Starting phenix.real_space_refine on Sat Aug 23 09:41:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wse_32755/08_2025/7wse_32755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wse_32755/08_2025/7wse_32755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wse_32755/08_2025/7wse_32755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wse_32755/08_2025/7wse_32755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wse_32755/08_2025/7wse_32755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wse_32755/08_2025/7wse_32755.map" } resolution = 2.93 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 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5923 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 4115 2.51 5 N 1069 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6431 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4887 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 566} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.24 Number of scatterers: 6431 At special positions: 0 Unit cell: (72.921, 82.287, 117.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 1211 8.00 N 1069 7.00 C 4115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 311.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 377 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 52.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.672A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.624A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.529A pdb=" N ARG A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.768A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 156 through 193 removed outlier: 3.794A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.616A pdb=" N GLU A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 219 through 251 removed outlier: 3.824A pdb=" N ALA A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 3.709A pdb=" N GLN A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.594A pdb=" N GLN A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.770A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.760A pdb=" N GLN A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.085A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 483 removed outlier: 3.912A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.965A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.700A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.960A pdb=" N ASP A 614 " --> pdb=" O PRO A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.685A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.793A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.081A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 333 removed outlier: 8.336A pdb=" N LEU A 332 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.525A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 272 hydrogen bonds defined for protein. 777 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: 0.80 Time building geometry restraints manager: 0.61 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: 2071 1.34 - 1.46: 1664 1.46 - 1.58: 2822 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 6612 Sorted by residual: bond pdb=" CG PRO A 145 " pdb=" CD PRO A 145 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.19e-01 bond pdb=" C ILE A 467 " pdb=" O ILE A 467 " ideal model delta sigma weight residual 1.240 1.231 0.008 1.26e-02 6.30e+03 4.54e-01 bond pdb=" C TYR A 278 " pdb=" N PRO A 279 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.72e-01 bond pdb=" CA ILE B 410 " pdb=" CB ILE B 410 " ideal model delta sigma weight residual 1.528 1.535 -0.007 1.34e-02 5.57e+03 2.99e-01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.461 1.455 0.006 1.23e-02 6.61e+03 2.48e-01 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 8925 2.26 - 4.52: 54 4.52 - 6.78: 4 6.78 - 9.04: 0 9.04 - 11.30: 1 Bond angle restraints: 8984 Sorted by residual: angle pdb=" C GLN B 409 " pdb=" N ILE B 410 " pdb=" CA ILE B 410 " ideal model delta sigma weight residual 122.59 120.26 2.33 1.10e+00 8.26e-01 4.48e+00 angle pdb=" C THR A 361 " pdb=" N LYS A 362 " pdb=" CA LYS A 362 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.38e+00 angle pdb=" N ILE B 410 " pdb=" CA ILE B 410 " pdb=" C ILE B 410 " ideal model delta sigma weight residual 106.32 109.60 -3.28 1.61e+00 3.86e-01 4.15e+00 angle pdb=" C LEU A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 121.41 132.71 -11.30 5.58e+00 3.21e-02 4.10e+00 angle pdb=" C VAL A 363 " pdb=" N THR A 364 " pdb=" CA THR A 364 " ideal model delta sigma weight residual 121.63 125.28 -3.65 1.92e+00 2.71e-01 3.62e+00 ... (remaining 8979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3684 16.42 - 32.83: 188 32.83 - 49.25: 37 49.25 - 65.66: 4 65.66 - 82.08: 2 Dihedral angle restraints: 3915 sinusoidal: 1589 harmonic: 2326 Sorted by residual: dihedral pdb=" CA LYS A 362 " pdb=" C LYS A 362 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta harmonic sigma weight residual -180.00 -145.98 -34.02 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual 93.00 148.62 -55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -124.50 38.50 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 3912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 519 0.025 - 0.050: 268 0.050 - 0.076: 86 0.076 - 0.101: 43 0.101 - 0.126: 19 Chirality restraints: 935 Sorted by residual: chirality pdb=" CA VAL B 362 " pdb=" N VAL B 362 " pdb=" C VAL B 362 " pdb=" CB VAL B 362 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL A 282 " pdb=" N VAL A 282 " pdb=" C VAL A 282 " pdb=" CB VAL A 282 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 932 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO B 337 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 134 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 135 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 463 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.016 5.00e-02 4.00e+02 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 333 2.73 - 3.28: 6510 3.28 - 3.82: 10557 3.82 - 4.36: 13505 4.36 - 4.90: 22692 Nonbonded interactions: 53597 Sorted by model distance: nonbonded pdb=" OH TYR A 182 " pdb=" OD1 ASP A 508 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLU A 401 " pdb="ZN ZN A 801 " model vdw 2.253 2.230 nonbonded pdb=" OD1 ASP A 381 " pdb=" OH TYR A 384 " model vdw 2.263 3.040 nonbonded pdb=" NZ LYS A 81 " pdb=" O GLN A 101 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASP A 38 " pdb=" OH TYR B 449 " model vdw 2.334 3.040 ... (remaining 53592 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.002 0.023 6620 Z= 0.082 Angle : 0.445 11.304 8996 Z= 0.227 Chirality : 0.038 0.126 935 Planarity : 0.004 0.034 1164 Dihedral : 10.168 82.077 2407 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.01 % Allowed : 3.75 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.30), residues: 787 helix: -0.57 (0.27), residues: 376 sheet: 1.53 (0.82), residues: 47 loop : -0.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.012 0.001 TYR A 384 PHE 0.006 0.001 PHE A 522 TRP 0.004 0.001 TRP A 477 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00169 ( 6612) covalent geometry : angle 0.44496 ( 8984) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.58667 ( 12) hydrogen bonds : bond 0.27180 ( 272) hydrogen bonds : angle 8.86304 ( 777) metal coordination : bond 0.00103 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8455 (mmt) cc_final: 0.7971 (mmt) REVERT: B 454 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7365 (ttm-80) outliers start: 7 outliers final: 2 residues processed: 139 average time/residue: 0.4897 time to fit residues: 71.6313 Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 585 ASN B 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124430 restraints weight = 7611.647| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.64 r_work: 0.3320 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6620 Z= 0.223 Angle : 0.611 8.598 8996 Z= 0.319 Chirality : 0.045 0.164 935 Planarity : 0.005 0.053 1164 Dihedral : 5.138 54.593 873 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.17 % Allowed : 11.69 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.30), residues: 787 helix: -0.14 (0.26), residues: 394 sheet: 1.10 (0.81), residues: 49 loop : -0.27 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 599 TYR 0.016 0.002 TYR A 384 PHE 0.021 0.002 PHE B 374 TRP 0.013 0.002 TRP A 164 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 6612) covalent geometry : angle 0.61128 ( 8984) SS BOND : bond 0.00324 ( 6) SS BOND : angle 0.70325 ( 12) hydrogen bonds : bond 0.05533 ( 272) hydrogen bonds : angle 5.18690 ( 777) metal coordination : bond 0.00577 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7325 (tt) REVERT: A 153 ASN cc_start: 0.8471 (m-40) cc_final: 0.8258 (m-40) REVERT: A 490 LEU cc_start: 0.7589 (mt) cc_final: 0.7360 (mt) REVERT: A 535 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: A 596 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: A 599 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7203 (mtm110) REVERT: B 438 SER cc_start: 0.8358 (t) cc_final: 0.8138 (t) REVERT: B 454 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6797 (ttm-80) REVERT: B 509 ARG cc_start: 0.6269 (mtt180) cc_final: 0.5961 (mtt180) outliers start: 22 outliers final: 8 residues processed: 121 average time/residue: 0.4635 time to fit residues: 59.1161 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 585 ASN B 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.172401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127124 restraints weight = 7624.722| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.63 r_work: 0.3361 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6620 Z= 0.128 Angle : 0.541 8.042 8996 Z= 0.275 Chirality : 0.042 0.145 935 Planarity : 0.004 0.044 1164 Dihedral : 5.051 59.769 873 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.90 % Allowed : 13.42 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.30), residues: 787 helix: 0.03 (0.26), residues: 400 sheet: 1.05 (0.79), residues: 48 loop : -0.20 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.012 0.001 TYR A 384 PHE 0.011 0.001 PHE A 522 TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6612) covalent geometry : angle 0.54067 ( 8984) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.82308 ( 12) hydrogen bonds : bond 0.04665 ( 272) hydrogen bonds : angle 4.72607 ( 777) metal coordination : bond 0.00212 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 79 ILE cc_start: 0.8275 (mm) cc_final: 0.7942 (mp) REVERT: A 151 MET cc_start: 0.8013 (mmm) cc_final: 0.7206 (mmt) REVERT: A 490 LEU cc_start: 0.7571 (mt) cc_final: 0.7273 (mt) REVERT: A 535 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: A 596 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: B 438 SER cc_start: 0.8277 (t) cc_final: 0.8052 (t) REVERT: B 454 ARG cc_start: 0.7025 (ttm-80) cc_final: 0.6789 (ttm-80) REVERT: B 509 ARG cc_start: 0.6085 (mtt180) cc_final: 0.5859 (mtt180) outliers start: 27 outliers final: 10 residues processed: 116 average time/residue: 0.4714 time to fit residues: 57.6817 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 0.0170 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.0020 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 overall best weight: 0.2826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 474 GLN A 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130381 restraints weight = 7596.395| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.62 r_work: 0.3370 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6620 Z= 0.098 Angle : 0.512 8.532 8996 Z= 0.258 Chirality : 0.040 0.143 935 Planarity : 0.004 0.052 1164 Dihedral : 4.854 56.292 873 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.31 % Allowed : 14.57 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.30), residues: 787 helix: 0.30 (0.26), residues: 404 sheet: 1.22 (0.80), residues: 48 loop : -0.17 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 599 TYR 0.015 0.001 TYR A 50 PHE 0.012 0.001 PHE A 522 TRP 0.014 0.001 TRP A 164 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 6612) covalent geometry : angle 0.51164 ( 8984) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.79928 ( 12) hydrogen bonds : bond 0.04012 ( 272) hydrogen bonds : angle 4.38295 ( 777) metal coordination : bond 0.00120 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7053 (ttp) cc_final: 0.6795 (ttm) REVERT: A 79 ILE cc_start: 0.8237 (mm) cc_final: 0.7934 (mp) REVERT: A 151 MET cc_start: 0.7880 (mmm) cc_final: 0.6920 (mmt) REVERT: A 269 MET cc_start: 0.8554 (mmm) cc_final: 0.8346 (tpt) REVERT: A 348 TRP cc_start: 0.7100 (m100) cc_final: 0.6748 (m100) REVERT: A 490 LEU cc_start: 0.7545 (mt) cc_final: 0.7269 (mt) REVERT: A 507 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 596 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: A 599 ARG cc_start: 0.7389 (mtm110) cc_final: 0.6965 (mtm110) REVERT: B 438 SER cc_start: 0.8227 (t) cc_final: 0.7988 (t) REVERT: B 454 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.6739 (ttm-80) outliers start: 16 outliers final: 8 residues processed: 114 average time/residue: 0.4357 time to fit residues: 52.5210 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 70 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.171558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125766 restraints weight = 7691.952| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.64 r_work: 0.3303 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6620 Z= 0.155 Angle : 0.554 8.765 8996 Z= 0.277 Chirality : 0.043 0.141 935 Planarity : 0.004 0.045 1164 Dihedral : 4.892 56.354 873 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.61 % Allowed : 14.57 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.30), residues: 787 helix: 0.35 (0.27), residues: 401 sheet: 1.19 (0.77), residues: 48 loop : -0.18 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 66 TYR 0.015 0.001 TYR A 50 PHE 0.013 0.001 PHE A 522 TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6612) covalent geometry : angle 0.55339 ( 8984) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.80618 ( 12) hydrogen bonds : bond 0.04284 ( 272) hydrogen bonds : angle 4.39371 ( 777) metal coordination : bond 0.00249 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7077 (ttp) cc_final: 0.6781 (ttm) REVERT: A 79 ILE cc_start: 0.8223 (mm) cc_final: 0.7945 (mp) REVERT: A 151 MET cc_start: 0.7919 (mmm) cc_final: 0.7025 (mmt) REVERT: A 407 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7435 (mmt) REVERT: A 490 LEU cc_start: 0.7511 (mt) cc_final: 0.7237 (mt) REVERT: A 507 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 535 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: A 596 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7920 (tp30) REVERT: A 599 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7075 (mtm110) REVERT: B 438 SER cc_start: 0.8188 (t) cc_final: 0.7860 (t) REVERT: B 454 ARG cc_start: 0.7027 (ttm-80) cc_final: 0.6764 (ttm-80) outliers start: 25 outliers final: 11 residues processed: 115 average time/residue: 0.4444 time to fit residues: 53.9091 Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.0000 chunk 66 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 27 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127971 restraints weight = 7600.900| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.60 r_work: 0.3337 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6620 Z= 0.115 Angle : 0.538 8.755 8996 Z= 0.267 Chirality : 0.042 0.141 935 Planarity : 0.004 0.046 1164 Dihedral : 4.850 55.634 873 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.74 % Allowed : 16.59 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.30), residues: 787 helix: 0.47 (0.26), residues: 401 sheet: 1.16 (0.76), residues: 48 loop : -0.14 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 66 TYR 0.018 0.001 TYR A 50 PHE 0.016 0.001 PHE B 347 TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6612) covalent geometry : angle 0.53789 ( 8984) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.80702 ( 12) hydrogen bonds : bond 0.03958 ( 272) hydrogen bonds : angle 4.30711 ( 777) metal coordination : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7085 (ttp) cc_final: 0.6878 (ttm) REVERT: A 79 ILE cc_start: 0.8210 (mm) cc_final: 0.7948 (mp) REVERT: A 151 MET cc_start: 0.7846 (mmm) cc_final: 0.6905 (mmt) REVERT: A 269 MET cc_start: 0.8545 (tpt) cc_final: 0.7961 (tpt) REVERT: A 407 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7398 (mmt) REVERT: A 471 GLN cc_start: 0.7672 (mt0) cc_final: 0.7347 (mt0) REVERT: A 490 LEU cc_start: 0.7528 (mt) cc_final: 0.7253 (mt) REVERT: A 507 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 535 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: A 596 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: A 599 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7164 (mtm110) REVERT: B 438 SER cc_start: 0.8122 (t) cc_final: 0.7787 (t) REVERT: B 454 ARG cc_start: 0.6987 (ttm-80) cc_final: 0.6730 (ttm-80) REVERT: B 455 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7483 (tp) outliers start: 19 outliers final: 9 residues processed: 109 average time/residue: 0.5708 time to fit residues: 65.6165 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 585 ASN A 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127532 restraints weight = 7627.712| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.61 r_work: 0.3330 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6620 Z= 0.123 Angle : 0.538 9.063 8996 Z= 0.268 Chirality : 0.041 0.140 935 Planarity : 0.004 0.046 1164 Dihedral : 4.817 55.278 873 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.75 % Allowed : 16.02 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.30), residues: 787 helix: 0.59 (0.27), residues: 400 sheet: 1.19 (0.75), residues: 48 loop : -0.16 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 66 TYR 0.018 0.001 TYR A 50 PHE 0.013 0.001 PHE B 347 TRP 0.013 0.001 TRP A 164 HIS 0.002 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6612) covalent geometry : angle 0.53754 ( 8984) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.80881 ( 12) hydrogen bonds : bond 0.03931 ( 272) hydrogen bonds : angle 4.23626 ( 777) metal coordination : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8390 (t70) cc_final: 0.7420 (m-30) REVERT: A 66 ARG cc_start: 0.7459 (ttm110) cc_final: 0.7193 (ttm110) REVERT: A 79 ILE cc_start: 0.8227 (mm) cc_final: 0.7984 (mp) REVERT: A 151 MET cc_start: 0.7879 (mmm) cc_final: 0.6942 (mmt) REVERT: A 226 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: A 269 MET cc_start: 0.8546 (tpt) cc_final: 0.7919 (tpt) REVERT: A 280 LEU cc_start: 0.8119 (mt) cc_final: 0.7914 (mp) REVERT: A 407 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7129 (mmt) REVERT: A 471 GLN cc_start: 0.7684 (mt0) cc_final: 0.7279 (mt0) REVERT: A 490 LEU cc_start: 0.7506 (mt) cc_final: 0.7239 (mt) REVERT: A 507 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8025 (mt-10) REVERT: A 526 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: A 535 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: A 596 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: A 599 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7189 (mtm110) REVERT: B 414 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8001 (mm-40) REVERT: B 438 SER cc_start: 0.8051 (t) cc_final: 0.7679 (t) REVERT: B 454 ARG cc_start: 0.7060 (ttm-80) cc_final: 0.6796 (ttm-80) outliers start: 26 outliers final: 15 residues processed: 114 average time/residue: 0.5139 time to fit residues: 61.8356 Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9333 > 50: distance: 0 - 1: 7.860 distance: 1 - 2: 7.298 distance: 1 - 4: 9.894 distance: 2 - 3: 13.548 distance: 2 - 7: 9.912 distance: 4 - 5: 7.333 distance: 4 - 6: 10.476 distance: 7 - 8: 10.708 distance: 8 - 9: 4.245 distance: 8 - 11: 14.237 distance: 9 - 10: 23.045 distance: 9 - 15: 15.813 distance: 11 - 12: 10.306 distance: 12 - 13: 16.377 distance: 12 - 14: 22.236 distance: 15 - 16: 15.611 distance: 16 - 17: 15.595 distance: 16 - 19: 17.277 distance: 17 - 18: 12.738 distance: 17 - 23: 19.356 distance: 19 - 20: 7.713 distance: 20 - 21: 11.638 distance: 20 - 22: 21.348 distance: 23 - 24: 17.907 distance: 24 - 25: 22.975 distance: 24 - 27: 13.021 distance: 25 - 26: 22.179 distance: 25 - 29: 33.781 distance: 27 - 28: 13.113 distance: 28 - 100: 19.853 distance: 29 - 30: 35.317 distance: 29 - 35: 26.460 distance: 30 - 31: 6.809 distance: 30 - 33: 19.102 distance: 31 - 32: 18.291 distance: 31 - 36: 13.715 distance: 33 - 34: 33.672 distance: 34 - 35: 28.917 distance: 36 - 37: 25.749 distance: 37 - 38: 28.449 distance: 37 - 40: 11.264 distance: 38 - 39: 16.839 distance: 38 - 47: 20.409 distance: 39 - 67: 11.433 distance: 40 - 41: 9.919 distance: 41 - 42: 14.088 distance: 41 - 43: 16.320 distance: 42 - 44: 28.107 distance: 43 - 45: 20.717 distance: 44 - 46: 14.906 distance: 45 - 46: 21.352 distance: 47 - 48: 4.929 distance: 48 - 49: 5.496 distance: 49 - 50: 8.047 distance: 49 - 51: 6.745 distance: 50 - 76: 9.671 distance: 51 - 52: 14.570 distance: 52 - 53: 17.820 distance: 52 - 55: 10.619 distance: 53 - 54: 6.894 distance: 53 - 60: 10.556 distance: 55 - 56: 9.230 distance: 56 - 57: 9.924 distance: 57 - 58: 14.907 distance: 57 - 59: 8.799 distance: 60 - 61: 4.008 distance: 61 - 62: 16.666 distance: 61 - 64: 14.842 distance: 62 - 63: 17.592 distance: 62 - 67: 24.619 distance: 64 - 65: 22.272 distance: 64 - 66: 25.660