Starting phenix.real_space_refine on Mon Feb 10 21:40:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsm_38622/02_2025/8xsm_38622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsm_38622/02_2025/8xsm_38622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsm_38622/02_2025/8xsm_38622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsm_38622/02_2025/8xsm_38622.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsm_38622/02_2025/8xsm_38622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsm_38622/02_2025/8xsm_38622.cif" } resolution = 3.01 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= 0.139 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 16 5.16 5 C 1842 2.51 5 N 466 2.21 5 O 464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2788 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2734 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'RBF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.34, per 1000 atoms: 1.20 Number of scatterers: 2788 At special positions: 0 Unit cell: (73.1, 62.9, 75.65, 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 16 16.00 O 464 8.00 N 466 7.00 C 1842 6.00 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 - 3.00 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: 0.78 Conformation dependent library (CDL) restraints added in 381.9 milliseconds 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 1 sheets defined 81.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 8 through 22 Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.904A pdb=" N VAL A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix removed outlier: 3.862A pdb=" N LYS A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.521A pdb=" N TYR A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 72 removed outlier: 4.212A pdb=" N LEU A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 98 removed outlier: 4.511A pdb=" N ILE A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 133 removed outlier: 4.009A pdb=" N ASN A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.713A pdb=" N HIS A 138 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 143 through 166 removed outlier: 3.993A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 192 through 218 removed outlier: 3.737A pdb=" N PHE A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.854A pdb=" N LEU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 5.740A pdb=" N SER A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 331 removed outlier: 3.803A pdb=" N TYR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 335 through 359 removed outlier: 3.907A pdb=" N CYS A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 398 removed outlier: 3.862A pdb=" N VAL A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 429 removed outlier: 3.532A pdb=" N ALA A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 105 206 hydrogen bonds defined for protein. 612 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: 0.84 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 412 1.30 - 1.43: 753 1.43 - 1.55: 1675 1.55 - 1.68: 0 1.68 - 1.81: 21 Bond restraints: 2861 Sorted by residual: bond pdb=" C4 RBF A 501 " pdb=" C4A RBF A 501 " ideal model delta sigma weight residual 1.481 1.343 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C4 RBF A 502 " pdb=" C4A RBF A 502 " ideal model delta sigma weight residual 1.481 1.353 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C10 RBF A 501 " pdb=" C4A RBF A 501 " ideal model delta sigma weight residual 1.440 1.337 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C ALA A 404 " pdb=" O ALA A 404 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.19e-02 7.06e+03 1.96e+01 bond pdb=" C LEU A 406 " pdb=" O LEU A 406 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.17e-02 7.31e+03 1.80e+01 ... (remaining 2856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 3801 2.37 - 4.73: 100 4.73 - 7.10: 21 7.10 - 9.47: 5 9.47 - 11.84: 1 Bond angle restraints: 3928 Sorted by residual: angle pdb=" C ARG A 402 " pdb=" N PRO A 403 " pdb=" CA PRO A 403 " ideal model delta sigma weight residual 119.05 126.50 -7.45 1.11e+00 8.12e-01 4.50e+01 angle pdb=" N GLY A 400 " pdb=" CA GLY A 400 " pdb=" C GLY A 400 " ideal model delta sigma weight residual 112.73 120.18 -7.45 1.20e+00 6.94e-01 3.86e+01 angle pdb=" C GLY A 399 " pdb=" N GLY A 400 " pdb=" CA GLY A 400 " ideal model delta sigma weight residual 119.98 126.16 -6.18 1.11e+00 8.12e-01 3.10e+01 angle pdb=" C HIS A 398 " pdb=" N GLY A 399 " pdb=" CA GLY A 399 " ideal model delta sigma weight residual 119.98 125.90 -5.92 1.11e+00 8.12e-01 2.84e+01 angle pdb=" C3' RBF A 501 " pdb=" C4' RBF A 501 " pdb=" O4' RBF A 501 " ideal model delta sigma weight residual 113.84 102.00 11.84 3.00e+00 1.11e-01 1.56e+01 ... (remaining 3923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.40: 1445 13.40 - 26.80: 141 26.80 - 40.20: 50 40.20 - 53.60: 16 53.60 - 66.99: 6 Dihedral angle restraints: 1658 sinusoidal: 600 harmonic: 1058 Sorted by residual: dihedral pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" CB LEU A 217 " pdb=" CG LEU A 217 " ideal model delta sinusoidal sigma weight residual -180.00 -126.91 -53.09 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA LEU A 359 " pdb=" CB LEU A 359 " pdb=" CG LEU A 359 " pdb=" CD1 LEU A 359 " ideal model delta sinusoidal sigma weight residual 60.00 110.69 -50.69 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N CYS A 302 " pdb=" CA CYS A 302 " ideal model delta harmonic sigma weight residual -180.00 -165.27 -14.73 0 5.00e+00 4.00e-02 8.67e+00 ... (remaining 1655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 410 0.061 - 0.122: 63 0.122 - 0.183: 3 0.183 - 0.244: 4 0.244 - 0.305: 2 Chirality restraints: 482 Sorted by residual: chirality pdb=" C4' RBF A 501 " pdb=" C3' RBF A 501 " pdb=" C5' RBF A 501 " pdb=" O4' RBF A 501 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU A 405 " pdb=" N LEU A 405 " pdb=" C LEU A 405 " pdb=" CB LEU A 405 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C4' RBF A 502 " pdb=" C3' RBF A 502 " pdb=" C5' RBF A 502 " pdb=" O4' RBF A 502 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 479 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 403 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO A 403 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO A 403 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA A 404 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 404 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.77e+00 pdb=" C ALA A 404 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 404 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 405 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 405 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C LEU A 405 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A 405 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 406 " 0.012 2.00e-02 2.50e+03 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 68 2.71 - 3.26: 2759 3.26 - 3.80: 4197 3.80 - 4.35: 5369 4.35 - 4.90: 9243 Nonbonded interactions: 21636 Sorted by model distance: nonbonded pdb=" O GLN A 270 " pdb=" OG SER A 276 " model vdw 2.161 3.040 nonbonded pdb=" O3' RBF A 501 " pdb=" O5' RBF A 501 " model vdw 2.186 3.040 nonbonded pdb=" O CYS A 125 " pdb=" OG SER A 128 " model vdw 2.251 3.040 nonbonded pdb=" O2' RBF A 501 " pdb=" O4' RBF A 501 " model vdw 2.381 3.040 nonbonded pdb=" O2' RBF A 502 " pdb=" O4' RBF A 502 " model vdw 2.421 3.040 ... (remaining 21631 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: 1.600 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.060 Find NCS groups from input model: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.008 0.138 2861 Z= 0.597 Angle : 0.926 11.836 3928 Z= 0.495 Chirality : 0.050 0.305 482 Planarity : 0.007 0.046 476 Dihedral : 13.813 66.994 978 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.40 % Allowed : 11.54 % Favored : 87.06 % 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: -1.76 (0.38), residues: 369 helix: -0.68 (0.27), residues: 278 sheet: None (None), residues: 0 loop : -2.33 (0.58), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 379 HIS 0.008 0.001 HIS A 398 PHE 0.011 0.001 PHE A 191 TYR 0.005 0.001 TYR A 430 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.271 Fit side-chains REVERT: A 70 ARG cc_start: 0.6940 (mpt180) cc_final: 0.6585 (mmt180) REVERT: A 169 ARG cc_start: 0.6203 (mtp-110) cc_final: 0.5977 (mtm-85) REVERT: A 402 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8192 (ttt-90) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.2229 time to fit residues: 9.7565 Evaluate side-chains 29 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 402 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 291 ASN A 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115396 restraints weight = 3060.660| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.84 r_work: 0.3196 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2861 Z= 0.242 Angle : 0.651 6.517 3928 Z= 0.312 Chirality : 0.039 0.125 482 Planarity : 0.006 0.042 476 Dihedral : 9.477 59.677 428 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.75 % Allowed : 14.34 % Favored : 83.92 % 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: 0.25 (0.42), residues: 369 helix: 0.77 (0.30), residues: 273 sheet: None (None), residues: 0 loop : -1.44 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 379 HIS 0.005 0.001 HIS A 13 PHE 0.010 0.001 PHE A 191 TYR 0.007 0.001 TYR A 430 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.278 Fit side-chains REVERT: A 70 ARG cc_start: 0.6943 (mpt180) cc_final: 0.6507 (mmt180) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.1275 time to fit residues: 5.1657 Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118386 restraints weight = 2993.764| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.83 r_work: 0.3237 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2861 Z= 0.194 Angle : 0.584 6.074 3928 Z= 0.281 Chirality : 0.037 0.119 482 Planarity : 0.005 0.038 476 Dihedral : 8.454 53.078 424 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.05 % Allowed : 15.03 % Favored : 83.92 % 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: 1.20 (0.43), residues: 369 helix: 1.52 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -1.26 (0.59), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 45 HIS 0.005 0.001 HIS A 13 PHE 0.009 0.001 PHE A 348 TYR 0.005 0.001 TYR A 430 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.287 Fit side-chains REVERT: A 70 ARG cc_start: 0.6811 (mpt180) cc_final: 0.6350 (mmt180) REVERT: A 272 LEU cc_start: 0.7547 (mp) cc_final: 0.7249 (mm) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.1027 time to fit residues: 3.7058 Evaluate side-chains 25 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119103 restraints weight = 3034.852| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.86 r_work: 0.3248 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2861 Z= 0.180 Angle : 0.567 6.048 3928 Z= 0.273 Chirality : 0.037 0.118 482 Planarity : 0.005 0.037 476 Dihedral : 8.104 55.409 424 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.80 % Allowed : 13.29 % Favored : 83.92 % 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: 1.73 (0.44), residues: 369 helix: 1.92 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -1.13 (0.59), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 68 HIS 0.005 0.001 HIS A 13 PHE 0.008 0.001 PHE A 191 TYR 0.004 0.001 TYR A 430 ARG 0.001 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.288 Fit side-chains REVERT: A 70 ARG cc_start: 0.6873 (mpt180) cc_final: 0.6401 (mmt180) REVERT: A 272 LEU cc_start: 0.7538 (mp) cc_final: 0.7265 (mm) REVERT: A 345 LEU cc_start: 0.5891 (mt) cc_final: 0.5644 (tp) REVERT: A 354 MET cc_start: 0.7816 (ttp) cc_final: 0.7426 (tpp) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.1448 time to fit residues: 5.8551 Evaluate side-chains 26 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114427 restraints weight = 3042.974| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.85 r_work: 0.3219 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2861 Z= 0.221 Angle : 0.597 6.039 3928 Z= 0.288 Chirality : 0.038 0.121 482 Planarity : 0.005 0.038 476 Dihedral : 8.117 54.490 424 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 13.99 % Favored : 83.57 % 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: 1.66 (0.43), residues: 369 helix: 1.86 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 24 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE A 19 TYR 0.004 0.001 TYR A 430 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.285 Fit side-chains REVERT: A 70 ARG cc_start: 0.6931 (mpt180) cc_final: 0.6485 (mmt180) REVERT: A 272 LEU cc_start: 0.7584 (mp) cc_final: 0.7289 (mm) REVERT: A 345 LEU cc_start: 0.5859 (mt) cc_final: 0.5629 (tp) outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.1157 time to fit residues: 4.6184 Evaluate side-chains 28 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.0474 > 50: distance: 29 - 46: 20.634 distance: 32 - 38: 14.513 distance: 38 - 39: 9.133 distance: 39 - 40: 22.875 distance: 39 - 42: 6.708 distance: 40 - 41: 9.095 distance: 40 - 46: 27.082 distance: 42 - 43: 13.192 distance: 43 - 44: 4.885 distance: 43 - 45: 7.531 distance: 46 - 47: 17.219 distance: 47 - 48: 14.795 distance: 47 - 50: 13.075 distance: 48 - 49: 17.062 distance: 48 - 52: 15.362 distance: 50 - 51: 15.689 distance: 52 - 53: 9.377 distance: 53 - 54: 6.236 distance: 53 - 56: 9.521 distance: 54 - 55: 14.600 distance: 54 - 62: 10.736 distance: 56 - 57: 9.854 distance: 57 - 59: 6.438 distance: 58 - 60: 5.983 distance: 59 - 61: 3.467 distance: 60 - 61: 4.094 distance: 62 - 63: 13.011 distance: 63 - 64: 14.278 distance: 63 - 66: 11.889 distance: 64 - 65: 14.968 distance: 64 - 70: 11.521 distance: 66 - 67: 13.436 distance: 67 - 68: 7.359 distance: 67 - 69: 6.634 distance: 70 - 71: 15.661 distance: 70 - 76: 21.338 distance: 71 - 72: 21.911 distance: 71 - 74: 18.031 distance: 72 - 73: 15.259 distance: 72 - 77: 25.150 distance: 74 - 75: 20.068 distance: 75 - 76: 28.564 distance: 77 - 78: 13.401 distance: 77 - 83: 12.526 distance: 78 - 79: 24.431 distance: 78 - 81: 16.076 distance: 79 - 80: 12.617 distance: 79 - 84: 25.689 distance: 81 - 82: 24.939 distance: 82 - 83: 31.029 distance: 84 - 85: 24.187 distance: 85 - 86: 18.643 distance: 85 - 88: 20.960 distance: 86 - 87: 29.567 distance: 86 - 95: 3.401 distance: 88 - 89: 30.962 distance: 89 - 90: 10.047 distance: 90 - 91: 4.868 distance: 91 - 92: 3.949 distance: 95 - 96: 18.416 distance: 96 - 97: 10.576 distance: 96 - 99: 7.701 distance: 97 - 98: 17.055 distance: 97 - 106: 6.672 distance: 98 - 131: 23.584 distance: 99 - 100: 14.093 distance: 100 - 101: 6.831 distance: 100 - 102: 17.314 distance: 101 - 103: 14.005 distance: 102 - 104: 11.615 distance: 103 - 105: 9.696 distance: 104 - 105: 10.396 distance: 106 - 107: 7.263 distance: 107 - 108: 12.632 distance: 107 - 110: 11.068 distance: 108 - 109: 11.668 distance: 108 - 114: 13.364 distance: 109 - 142: 12.808 distance: 110 - 111: 15.369 distance: 111 - 112: 12.107 distance: 111 - 113: 8.362 distance: 114 - 115: 9.189 distance: 115 - 116: 10.844 distance: 115 - 118: 6.354 distance: 116 - 117: 8.553 distance: 116 - 125: 10.210 distance: 117 - 152: 17.801 distance: 118 - 119: 8.845 distance: 119 - 120: 5.309 distance: 120 - 121: 5.720