 50: 8.502 distance: 48 - 49: 14.870 distance: 48 - 58: 17.961 distance: 50 - 51: 13.342 distance: 51 - 52: 15.372 distance: 51 - 53: 9.421 distance: 52 - 54: 10.901 distance: 53 - 55: 6.109 distance: 54 - 56: 9.497 distance: 55 - 56: 14.703 distance: 56 - 57: 15.845 distance: 58 - 59: 29.213 distance: 59 - 60: 10.277 distance: 59 - 62: 8.910 distance: 60 - 61: 9.811 distance: 60 - 67: 11.005 distance: 62 - 63: 15.798 distance: 63 - 64: 19.225 distance: 64 - 65: 24.481 distance: 64 - 66: 25.008 distance: 67 - 68: 7.607 distance: 68 - 69: 6.545 distance: 69 - 70: 14.418 distance: 69 - 71: 8.750 distance: 71 - 72: 13.837 distance: 72 - 73: 8.147 distance: 72 - 75: 7.965 distance: 73 - 74: 11.628 distance: 73 - 82: 11.884 distance: 75 - 76: 16.044 distance: 76 - 77: 14.223 distance: 77 - 78: 13.838 distance: 78 - 79: 9.908 distance: 79 - 80: 8.659 distance: 79 - 81: 11.722 distance: 82 - 83: 3.409 distance: 83 - 84: 10.972 distance: 83 - 86: 11.786 distance: 84 - 85: 19.676 distance: 84 - 90: 10.841 distance: 86 - 87: 4.937 distance: 87 - 88: 10.717 distance: 87 - 89: 6.475 distance: 90 - 91: 4.488 distance: 90 - 165: 8.359 distance: 91 - 92: 3.319 distance: 91 - 94: 5.281 distance: 92 - 93: 6.224 distance: 92 - 96: 3.118 distance: 93 - 162: 5.288 distance: 94 - 95: 6.495 distance: 97 - 98: 7.013 distance: 97 - 100: 5.831 distance: 98 - 99: 17.983 distance: 98 - 104: 11.901 distance: 100 - 101: 8.115 distance: 101 - 102: 6.774 distance: 104 - 151: 8.569 distance: 105 - 106: 9.078 distance: 105 - 108: 11.244 distance: 106 - 107: 18.486 distance: 106 - 112: 11.013 distance: 107 - 148: 26.932 distance: 108 - 109: 7.719 distance: 109 - 110: 9.761 distance: 109 - 111: 11.674 distance: 112 - 113: 20.412 distance: 113 - 114: 3.536 distance: 113 - 116: 17.208 distance: 114 - 115: 29.391 distance: 114 - 121: 17.075 distance: 116 - 117: 5.964 distance: 117 - 118: 14.822 distance: 118 - 119: 6.966 distance: 118 - 120: 9.809 distance: 121 - 122: 6.145 distance: 122 - 123: 12.979 distance: 122 - 125: 4.591 distance: 123 - 124: 18.730 distance: 123 - 130: 19.937 distance: 125 - 126: 13.160 distance: 126 - 127: 23.797 distance: 127 - 128: 4.356 distance: 127 - 129: 18.965