Starting phenix.real_space_refine on Tue Dec 12 06:57:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/12_2023/6h3i_0133.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/12_2023/6h3i_0133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/12_2023/6h3i_0133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/12_2023/6h3i_0133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/12_2023/6h3i_0133.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/12_2023/6h3i_0133.pdb" } resolution = 3.5 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= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 C 12990 2.51 5 N 3461 2.21 5 O 4049 1.98 5 H 53 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1311": "NH1" <-> "NH2" Residue "A PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1745": "NH1" <-> "NH2" Residue "A TYR 1766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1988": "NH1" <-> "NH2" Residue "A TYR 2045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20599 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2124, 16848 Classifications: {'peptide': 2124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 97, 'TRANS': 2026} Chain breaks: 11 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2708 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 4 Time building chain proxies: 10.88, per 1000 atoms: 0.53 Number of scatterers: 20599 At special positions: 0 Unit cell: (117.26, 127.1, 135.3, 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) S 46 16.00 O 4049 8.00 N 3461 7.00 C 12990 6.00 H 53 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 3.4 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 10.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.906A pdb=" N THR A 185 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.398A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.709A pdb=" N GLU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.261A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.533A pdb=" N GLY A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.869A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 627 through 634 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.686A pdb=" N MET A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.534A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 914 through 920 removed outlier: 4.306A pdb=" N TYR A 918 " --> pdb=" O ASP A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 944 removed outlier: 3.896A pdb=" N LEU A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.547A pdb=" N ASN A 986 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1081 through 1089 removed outlier: 4.267A pdb=" N ASN A1087 " --> pdb=" O ASP A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 4.272A pdb=" N TYR A1132 " --> pdb=" O VAL A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1426 through 1439 removed outlier: 3.995A pdb=" N LEU A1430 " --> pdb=" O ALA A1426 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG A1432 " --> pdb=" O ASP A1428 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1576 Processing helix chain 'A' and resid 1607 through 1613 Processing helix chain 'A' and resid 1617 through 1622 Processing helix chain 'A' and resid 1856 through 1861 removed outlier: 3.647A pdb=" N SER A1860 " --> pdb=" O SER A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1982 Processing helix chain 'A' and resid 1989 through 1995 removed outlier: 3.705A pdb=" N GLY A1995 " --> pdb=" O ALA A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2072 through 2076 removed outlier: 4.214A pdb=" N PHE A2076 " --> pdb=" O LYS A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2104 removed outlier: 3.965A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2111 removed outlier: 3.521A pdb=" N VAL A2110 " --> pdb=" O GLY A2107 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA A2111 " --> pdb=" O SER A2108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2107 through 2111' Processing helix chain 'A' and resid 2129 through 2135 Processing helix chain 'A' and resid 2147 through 2152 removed outlier: 3.528A pdb=" N LEU A2151 " --> pdb=" O ASN A2147 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2161 Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 286 through 297 removed outlier: 4.225A pdb=" N TYR F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.764A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 291 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: 4.45 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 53 1.03 - 1.23: 244 1.23 - 1.42: 8887 1.42 - 1.62: 11763 1.62 - 1.81: 90 Bond restraints: 21037 Sorted by residual: bond pdb=" CD2 TYR A 309 " pdb=" CE2 TYR A 309 " ideal model delta sigma weight residual 1.382 1.310 0.072 3.00e-02 1.11e+03 5.83e+00 bond pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 1.512 1.467 0.045 2.20e-02 2.07e+03 4.10e+00 bond pdb=" C ASP A1600 " pdb=" N PRO A1601 " ideal model delta sigma weight residual 1.334 1.288 0.046 2.34e-02 1.83e+03 3.88e+00 bond pdb=" CB ILE A 990 " pdb=" CG2 ILE A 990 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.83e+00 bond pdb=" CB VAL A1345 " pdb=" CG1 VAL A1345 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 ... (remaining 21032 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.03: 394 105.03 - 112.31: 10095 112.31 - 119.59: 7042 119.59 - 126.88: 10845 126.88 - 134.16: 182 Bond angle restraints: 28558 Sorted by residual: angle pdb=" N GLN F 58 " pdb=" CA GLN F 58 " pdb=" C GLN F 58 " ideal model delta sigma weight residual 114.04 107.91 6.13 1.24e+00 6.50e-01 2.44e+01 angle pdb=" C GLU A1035 " pdb=" N ILE A1036 " pdb=" CA ILE A1036 " ideal model delta sigma weight residual 120.49 126.64 -6.15 1.38e+00 5.25e-01 1.99e+01 angle pdb=" N ASN A 822 " pdb=" CA ASN A 822 " pdb=" C ASN A 822 " ideal model delta sigma weight residual 110.80 118.76 -7.96 2.13e+00 2.20e-01 1.40e+01 angle pdb=" N GLY F 43 " pdb=" CA GLY F 43 " pdb=" C GLY F 43 " ideal model delta sigma weight residual 115.46 109.67 5.79 1.63e+00 3.76e-01 1.26e+01 angle pdb=" CA TYR F 330 " pdb=" CB TYR F 330 " pdb=" CG TYR F 330 " ideal model delta sigma weight residual 113.90 107.51 6.39 1.80e+00 3.09e-01 1.26e+01 ... (remaining 28553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 11771 15.29 - 30.58: 639 30.58 - 45.87: 81 45.87 - 61.17: 3 61.17 - 76.46: 19 Dihedral angle restraints: 12513 sinusoidal: 4972 harmonic: 7541 Sorted by residual: dihedral pdb=" CA GLN A 501 " pdb=" C GLN A 501 " pdb=" N SER A 502 " pdb=" CA SER A 502 " ideal model delta harmonic sigma weight residual -180.00 -149.73 -30.27 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA GLN A1563 " pdb=" C GLN A1563 " pdb=" N TYR A1564 " pdb=" CA TYR A1564 " ideal model delta harmonic sigma weight residual 180.00 149.89 30.11 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA ASN A 308 " pdb=" C ASN A 308 " pdb=" N TYR A 309 " pdb=" CA TYR A 309 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 12510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2027 0.049 - 0.098: 811 0.098 - 0.147: 241 0.147 - 0.196: 13 0.196 - 0.245: 2 Chirality restraints: 3094 Sorted by residual: chirality pdb=" CA ASN A 998 " pdb=" N ASN A 998 " pdb=" C ASN A 998 " pdb=" CB ASN A 998 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A2178 " pdb=" N PRO A2178 " pdb=" C PRO A2178 " pdb=" CB PRO A2178 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TYR F 330 " pdb=" N TYR F 330 " pdb=" C TYR F 330 " pdb=" CB TYR F 330 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 3091 not shown) Planarity restraints: 3766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2250 " 0.048 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO A2251 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A2251 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2251 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 129 " 0.022 2.00e-02 2.50e+03 1.60e-02 7.05e+00 pdb=" CG TRP B 129 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 129 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 129 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 129 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 129 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP B 129 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A2177 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.50e+00 pdb=" N PRO A2178 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A2178 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2178 " -0.035 5.00e-02 4.00e+02 ... (remaining 3763 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.53: 223 2.53 - 3.05: 15822 3.05 - 3.56: 22878 3.56 - 4.08: 36865 4.08 - 4.60: 53899 Nonbonded interactions: 129687 Sorted by model distance: nonbonded pdb=" OH TYR B 101 " pdb=" HH TYR B 120 " model vdw 2.010 1.850 nonbonded pdb=" OD1 ASP A2030 " pdb=" OG SER A2181 " model vdw 2.012 2.200 nonbonded pdb=" OG1 THR A1847 " pdb=" OG SER A1881 " model vdw 2.014 2.200 nonbonded pdb=" O GLN A1338 " pdb=" OG SER A1492 " model vdw 2.024 2.200 nonbonded pdb=" O LEU F 146 " pdb=" OG SER F 153 " model vdw 2.043 2.200 ... (remaining 129682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.160 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: 0.500 Extract box with map and model: 6.720 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 50.530 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.009 0.072 20984 Z= 0.595 Angle : 0.921 12.509 28466 Z= 0.502 Chirality : 0.054 0.245 3094 Planarity : 0.006 0.071 3766 Dihedral : 10.079 76.457 7671 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 39.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.41 % Favored : 78.43 % Rotamer: Outliers : 0.40 % Allowed : 3.41 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.64 (0.13), residues: 2559 helix: -3.64 (0.20), residues: 251 sheet: -3.59 (0.15), residues: 898 loop : -3.96 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B 129 HIS 0.009 0.002 HIS A1672 PHE 0.039 0.003 PHE A 656 TYR 0.039 0.003 TYR A1120 ARG 0.010 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 226 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 234 average time/residue: 0.3610 time to fit residues: 128.3208 Evaluate side-chains 122 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1817 time to fit residues: 3.4619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1742 GLN ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2120 ASN ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2236 ASN ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20984 Z= 0.155 Angle : 0.527 11.877 28466 Z= 0.276 Chirality : 0.042 0.142 3094 Planarity : 0.003 0.043 3766 Dihedral : 5.687 26.120 2836 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 51.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.41 % Favored : 83.47 % Rotamer: Outliers : 1.28 % Allowed : 7.09 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.15), residues: 2559 helix: -2.72 (0.26), residues: 248 sheet: -3.25 (0.16), residues: 879 loop : -3.59 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.028 0.001 PHE A2257 TYR 0.016 0.001 TYR F 292 ARG 0.003 0.000 ARG A2094 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 2.381 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 163 average time/residue: 0.3224 time to fit residues: 85.0804 Evaluate side-chains 127 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 2.408 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2163 time to fit residues: 10.6639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 188 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 ASN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 20984 Z= 0.320 Angle : 0.574 10.336 28466 Z= 0.299 Chirality : 0.043 0.151 3094 Planarity : 0.004 0.053 3766 Dihedral : 5.569 27.080 2836 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 49.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.34 % Favored : 80.54 % Rotamer: Outliers : 1.24 % Allowed : 8.46 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.15), residues: 2559 helix: -2.51 (0.27), residues: 250 sheet: -3.15 (0.16), residues: 885 loop : -3.49 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1996 HIS 0.004 0.001 HIS F 344 PHE 0.030 0.002 PHE A2257 TYR 0.022 0.002 TYR A1120 ARG 0.004 0.001 ARG A1484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 2.444 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 0.3229 time to fit residues: 71.5957 Evaluate side-chains 117 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2065 time to fit residues: 9.4569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 20984 Z= 0.237 Angle : 0.528 8.943 28466 Z= 0.275 Chirality : 0.042 0.144 3094 Planarity : 0.003 0.049 3766 Dihedral : 5.276 25.635 2836 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 49.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 17.43 % Favored : 82.45 % Rotamer: Outliers : 1.15 % Allowed : 9.70 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.15), residues: 2559 helix: -2.28 (0.28), residues: 248 sheet: -2.94 (0.17), residues: 862 loop : -3.33 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.003 0.001 HIS F 344 PHE 0.024 0.001 PHE A2257 TYR 0.017 0.001 TYR A1120 ARG 0.003 0.000 ARG A1484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 2.393 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 128 average time/residue: 0.3118 time to fit residues: 65.9194 Evaluate side-chains 116 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2208 time to fit residues: 8.4366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 57.2181 > 50: distance: 44 - 50: 4.193 distance: 50 - 51: 10.961 distance: 50 - 56: 3.966 distance: 51 - 52: 20.925 distance: 51 - 54: 19.275 distance: 52 - 53: 26.813 distance: 52 - 57: 34.798 distance: 54 - 55: 14.211 distance: 55 - 56: 28.052 distance: 58 - 59: 31.488 distance: 58 - 61: 6.533 distance: 59 - 60: 11.610 distance: 59 - 66: 7.853 distance: 66 - 67: 5.200 distance: 67 - 68: 8.777 distance: 67 - 70: 6.501 distance: 68 - 69: 10.387 distance: 68 - 75: 5.319 distance: 70 - 71: 5.642 distance: 71 - 72: 11.053 distance: 72 - 73: 6.586 distance: 73 - 74: 22.980 distance: 75 - 76: 7.083 distance: 76 - 77: 6.035 distance: 76 - 79: 6.544 distance: 77 - 78: 4.198 distance: 77 - 89: 10.327 distance: 79 - 80: 4.919 distance: 80 - 81: 7.456 distance: 80 - 82: 5.854 distance: 81 - 83: 8.301 distance: 82 - 84: 4.772 distance: 82 - 85: 8.096 distance: 83 - 84: 7.142 distance: 84 - 86: 5.183 distance: 86 - 88: 5.406 distance: 87 - 88: 8.506 distance: 89 - 90: 11.564 distance: 90 - 91: 8.486 distance: 91 - 92: 7.758 distance: 91 - 93: 9.330 distance: 93 - 94: 5.048 distance: 94 - 95: 6.487 distance: 95 - 96: 4.645 distance: 95 - 101: 6.920 distance: 97 - 98: 8.811 distance: 97 - 99: 6.612 distance: 98 - 100: 13.230 distance: 101 - 102: 5.029 distance: 102 - 103: 5.133 distance: 102 - 105: 8.353 distance: 103 - 104: 17.683 distance: 103 - 109: 9.451 distance: 105 - 106: 7.042 distance: 106 - 107: 3.747 distance: 106 - 108: 12.423 distance: 109 - 110: 4.970 distance: 110 - 111: 7.193 distance: 111 - 112: 16.056 distance: 111 - 117: 6.075 distance: 113 - 114: 10.066 distance: 114 - 115: 4.468 distance: 114 - 116: 5.794 distance: 117 - 118: 6.168 distance: 117 - 123: 10.482 distance: 118 - 121: 10.644 distance: 119 - 120: 10.565 distance: 119 - 124: 3.284 distance: 121 - 122: 6.822 distance: 122 - 123: 9.591 distance: 124 - 125: 7.791 distance: 125 - 126: 11.526 distance: 125 - 128: 4.430 distance: 126 - 127: 16.585 distance: 126 - 135: 6.994 distance: 128 - 129: 4.178 distance: 129 - 130: 12.033 distance: 129 - 131: 8.053 distance: 130 - 132: 9.851 distance: 131 - 133: 13.451 distance: 132 - 134: 11.533 distance: 133 - 134: 15.890