Starting phenix.real_space_refine on Tue Sep 24 15:25:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/09_2024/7y1t_33572.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/09_2024/7y1t_33572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/09_2024/7y1t_33572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/09_2024/7y1t_33572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/09_2024/7y1t_33572.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1t_33572/09_2024/7y1t_33572.cif" } resolution = 3.24 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mn 1 7.51 5 S 38 5.16 5 C 5127 2.51 5 N 1357 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8112 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4114 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 507} Chain breaks: 3 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2714 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1038 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 131 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.62, per 1000 atoms: 0.69 Number of scatterers: 8112 At special positions: 0 Unit cell: (100.225, 75.96, 150.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 Ca 5 19.99 S 38 16.00 O 1584 8.00 N 1357 7.00 C 5127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS B 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 6 " ALPHA1-4 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " MAN G 4 " - " MAN G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 701 " - " ASN A 525 " " NAG B 501 " - " ASN B 389 " " NAG B 502 " - " ASN B 191 " " NAG B 503 " - " ASN B 360 " " NAG C 1 " - " ASN A 260 " " NAG D 401 " - " ASN D 107 " " NAG E 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 414 " " NAG G 1 " - " ASN A 266 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 945.1 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 14.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.459A pdb=" N GLY A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.609A pdb=" N THR A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.816A pdb=" N HIS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 126 through 136 removed outlier: 3.985A pdb=" N ASP B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.770A pdb=" N HIS B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 254 removed outlier: 4.083A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 330 through 345 Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.989A pdb=" N LEU D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 removed outlier: 4.020A pdb=" N SER D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.921A pdb=" N ASP A 422 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 412 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 408 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 4.016A pdb=" N ALA A 81 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 4.046A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.958A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.754A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 283 removed outlier: 4.020A pdb=" N SER A 279 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 293 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 348 removed outlier: 6.330A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.737A pdb=" N GLU A 537 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 478 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A 476 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 524 through 529 removed outlier: 4.043A pdb=" N LYS A 524 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 496 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 528 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 492 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.669A pdb=" N HIS B 422 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 407 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 409 " --> pdb=" O GLN B 349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 97 removed outlier: 3.566A pdb=" N VAL B 392 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 390 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 95 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 393 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 97 removed outlier: 3.566A pdb=" N VAL B 392 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 390 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 95 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 189 removed outlier: 6.411A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE B 146 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 109 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 111 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 149 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 296 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.052A pdb=" N PHE D 228 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 127 " --> pdb=" O PHE D 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 106 removed outlier: 3.746A pdb=" N ILE D 102 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 190 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D 104 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY D 187 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 144 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 139 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG D 156 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU D 141 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER D 154 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN D 143 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR D 152 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR D 145 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP D 150 " --> pdb=" O TYR D 145 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 594 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: 2.44 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2645 1.34 - 1.46: 1943 1.46 - 1.58: 3630 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 8278 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C1 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.399 1.434 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 MAN G 6 " pdb=" C2 MAN G 6 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 8273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 10800 1.31 - 2.63: 318 2.63 - 3.94: 81 3.94 - 5.26: 20 5.26 - 6.57: 11 Bond angle restraints: 11230 Sorted by residual: angle pdb=" C ASP A 288 " pdb=" N ASP A 289 " pdb=" CA ASP A 289 " ideal model delta sigma weight residual 124.31 130.49 -6.18 1.67e+00 3.59e-01 1.37e+01 angle pdb=" C SER A 201 " pdb=" N ILE A 202 " pdb=" CA ILE A 202 " ideal model delta sigma weight residual 121.97 126.30 -4.33 1.80e+00 3.09e-01 5.80e+00 angle pdb=" CA ASP A 289 " pdb=" CB ASP A 289 " pdb=" CG ASP A 289 " ideal model delta sigma weight residual 112.60 114.90 -2.30 1.00e+00 1.00e+00 5.27e+00 angle pdb=" CA CYS B 259 " pdb=" CB CYS B 259 " pdb=" SG CYS B 259 " ideal model delta sigma weight residual 114.40 119.52 -5.12 2.30e+00 1.89e-01 4.96e+00 angle pdb=" C PHE B 195 " pdb=" N GLU B 196 " pdb=" CA GLU B 196 " ideal model delta sigma weight residual 120.31 117.19 3.12 1.52e+00 4.33e-01 4.21e+00 ... (remaining 11225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 4778 22.77 - 45.55: 283 45.55 - 68.32: 58 68.32 - 91.10: 20 91.10 - 113.87: 19 Dihedral angle restraints: 5158 sinusoidal: 2207 harmonic: 2951 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -38.55 -47.45 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CB CYS A 401 " pdb=" SG CYS A 401 " pdb=" SG CYS B 259 " pdb=" CB CYS B 259 " ideal model delta sinusoidal sigma weight residual -86.00 -126.14 40.14 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA ALA B 329 " pdb=" C ALA B 329 " pdb=" N ASN B 330 " pdb=" CA ASN B 330 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 1286 0.316 - 0.633: 2 0.633 - 0.949: 1 0.949 - 1.266: 0 1.266 - 1.582: 3 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.47e+02 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 266 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.26e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 414 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.95 -1.45 2.00e-01 2.50e+01 5.28e+01 ... (remaining 1289 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 266 " -0.163 2.00e-02 2.50e+03 2.04e-01 5.21e+02 pdb=" CG ASN A 266 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 266 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 266 " 0.340 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.248 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 414 " -0.152 2.00e-02 2.50e+03 1.93e-01 4.67e+02 pdb=" CG ASN B 414 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B 414 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 414 " 0.325 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 525 " -0.115 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" CG ASN A 525 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 525 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 525 " 0.217 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.163 2.00e-02 2.50e+03 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 88 2.58 - 3.16: 6368 3.16 - 3.74: 11799 3.74 - 4.32: 16459 4.32 - 4.90: 27765 Nonbonded interactions: 62479 Sorted by model distance: nonbonded pdb=" OD1 ASP D 217 " pdb="MN MN B 505 " model vdw 1.998 2.320 nonbonded pdb=" OG SER A 144 " pdb=" OD1 ASP A 146 " model vdw 2.130 3.040 nonbonded pdb=" NZ LYS B 327 " pdb=" O ALA B 329 " model vdw 2.182 3.120 nonbonded pdb=" OD1 ASP B 130 " pdb=" ND2 ASN B 332 " model vdw 2.190 3.120 nonbonded pdb=" OD1 ASP A 24 " pdb=" N PHE A 25 " model vdw 2.233 3.120 ... (remaining 62474 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 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.003 0.083 8278 Z= 0.214 Angle : 0.588 6.573 11230 Z= 0.277 Chirality : 0.087 1.582 1292 Planarity : 0.004 0.104 1449 Dihedral : 16.885 113.873 3244 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.76 (0.27), residues: 1014 helix: 1.39 (0.57), residues: 98 sheet: 0.21 (0.29), residues: 337 loop : -1.33 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.002 0.000 HIS A 113 PHE 0.017 0.001 PHE B 137 TYR 0.011 0.001 TYR A 200 ARG 0.005 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 474 PHE cc_start: 0.3816 (p90) cc_final: 0.3565 (p90) REVERT: B 250 LEU cc_start: 0.8421 (mt) cc_final: 0.8081 (mt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1940 time to fit residues: 33.9305 Evaluate side-chains 87 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8278 Z= 0.270 Angle : 0.663 9.527 11230 Z= 0.320 Chirality : 0.048 0.276 1292 Planarity : 0.004 0.078 1449 Dihedral : 12.286 96.049 1472 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.22 % Allowed : 10.34 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.69 (0.27), residues: 1014 helix: 1.74 (0.56), residues: 100 sheet: -0.02 (0.27), residues: 373 loop : -1.21 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.004 0.001 HIS A 113 PHE 0.029 0.002 PHE B 137 TYR 0.013 0.002 TYR A 178 ARG 0.005 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 CYS cc_start: 0.6299 (m) cc_final: 0.6071 (m) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1872 time to fit residues: 25.6042 Evaluate side-chains 86 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 8278 Z= 0.427 Angle : 0.752 13.217 11230 Z= 0.375 Chirality : 0.052 0.380 1292 Planarity : 0.005 0.062 1449 Dihedral : 10.739 93.107 1472 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.68 % Allowed : 13.38 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.01 (0.27), residues: 1014 helix: 1.17 (0.56), residues: 102 sheet: -0.27 (0.27), residues: 371 loop : -1.32 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 61 HIS 0.006 0.001 HIS A 113 PHE 0.027 0.002 PHE B 137 TYR 0.024 0.002 TYR A 420 ARG 0.004 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.868 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 95 average time/residue: 0.2004 time to fit residues: 26.4388 Evaluate side-chains 85 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8278 Z= 0.246 Angle : 0.646 13.858 11230 Z= 0.315 Chirality : 0.047 0.304 1292 Planarity : 0.004 0.048 1449 Dihedral : 10.288 93.898 1472 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.95 % Allowed : 16.30 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.96 (0.27), residues: 1014 helix: 1.26 (0.56), residues: 102 sheet: -0.31 (0.27), residues: 372 loop : -1.23 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.024 0.002 PHE B 137 TYR 0.013 0.001 TYR A 420 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.956 Fit side-chains REVERT: A 368 ASP cc_start: 0.7927 (t0) cc_final: 0.7648 (t0) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1996 time to fit residues: 25.1884 Evaluate side-chains 84 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 421 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8278 Z= 0.280 Angle : 0.639 13.327 11230 Z= 0.313 Chirality : 0.048 0.299 1292 Planarity : 0.004 0.046 1449 Dihedral : 10.024 92.997 1472 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.31 % Allowed : 17.15 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.91 (0.27), residues: 1014 helix: 1.32 (0.56), residues: 102 sheet: -0.29 (0.27), residues: 372 loop : -1.20 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.032 0.002 PHE B 137 TYR 0.012 0.001 TYR A 562 ARG 0.004 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.881 Fit side-chains REVERT: A 275 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: A 368 ASP cc_start: 0.7814 (t0) cc_final: 0.7560 (t0) REVERT: D 140 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5736 (tp30) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.1912 time to fit residues: 24.4479 Evaluate side-chains 92 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8278 Z= 0.195 Angle : 0.604 12.636 11230 Z= 0.294 Chirality : 0.047 0.291 1292 Planarity : 0.004 0.047 1449 Dihedral : 9.735 92.860 1472 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.68 % Allowed : 17.64 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.80 (0.27), residues: 1014 helix: 1.44 (0.56), residues: 102 sheet: -0.24 (0.27), residues: 372 loop : -1.12 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 PHE 0.029 0.001 PHE B 137 TYR 0.010 0.001 TYR A 562 ARG 0.003 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.920 Fit side-chains REVERT: A 275 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: A 368 ASP cc_start: 0.7809 (t0) cc_final: 0.7562 (t0) REVERT: D 140 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5850 (tp30) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 0.1955 time to fit residues: 27.9128 Evaluate side-chains 92 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain D residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.0010 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 58 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8278 Z= 0.242 Angle : 0.614 12.619 11230 Z= 0.299 Chirality : 0.047 0.291 1292 Planarity : 0.004 0.048 1449 Dihedral : 9.588 91.787 1472 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.80 % Allowed : 17.40 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.75 (0.27), residues: 1014 helix: 1.44 (0.56), residues: 102 sheet: -0.22 (0.27), residues: 373 loop : -1.06 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.003 0.001 HIS B 307 PHE 0.026 0.001 PHE B 137 TYR 0.011 0.001 TYR A 562 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.922 Fit side-chains REVERT: A 275 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: A 368 ASP cc_start: 0.7846 (t0) cc_final: 0.7581 (t0) REVERT: D 140 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5860 (tp30) outliers start: 23 outliers final: 19 residues processed: 97 average time/residue: 0.1838 time to fit residues: 25.4517 Evaluate side-chains 98 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 222 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8278 Z= 0.195 Angle : 0.594 11.125 11230 Z= 0.289 Chirality : 0.046 0.286 1292 Planarity : 0.004 0.050 1449 Dihedral : 9.340 90.875 1472 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.68 % Allowed : 17.88 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.68 (0.27), residues: 1014 helix: 1.43 (0.56), residues: 103 sheet: -0.19 (0.27), residues: 372 loop : -0.99 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 61 HIS 0.002 0.001 HIS B 307 PHE 0.024 0.001 PHE B 137 TYR 0.010 0.001 TYR A 178 ARG 0.002 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.855 Fit side-chains REVERT: A 162 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7841 (t70) REVERT: A 275 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: A 368 ASP cc_start: 0.7869 (t0) cc_final: 0.7610 (t0) REVERT: D 140 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5856 (tp30) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.1789 time to fit residues: 24.5018 Evaluate side-chains 92 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 222 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 56.8718 > 50: distance: 10 - 16: 10.547 distance: 16 - 17: 15.394 distance: 17 - 18: 38.222 distance: 17 - 20: 26.721 distance: 18 - 19: 26.517 distance: 18 - 24: 37.989 distance: 20 - 21: 14.842 distance: 20 - 22: 29.535 distance: 21 - 23: 15.774 distance: 24 - 25: 28.447 distance: 24 - 146: 20.863 distance: 25 - 26: 29.561 distance: 25 - 28: 28.825 distance: 26 - 27: 11.710 distance: 26 - 31: 13.338 distance: 27 - 143: 3.173 distance: 28 - 29: 18.435 distance: 28 - 30: 19.257 distance: 31 - 32: 21.068 distance: 32 - 33: 23.872 distance: 32 - 35: 19.951 distance: 33 - 34: 25.454 distance: 33 - 36: 14.547 distance: 36 - 37: 22.762 distance: 36 - 131: 22.417 distance: 37 - 38: 24.987 distance: 37 - 40: 13.881 distance: 38 - 39: 17.526 distance: 38 - 44: 13.197 distance: 39 - 128: 25.536 distance: 40 - 41: 35.099 distance: 40 - 42: 32.219 distance: 41 - 43: 30.689 distance: 44 - 45: 22.763 distance: 45 - 46: 31.692 distance: 45 - 48: 9.264 distance: 46 - 47: 40.932 distance: 46 - 50: 34.886 distance: 48 - 49: 16.373 distance: 49 - 108: 12.101 distance: 50 - 51: 3.136 distance: 50 - 56: 24.248 distance: 51 - 52: 19.630 distance: 51 - 54: 12.416 distance: 52 - 53: 17.434 distance: 52 - 57: 3.708 distance: 54 - 55: 6.620 distance: 55 - 56: 18.133 distance: 57 - 58: 20.709 distance: 58 - 59: 12.825 distance: 58 - 61: 5.548 distance: 59 - 60: 30.447 distance: 59 - 65: 21.415 distance: 61 - 62: 35.906 distance: 62 - 63: 29.997 distance: 62 - 64: 13.668 distance: 65 - 66: 10.189 distance: 66 - 67: 22.890 distance: 67 - 68: 40.638 distance: 67 - 69: 33.142 distance: 69 - 70: 7.665 distance: 70 - 71: 3.208 distance: 70 - 73: 11.639 distance: 71 - 72: 10.246 distance: 71 - 75: 5.108 distance: 73 - 74: 14.052 distance: 75 - 76: 9.036 distance: 76 - 77: 5.440 distance: 76 - 79: 9.617 distance: 77 - 78: 13.109 distance: 77 - 86: 7.662 distance: 79 - 80: 7.444 distance: 80 - 81: 5.941 distance: 81 - 82: 4.614