Starting phenix.real_space_refine on Fri Aug 2 18:32:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb4_38210/08_2024/8xb4_38210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb4_38210/08_2024/8xb4_38210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb4_38210/08_2024/8xb4_38210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb4_38210/08_2024/8xb4_38210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb4_38210/08_2024/8xb4_38210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb4_38210/08_2024/8xb4_38210.cif" } resolution = 2.92 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= -0.001 sd= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2894 2.51 5 N 665 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4307 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4293 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.73 Number of scatterers: 4307 At special positions: 0 Unit cell: (65.88, 66.96, 95.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 728 8.00 N 665 7.00 C 2894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 184 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 766.3 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 66 through 74 removed outlier: 4.005A pdb=" N PHE A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.525A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.652A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.524A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.870A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.805A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.505A pdb=" N PHE A 207 " --> pdb=" O LYS A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 208 through 218 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 264 through 283 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.865A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.788A pdb=" N LEU A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.542A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.731A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 4.293A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.038A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 603' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.316A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 819 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: 1.17 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1257 1.34 - 1.46: 1195 1.46 - 1.58: 1964 1.58 - 1.70: 0 1.70 - 1.81: 31 Bond restraints: 4447 Sorted by residual: bond pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.86e-01 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.432 -0.019 2.00e-02 2.50e+03 9.34e-01 bond pdb=" CG LEU A 390 " pdb=" CD2 LEU A 390 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.20e-01 bond pdb=" C PHE A 82 " pdb=" O PHE A 82 " ideal model delta sigma weight residual 1.244 1.235 0.008 9.80e-03 1.04e+04 6.95e-01 bond pdb=" CB VAL A 535 " pdb=" CG1 VAL A 535 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.43e-01 ... (remaining 4442 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.65: 118 106.65 - 113.49: 2408 113.49 - 120.34: 1759 120.34 - 127.18: 1717 127.18 - 134.03: 67 Bond angle restraints: 6069 Sorted by residual: angle pdb=" N GLY A 478 " pdb=" CA GLY A 478 " pdb=" C GLY A 478 " ideal model delta sigma weight residual 113.18 107.55 5.63 2.37e+00 1.78e-01 5.64e+00 angle pdb=" C ASN A 596 " pdb=" N GLU A 597 " pdb=" CA GLU A 597 " ideal model delta sigma weight residual 123.17 120.08 3.09 1.49e+00 4.50e-01 4.30e+00 angle pdb=" CA TYR A 391 " pdb=" C TYR A 391 " pdb=" N PRO A 392 " ideal model delta sigma weight residual 118.44 121.69 -3.25 1.59e+00 3.96e-01 4.17e+00 angle pdb=" C VAL A 282 " pdb=" N THR A 283 " pdb=" CA THR A 283 " ideal model delta sigma weight residual 121.94 118.02 3.92 2.00e+00 2.50e-01 3.85e+00 angle pdb=" CA TYR A 111 " pdb=" CB TYR A 111 " pdb=" CG TYR A 111 " ideal model delta sigma weight residual 113.90 117.28 -3.38 1.80e+00 3.09e-01 3.53e+00 ... (remaining 6064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 2352 21.48 - 42.95: 121 42.95 - 64.43: 8 64.43 - 85.90: 7 85.90 - 107.38: 7 Dihedral angle restraints: 2495 sinusoidal: 944 harmonic: 1551 Sorted by residual: dihedral pdb=" CA THR A 544 " pdb=" C THR A 544 " pdb=" N TYR A 545 " pdb=" CA TYR A 545 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual 53.78 -53.60 107.38 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 68.05 107.06 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 2492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 360 0.029 - 0.058: 208 0.058 - 0.087: 78 0.087 - 0.116: 27 0.116 - 0.145: 8 Chirality restraints: 681 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 549 " pdb=" N ILE A 549 " pdb=" C ILE A 549 " pdb=" CB ILE A 549 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 678 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 83 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 111 " -0.014 2.00e-02 2.50e+03 1.23e-02 3.01e+00 pdb=" CG TYR A 111 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 111 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 111 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 111 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 392 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.024 5.00e-02 4.00e+02 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1130 2.79 - 3.32: 4134 3.32 - 3.84: 7479 3.84 - 4.37: 9160 4.37 - 4.90: 15607 Nonbonded interactions: 37510 Sorted by model distance: nonbonded pdb=" OH TYR A 496 " pdb=" OD2 ASP A 504 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU A 425 " pdb=" OG1 THR A 429 " model vdw 2.279 3.040 nonbonded pdb=" NH1 ARG A 121 " pdb=" O ASN A 333 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP A 75 " pdb=" OD1 ASN A 78 " model vdw 2.335 3.040 nonbonded pdb=" O ALA A 589 " pdb=" OG1 THR A 593 " model vdw 2.369 3.040 ... (remaining 37505 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.580 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.005 0.038 4447 Z= 0.292 Angle : 0.606 5.903 6069 Z= 0.329 Chirality : 0.043 0.145 681 Planarity : 0.005 0.045 736 Dihedral : 14.468 107.378 1504 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.32), residues: 530 helix: -1.09 (0.23), residues: 379 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 253 HIS 0.005 0.001 HIS A 280 PHE 0.012 0.001 PHE A 316 TYR 0.030 0.002 TYR A 111 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.456 Fit side-chains REVERT: A 88 LYS cc_start: 0.8339 (tttp) cc_final: 0.8021 (ttmt) REVERT: A 206 LYS cc_start: 0.7992 (pttm) cc_final: 0.7682 (ptpt) REVERT: A 531 PHE cc_start: 0.7634 (t80) cc_final: 0.7178 (t80) outliers start: 0 outliers final: 1 residues processed: 75 average time/residue: 0.6926 time to fit residues: 55.3106 Evaluate side-chains 54 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 610 GLN A 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4447 Z= 0.205 Angle : 0.559 6.841 6069 Z= 0.285 Chirality : 0.042 0.173 681 Planarity : 0.005 0.044 736 Dihedral : 5.985 31.440 600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.55 % Allowed : 9.07 % Favored : 89.38 % 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: -0.21 (0.35), residues: 530 helix: 0.09 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.39 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 222 PHE 0.012 0.001 PHE A 409 TYR 0.019 0.002 TYR A 111 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.477 Fit side-chains REVERT: A 206 LYS cc_start: 0.8116 (pttm) cc_final: 0.7771 (ptpt) outliers start: 7 outliers final: 1 residues processed: 68 average time/residue: 0.7498 time to fit residues: 54.2349 Evaluate side-chains 56 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4447 Z= 0.209 Angle : 0.530 5.968 6069 Z= 0.272 Chirality : 0.041 0.144 681 Planarity : 0.005 0.045 736 Dihedral : 4.666 31.163 600 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.99 % Allowed : 11.50 % Favored : 86.50 % 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: 0.42 (0.36), residues: 530 helix: 0.58 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.27 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.012 0.001 PHE A 409 TYR 0.018 0.001 TYR A 111 ARG 0.002 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.447 Fit side-chains REVERT: A 206 LYS cc_start: 0.8210 (pttm) cc_final: 0.7838 (ptpt) REVERT: A 421 MET cc_start: 0.7674 (ttm) cc_final: 0.7460 (ttm) outliers start: 9 outliers final: 1 residues processed: 65 average time/residue: 0.7243 time to fit residues: 50.1015 Evaluate side-chains 51 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.0070 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4447 Z= 0.152 Angle : 0.492 5.851 6069 Z= 0.252 Chirality : 0.039 0.139 681 Planarity : 0.004 0.044 736 Dihedral : 4.092 19.398 598 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.99 % Allowed : 13.50 % Favored : 84.51 % 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: 0.93 (0.37), residues: 530 helix: 0.97 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.14 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 220 PHE 0.011 0.001 PHE A 110 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.453 Fit side-chains REVERT: A 206 LYS cc_start: 0.8230 (pttm) cc_final: 0.7835 (ptpt) REVERT: A 310 ASP cc_start: 0.8254 (m-30) cc_final: 0.8027 (m-30) REVERT: A 421 MET cc_start: 0.7646 (ttm) cc_final: 0.7411 (ttm) REVERT: A 597 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7222 (pm20) outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.6802 time to fit residues: 50.8269 Evaluate side-chains 60 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4447 Z= 0.235 Angle : 0.533 5.875 6069 Z= 0.273 Chirality : 0.041 0.139 681 Planarity : 0.004 0.045 736 Dihedral : 4.254 20.830 598 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.88 % Allowed : 13.27 % Favored : 83.85 % 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: 0.95 (0.36), residues: 530 helix: 0.97 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.05 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.001 PHE A 316 TYR 0.018 0.002 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.498 Fit side-chains REVERT: A 206 LYS cc_start: 0.8345 (pttm) cc_final: 0.7928 (ptpt) REVERT: A 421 MET cc_start: 0.7628 (ttm) cc_final: 0.7424 (ttm) outliers start: 13 outliers final: 6 residues processed: 65 average time/residue: 0.6951 time to fit residues: 48.3099 Evaluate side-chains 57 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 42 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4447 Z= 0.161 Angle : 0.494 5.826 6069 Z= 0.252 Chirality : 0.039 0.143 681 Planarity : 0.004 0.044 736 Dihedral : 4.035 17.099 598 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.43 % Allowed : 14.38 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.37), residues: 530 helix: 1.20 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.13 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.014 0.001 PHE A 408 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.512 Fit side-chains REVERT: A 373 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7458 (mmmt) REVERT: A 421 MET cc_start: 0.7608 (ttm) cc_final: 0.7388 (ttm) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.6187 time to fit residues: 40.6020 Evaluate side-chains 60 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7846 > 50: distance: 43 - 64: 12.558 distance: 47 - 68: 22.733 distance: 52 - 76: 14.759 distance: 56 - 64: 16.257 distance: 64 - 65: 28.532 distance: 65 - 66: 43.336 distance: 66 - 67: 26.872 distance: 66 - 68: 25.889 distance: 68 - 69: 34.115 distance: 69 - 70: 35.143 distance: 69 - 72: 19.435 distance: 70 - 71: 27.745 distance: 70 - 76: 11.424 distance: 72 - 73: 19.934 distance: 72 - 74: 13.325 distance: 73 - 75: 21.188 distance: 76 - 77: 14.552 distance: 77 - 78: 24.649 distance: 77 - 80: 9.506 distance: 78 - 79: 27.692 distance: 78 - 83: 25.872 distance: 80 - 81: 15.044 distance: 80 - 82: 12.162 distance: 83 - 84: 13.882 distance: 83 - 89: 27.345 distance: 84 - 85: 34.070 distance: 84 - 87: 18.752 distance: 85 - 86: 16.254 distance: 85 - 90: 39.775 distance: 86 - 107: 17.668 distance: 87 - 88: 21.038 distance: 88 - 89: 36.126 distance: 90 - 91: 17.751 distance: 91 - 92: 27.486 distance: 91 - 94: 23.164 distance: 92 - 93: 19.692 distance: 92 - 99: 31.322 distance: 94 - 95: 19.126 distance: 95 - 96: 8.241 distance: 96 - 97: 14.382 distance: 96 - 98: 9.385 distance: 99 - 100: 20.875 distance: 100 - 101: 21.576 distance: 100 - 103: 26.504 distance: 101 - 102: 11.826 distance: 101 - 107: 30.947 distance: 103 - 104: 15.463 distance: 104 - 105: 35.515 distance: 104 - 106: 34.021 distance: 107 - 108: 18.424 distance: 108 - 109: 8.095 distance: 108 - 111: 14.665 distance: 109 - 110: 6.923 distance: 109 - 116: 12.783 distance: 111 - 112: 14.799 distance: 113 - 114: 7.638 distance: 113 - 115: 4.219 distance: 116 - 117: 32.474 distance: 117 - 118: 19.475 distance: 117 - 120: 23.253 distance: 118 - 119: 21.880 distance: 118 - 126: 5.892 distance: 120 - 121: 27.494 distance: 121 - 122: 14.603 distance: 121 - 123: 11.503 distance: 122 - 124: 5.410 distance: 123 - 125: 10.686 distance: 126 - 127: 28.196 distance: 127 - 128: 39.161 distance: 127 - 130: 38.595 distance: 128 - 129: 26.216 distance: 128 - 136: 48.294 distance: 130 - 131: 50.785 distance: 131 - 132: 44.006 distance: 131 - 133: 46.429 distance: 132 - 134: 40.106 distance: 133 - 135: 22.690 distance: 134 - 135: 41.068 distance: 136 - 137: 18.955 distance: 137 - 138: 24.320 distance: 137 - 140: 31.482 distance: 138 - 139: 15.787 distance: 138 - 144: 12.552 distance: 140 - 141: 6.894 distance: 141 - 142: 7.141 distance: 141 - 143: 15.316