Starting phenix.real_space_refine on Fri Aug 22 13:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3f_41860/08_2025/8u3f_41860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3f_41860/08_2025/8u3f_41860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u3f_41860/08_2025/8u3f_41860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3f_41860/08_2025/8u3f_41860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u3f_41860/08_2025/8u3f_41860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3f_41860/08_2025/8u3f_41860.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.073 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 17 5.16 5 C 2274 2.51 5 N 534 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3410 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 19, 'TRANS': 417} Chain breaks: 2 Time building chain proxies: 0.87, per 1000 atoms: 0.26 Number of scatterers: 3410 At special positions: 0 Unit cell: (58.1, 64.74, 86.32, 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 17 16.00 O 585 8.00 N 534 7.00 C 2274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 387 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 78.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.555A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.635A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.506A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Proline residue: A 215 - end of helix removed outlier: 3.712A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.648A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 311 removed outlier: 3.743A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 359 through 384 Proline residue: A 375 - end of helix removed outlier: 3.614A pdb=" N GLY A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.636A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.712A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 702 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: 0.38 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 920 1.46 - 1.58: 1565 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3513 Sorted by residual: bond pdb=" CA VAL A 280 " pdb=" CB VAL A 280 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.50e-01 bond pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 1.469 1.476 -0.007 7.40e-03 1.83e+04 9.44e-01 bond pdb=" CA ASN A 323 " pdb=" C ASN A 323 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.66e-01 bond pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 1.447 1.457 -0.011 1.18e-02 7.18e+03 8.22e-01 bond pdb=" CB VAL A 211 " pdb=" CG2 VAL A 211 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.47e-01 ... (remaining 3508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 4434 1.05 - 2.10: 286 2.10 - 3.15: 44 3.15 - 4.20: 21 4.20 - 5.25: 6 Bond angle restraints: 4791 Sorted by residual: angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 109.34 113.83 -4.49 2.08e+00 2.31e-01 4.66e+00 angle pdb=" C LEU A 447 " pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 122.89 120.51 2.38 1.12e+00 7.97e-01 4.51e+00 angle pdb=" CA THR A 153 " pdb=" C THR A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 118.44 121.64 -3.20 1.59e+00 3.96e-01 4.05e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 109.34 113.48 -4.14 2.08e+00 2.31e-01 3.97e+00 angle pdb=" CA LEU A 289 " pdb=" C LEU A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 118.44 121.58 -3.14 1.59e+00 3.96e-01 3.91e+00 ... (remaining 4786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1771 16.48 - 32.95: 182 32.95 - 49.43: 30 49.43 - 65.90: 3 65.90 - 82.38: 1 Dihedral angle restraints: 1987 sinusoidal: 737 harmonic: 1250 Sorted by residual: dihedral pdb=" CA ASN A 323 " pdb=" C ASN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASN A 323 " pdb=" CB ASN A 323 " pdb=" CG ASN A 323 " pdb=" OD1 ASN A 323 " ideal model delta sinusoidal sigma weight residual -90.00 -152.99 62.99 2 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CG LYS A 278 " pdb=" CD LYS A 278 " pdb=" CE LYS A 278 " pdb=" NZ LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -136.68 -43.32 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 1984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 356 0.037 - 0.073: 148 0.073 - 0.110: 33 0.110 - 0.146: 6 0.146 - 0.183: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA PRO A 192 " pdb=" N PRO A 192 " pdb=" C PRO A 192 " pdb=" CB PRO A 192 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 541 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " 0.014 2.00e-02 2.50e+03 1.40e-02 3.45e+00 pdb=" CG PHE A 305 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 290 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 163 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.022 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 911 2.79 - 3.32: 3343 3.32 - 3.85: 5797 3.85 - 4.37: 6821 4.37 - 4.90: 11982 Nonbonded interactions: 28854 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OE2 GLU A 175 " model vdw 2.265 3.120 nonbonded pdb=" OH TYR A 101 " pdb=" OD1 ASP A 158 " model vdw 2.286 3.040 nonbonded pdb=" O PRO A 192 " pdb=" NH2 ARG A 353 " model vdw 2.314 3.120 nonbonded pdb=" OG SER A 37 " pdb=" OE2 GLU A 262 " model vdw 2.352 3.040 nonbonded pdb=" O ALA A 444 " pdb=" OG1 THR A 448 " model vdw 2.358 3.040 ... (remaining 28849 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: 1.410 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.450 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 3514 Z= 0.197 Angle : 0.625 5.254 4793 Z= 0.369 Chirality : 0.041 0.183 544 Planarity : 0.005 0.046 581 Dihedral : 12.988 82.377 1188 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.37), residues: 431 helix: -0.90 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.011 0.001 TYR A 306 PHE 0.032 0.002 PHE A 305 TRP 0.012 0.001 TRP A 240 HIS 0.006 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 3513) covalent geometry : angle 0.62481 ( 4791) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.40530 ( 2) hydrogen bonds : bond 0.16164 ( 239) hydrogen bonds : angle 6.20821 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.124 Fit side-chains REVERT: A 256 LYS cc_start: 0.5750 (mmtt) cc_final: 0.4278 (tttp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0617 time to fit residues: 3.1896 Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101616 restraints weight = 3952.625| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.79 r_work: 0.3004 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3514 Z= 0.161 Angle : 0.566 5.382 4793 Z= 0.300 Chirality : 0.041 0.117 544 Planarity : 0.005 0.048 581 Dihedral : 4.329 19.928 463 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.55 % Allowed : 10.80 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.40), residues: 431 helix: 0.54 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.23 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.011 0.001 TYR A 306 PHE 0.011 0.001 PHE A 305 TRP 0.017 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3513) covalent geometry : angle 0.56543 ( 4791) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.91159 ( 2) hydrogen bonds : bond 0.04776 ( 239) hydrogen bonds : angle 4.56635 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.087 Fit side-chains REVERT: A 256 LYS cc_start: 0.6242 (mmtt) cc_final: 0.4095 (tttp) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.0646 time to fit residues: 2.8307 Evaluate side-chains 32 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.137973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102218 restraints weight = 3919.066| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.82 r_work: 0.2996 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3514 Z= 0.159 Angle : 0.559 5.251 4793 Z= 0.292 Chirality : 0.041 0.116 544 Planarity : 0.005 0.044 581 Dihedral : 4.313 21.547 463 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 12.47 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.40), residues: 431 helix: 1.00 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.10 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 364 TYR 0.012 0.001 TYR A 306 PHE 0.012 0.001 PHE A 51 TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3513) covalent geometry : angle 0.55904 ( 4791) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.83100 ( 2) hydrogen bonds : bond 0.04568 ( 239) hydrogen bonds : angle 4.44397 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.105 Fit side-chains REVERT: A 256 LYS cc_start: 0.6201 (mmtt) cc_final: 0.4017 (tttp) REVERT: A 317 LYS cc_start: 0.8359 (tppt) cc_final: 0.8095 (tppt) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.0767 time to fit residues: 3.4017 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103402 restraints weight = 3813.604| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.77 r_work: 0.2989 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.135 Angle : 0.532 5.241 4793 Z= 0.277 Chirality : 0.040 0.113 544 Planarity : 0.005 0.042 581 Dihedral : 4.232 22.942 463 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 12.47 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.41), residues: 431 helix: 1.36 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.94 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.011 0.001 TYR A 306 PHE 0.012 0.001 PHE A 51 TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3513) covalent geometry : angle 0.53159 ( 4791) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.89448 ( 2) hydrogen bonds : bond 0.04226 ( 239) hydrogen bonds : angle 4.30202 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.075 Fit side-chains REVERT: A 256 LYS cc_start: 0.6200 (mmtt) cc_final: 0.3986 (tttp) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.0513 time to fit residues: 2.6336 Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101639 restraints weight = 3964.496| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.82 r_work: 0.2972 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3514 Z= 0.154 Angle : 0.545 5.257 4793 Z= 0.282 Chirality : 0.041 0.116 544 Planarity : 0.005 0.043 581 Dihedral : 4.232 22.541 463 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 14.13 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.40), residues: 431 helix: 1.44 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.79 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.010 0.001 TYR A 306 PHE 0.013 0.001 PHE A 51 TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3513) covalent geometry : angle 0.54438 ( 4791) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.86378 ( 2) hydrogen bonds : bond 0.04298 ( 239) hydrogen bonds : angle 4.27230 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.126 Fit side-chains REVERT: A 256 LYS cc_start: 0.6302 (mmtt) cc_final: 0.4036 (tttp) REVERT: A 305 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6925 (t80) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.0685 time to fit residues: 3.0894 Evaluate side-chains 39 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104165 restraints weight = 3867.318| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.77 r_work: 0.3019 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3514 Z= 0.121 Angle : 0.518 5.208 4793 Z= 0.268 Chirality : 0.039 0.111 544 Planarity : 0.005 0.043 581 Dihedral : 4.131 22.484 463 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 14.40 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.41), residues: 431 helix: 1.70 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.69 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.011 0.001 TYR A 306 PHE 0.013 0.001 PHE A 51 TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3513) covalent geometry : angle 0.51780 ( 4791) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.70809 ( 2) hydrogen bonds : bond 0.03978 ( 239) hydrogen bonds : angle 4.20147 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.131 Fit side-chains REVERT: A 256 LYS cc_start: 0.6256 (mmtt) cc_final: 0.4032 (tttp) REVERT: A 305 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6985 (t80) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.0656 time to fit residues: 2.9699 Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.139186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103410 restraints weight = 3925.511| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.81 r_work: 0.3006 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.129 Angle : 0.522 5.216 4793 Z= 0.271 Chirality : 0.040 0.116 544 Planarity : 0.005 0.043 581 Dihedral : 4.150 22.878 463 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 14.40 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.41), residues: 431 helix: 1.75 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.60 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.010 0.001 TYR A 306 PHE 0.013 0.001 PHE A 51 TRP 0.013 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3513) covalent geometry : angle 0.52232 ( 4791) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.72990 ( 2) hydrogen bonds : bond 0.04040 ( 239) hydrogen bonds : angle 4.19277 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.116 Fit side-chains REVERT: A 256 LYS cc_start: 0.6269 (mmtt) cc_final: 0.3996 (tttp) REVERT: A 257 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7675 (ttm110) REVERT: A 305 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6987 (t80) outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.0690 time to fit residues: 2.9584 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.139669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104209 restraints weight = 3933.598| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.80 r_work: 0.3019 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.128 Angle : 0.520 5.208 4793 Z= 0.269 Chirality : 0.040 0.116 544 Planarity : 0.005 0.043 581 Dihedral : 4.126 22.803 463 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.68 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.41), residues: 431 helix: 1.80 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.52 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.010 0.001 TYR A 306 PHE 0.013 0.001 PHE A 51 TRP 0.013 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3513) covalent geometry : angle 0.51960 ( 4791) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.68805 ( 2) hydrogen bonds : bond 0.04006 ( 239) hydrogen bonds : angle 4.17322 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.115 Fit side-chains REVERT: A 67 MET cc_start: 0.7976 (ptp) cc_final: 0.7678 (ptp) REVERT: A 256 LYS cc_start: 0.6294 (mmtt) cc_final: 0.4013 (tttp) REVERT: A 257 ARG cc_start: 0.8288 (mtm110) cc_final: 0.7670 (ttm110) REVERT: A 305 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7060 (t80) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.0731 time to fit residues: 3.0656 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.139159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103539 restraints weight = 3904.975| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.79 r_work: 0.3010 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3514 Z= 0.136 Angle : 0.524 5.215 4793 Z= 0.271 Chirality : 0.040 0.122 544 Planarity : 0.005 0.043 581 Dihedral : 4.139 22.824 463 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.96 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.41), residues: 431 helix: 1.80 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.48 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 364 TYR 0.010 0.001 TYR A 306 PHE 0.013 0.001 PHE A 51 TRP 0.013 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3513) covalent geometry : angle 0.52394 ( 4791) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.64914 ( 2) hydrogen bonds : bond 0.04059 ( 239) hydrogen bonds : angle 4.17941 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.094 Fit side-chains REVERT: A 256 LYS cc_start: 0.6260 (mmtt) cc_final: 0.4049 (tttp) REVERT: A 257 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7718 (ttm110) REVERT: A 305 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7063 (t80) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.0815 time to fit residues: 3.4251 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.139269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103611 restraints weight = 3920.025| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.80 r_work: 0.3015 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.131 Angle : 0.520 5.212 4793 Z= 0.269 Chirality : 0.040 0.123 544 Planarity : 0.005 0.043 581 Dihedral : 4.126 22.788 463 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 15.51 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.41), residues: 431 helix: 1.83 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.48 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 364 TYR 0.010 0.001 TYR A 306 PHE 0.013 0.001 PHE A 51 TRP 0.013 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3513) covalent geometry : angle 0.52015 ( 4791) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.63273 ( 2) hydrogen bonds : bond 0.04028 ( 239) hydrogen bonds : angle 4.16611 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.087 Fit side-chains REVERT: A 256 LYS cc_start: 0.6313 (mmtt) cc_final: 0.4053 (tttp) REVERT: A 257 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7709 (ttm110) REVERT: A 305 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7046 (t80) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.0680 time to fit residues: 2.9280 Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5279 > 50: distance: 14 - 26: 8.132 distance: 21 - 26: 8.551 distance: 26 - 27: 19.107 distance: 27 - 28: 7.253 distance: 28 - 30: 3.148 distance: 29 - 52: 5.026 distance: 30 - 36: 5.518 distance: 31 - 32: 5.085 distance: 31 - 34: 4.587 distance: 32 - 33: 5.401 distance: 32 - 37: 8.203 distance: 33 - 57: 6.707 distance: 34 - 35: 10.000 distance: 35 - 36: 5.239 distance: 37 - 38: 7.751 distance: 38 - 39: 15.152 distance: 38 - 41: 8.220 distance: 39 - 40: 11.891 distance: 39 - 44: 27.664 distance: 40 - 66: 4.518 distance: 41 - 43: 7.715 distance: 44 - 45: 47.059 distance: 45 - 46: 43.285 distance: 45 - 48: 53.528 distance: 46 - 47: 21.000 distance: 46 - 52: 12.646 distance: 47 - 72: 9.552 distance: 48 - 49: 37.553 distance: 48 - 50: 26.452 distance: 49 - 51: 12.184 distance: 52 - 53: 7.328 distance: 53 - 54: 7.963 distance: 53 - 56: 4.891 distance: 55 - 80: 9.842 distance: 57 - 58: 8.549 distance: 58 - 59: 11.034 distance: 58 - 61: 14.973 distance: 59 - 60: 5.132 distance: 59 - 66: 7.414 distance: 61 - 62: 8.189 distance: 62 - 63: 9.868 distance: 63 - 64: 15.124 distance: 64 - 65: 12.223 distance: 66 - 67: 11.765 distance: 67 - 68: 9.283 distance: 67 - 70: 14.208 distance: 68 - 69: 6.172 distance: 68 - 72: 11.908 distance: 70 - 71: 11.887 distance: 72 - 73: 16.622 distance: 73 - 74: 16.299 distance: 73 - 76: 27.948 distance: 74 - 75: 10.161 distance: 74 - 80: 8.499 distance: 76 - 77: 15.082 distance: 77 - 78: 8.921 distance: 77 - 79: 10.643 distance: 80 - 81: 30.656 distance: 81 - 82: 29.982 distance: 81 - 84: 16.510 distance: 82 - 83: 12.435 distance: 82 - 87: 18.357 distance: 84 - 85: 11.870 distance: 84 - 86: 8.995 distance: 87 - 88: 9.510 distance: 87 - 93: 10.560 distance: 88 - 89: 9.403 distance: 88 - 91: 4.534 distance: 89 - 90: 11.123 distance: 89 - 94: 9.757 distance: 91 - 92: 12.686 distance: 92 - 93: 5.880