Starting phenix.real_space_refine on Wed Jul 1 22:50:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu8_60893/07_2026/9iu8_60893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu8_60893/07_2026/9iu8_60893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iu8_60893/07_2026/9iu8_60893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu8_60893/07_2026/9iu8_60893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu8_60893/07_2026/9iu8_60893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu8_60893/07_2026/9iu8_60893.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 50 5.49 5 S 10 5.16 5 C 2087 2.51 5 N 665 2.21 5 O 769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3582 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2556 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain breaks: 2 Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1299 SG CYS A 304 39.237 71.171 21.241 1.00229.33 S ATOM 1317 SG CYS A 307 39.849 68.304 19.028 1.00230.02 S ATOM 1468 SG CYS A 326 42.252 69.065 21.275 1.00223.79 S ATOM 1540 SG CYS A 335 41.923 71.881 18.609 1.00234.93 S Time building chain proxies: 1.17, per 1000 atoms: 0.33 Number of scatterers: 3582 At special positions: 0 Unit cell: (74.0773, 101.121, 63.4948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 10 16.00 P 50 15.00 O 769 8.00 N 665 7.00 C 2087 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: 0.39 Conformation dependent library (CDL) restraints added in 100.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " Number of angles added : 6 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 49.5% alpha, 13.5% beta 25 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.631A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.743A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.679A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.782A pdb=" N GLU A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 368 removed outlier: 5.184A pdb=" N GLN A 437 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU A 364 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 435 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 366 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 433 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 368 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU A 431 " --> pdb=" O VAL A 368 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 686 1.34 - 1.46: 1213 1.46 - 1.57: 1750 1.57 - 1.69: 98 1.69 - 1.81: 15 Bond restraints: 3762 Sorted by residual: bond pdb=" N1 DC F 30 " pdb=" C6 DC F 30 " ideal model delta sigma weight residual 1.367 1.331 0.036 6.00e-03 2.78e+04 3.68e+01 bond pdb=" C4 DC F 30 " pdb=" C5 DC F 30 " ideal model delta sigma weight residual 1.425 1.402 0.023 8.00e-03 1.56e+04 8.30e+00 bond pdb=" N1 DC E 21 " pdb=" C6 DC E 21 " ideal model delta sigma weight residual 1.367 1.350 0.017 6.00e-03 2.78e+04 8.14e+00 bond pdb=" P DG E 1 " pdb=" O5' DG E 1 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 8.00e+00 bond pdb=" C LYS A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 1.329 1.362 -0.034 1.20e-02 6.94e+03 7.87e+00 ... (remaining 3757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 4790 2.63 - 5.27: 478 5.27 - 7.90: 33 7.90 - 10.53: 3 10.53 - 13.17: 2 Bond angle restraints: 5306 Sorted by residual: angle pdb=" O3' DG F 32 " pdb=" P DT F 33 " pdb=" O5' DT F 33 " ideal model delta sigma weight residual 104.00 90.83 13.17 1.50e+00 4.44e-01 7.70e+01 angle pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 110.46 120.73 -10.27 1.57e+00 4.06e-01 4.28e+01 angle pdb=" O4' DG F 31 " pdb=" C1' DG F 31 " pdb=" C2' DG F 31 " ideal model delta sigma weight residual 105.90 100.89 5.01 8.00e-01 1.56e+00 3.92e+01 angle pdb=" C ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 109.72 98.91 10.81 1.92e+00 2.71e-01 3.17e+01 angle pdb=" O4' DT F 33 " pdb=" C1' DT F 33 " pdb=" N1 DT F 33 " ideal model delta sigma weight residual 108.00 111.83 -3.83 7.00e-01 2.04e+00 3.00e+01 ... (remaining 5301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1605 16.02 - 32.05: 255 32.05 - 48.07: 130 48.07 - 64.09: 98 64.09 - 80.12: 12 Dihedral angle restraints: 2100 sinusoidal: 1188 harmonic: 912 Sorted by residual: dihedral pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PRO A 197 " pdb=" C PRO A 197 " pdb=" N LEU A 198 " pdb=" CA LEU A 198 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C ARG A 155 " pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta harmonic sigma weight residual -122.60 -113.31 -9.29 0 2.50e+00 1.60e-01 1.38e+01 ... (remaining 2097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 508 0.130 - 0.260: 60 0.260 - 0.391: 2 0.391 - 0.521: 1 0.521 - 0.651: 2 Chirality restraints: 573 Sorted by residual: chirality pdb=" P DC F 28 " pdb=" OP1 DC F 28 " pdb=" OP2 DC F 28 " pdb=" O5' DC F 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DG E 1 " pdb=" OP1 DG E 1 " pdb=" OP2 DG E 1 " pdb=" O5' DG E 1 " both_signs ideal model delta sigma weight residual True 2.34 2.96 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" P DG F 31 " pdb=" OP1 DG F 31 " pdb=" OP2 DG F 31 " pdb=" O5' DG F 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 570 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 237 " 0.349 9.50e-02 1.11e+02 1.57e-01 1.75e+01 pdb=" NE ARG A 237 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 237 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 237 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 237 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 173 " 0.297 9.50e-02 1.11e+02 1.34e-01 1.32e+01 pdb=" NE ARG A 173 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 173 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 173 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 173 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG F 35 " -0.042 2.00e-02 2.50e+03 1.81e-02 9.86e+00 pdb=" N9 DG F 35 " 0.041 2.00e-02 2.50e+03 pdb=" C8 DG F 35 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG F 35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG F 35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG F 35 " -0.009 2.00e-02 2.50e+03 pdb=" O6 DG F 35 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG F 35 " -0.006 2.00e-02 2.50e+03 pdb=" C2 DG F 35 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG F 35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG F 35 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DG F 35 " 0.008 2.00e-02 2.50e+03 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 585 2.81 - 3.33: 3165 3.33 - 3.85: 6633 3.85 - 4.38: 7511 4.38 - 4.90: 11492 Nonbonded interactions: 29386 Sorted by model distance: nonbonded pdb=" OG SER A 157 " pdb=" O2 DC E 22 " model vdw 2.283 3.040 nonbonded pdb=" OG SER A 212 " pdb=" OP1 DG F 35 " model vdw 2.396 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" OE1 GLU A 186 " model vdw 2.459 3.120 nonbonded pdb=" O4' DC E 22 " pdb=" O2 DC E 22 " model vdw 2.499 3.040 nonbonded pdb=" O5' DG F 34 " pdb=" O4' DG F 34 " model vdw 2.526 2.432 ... (remaining 29381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.220 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 3766 Z= 0.628 Angle : 1.650 16.813 5312 Z= 1.109 Chirality : 0.091 0.651 573 Planarity : 0.018 0.157 516 Dihedral : 22.314 80.118 1512 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 4.53 % Favored : 93.21 % Cbeta Deviations : 0.34 % 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 are not related in a simple way. whole: -1.91 (0.40), residues: 313 helix: -1.25 (0.36), residues: 136 sheet: -1.33 (0.75), residues: 37 loop : -1.09 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.005 ARG A 237 TYR 0.020 0.005 TYR A 312 PHE 0.024 0.003 PHE A 217 TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.63 ( 3762) covalent geometry : angle 1.61556 / 1.11 ( 5306) hydrogen bonds : bond 0.17419 / 12.02 ( 185) hydrogen bonds : angle 6.90061 / 5.19 ( 466) metal coordination : bond 0.01390 / 0.73 ( 4) metal coordination : angle 10.04885 / 7.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.107 Fit side-chains REVERT: A 155 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6107 (ttp-110) REVERT: A 272 ARG cc_start: 0.5015 (ttp-110) cc_final: 0.4472 (ttm-80) REVERT: A 294 THR cc_start: 0.7699 (m) cc_final: 0.7468 (p) REVERT: A 324 TYR cc_start: 0.5490 (m-80) cc_final: 0.5237 (m-80) REVERT: A 371 SER cc_start: 0.6115 (t) cc_final: 0.5804 (m) REVERT: A 420 LEU cc_start: 0.5522 (mt) cc_final: 0.5319 (mt) REVERT: A 434 GLU cc_start: 0.7869 (mt-10) cc_final: 0.6820 (mm-30) REVERT: A 474 ILE cc_start: 0.7350 (mp) cc_final: 0.7136 (mp) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1323 time to fit residues: 7.0614 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.0000 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.222304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161305 restraints weight = 3995.260| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.82 r_work: 0.3506 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 3766 Z= 0.300 Angle : 0.789 9.831 5312 Z= 0.438 Chirality : 0.049 0.230 573 Planarity : 0.006 0.054 516 Dihedral : 25.544 88.212 897 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.89 % Allowed : 8.68 % Favored : 89.43 % 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 are not related in a simple way. whole: -0.15 (0.45), residues: 313 helix: 0.86 (0.42), residues: 140 sheet: -1.31 (0.57), residues: 63 loop : -0.40 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 223 TYR 0.026 0.003 TYR A 482 PHE 0.010 0.002 PHE A 348 TRP 0.011 0.002 TRP A 442 HIS 0.007 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.30 ( 3762) covalent geometry : angle 0.77311 / 0.44 ( 5306) hydrogen bonds : bond 0.06189 / 4.03 ( 185) hydrogen bonds : angle 4.29140 / 3.43 ( 466) metal coordination : bond 0.00896 / 0.45 ( 4) metal coordination : angle 4.69867 / 4.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.106 Fit side-chains REVERT: A 155 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7860 (ptt180) REVERT: A 226 GLN cc_start: 0.7599 (mp10) cc_final: 0.7335 (mp10) REVERT: A 272 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.7468 (ttm-80) REVERT: A 371 SER cc_start: 0.7648 (t) cc_final: 0.7161 (m) REVERT: A 434 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7447 (mm-30) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.0838 time to fit residues: 3.1529 Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.225855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.162769 restraints weight = 3908.898| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.82 r_work: 0.3475 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3766 Z= 0.150 Angle : 0.611 7.971 5312 Z= 0.354 Chirality : 0.040 0.202 573 Planarity : 0.004 0.027 516 Dihedral : 25.924 86.109 897 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.51 % Allowed : 10.94 % Favored : 87.55 % 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 are not related in a simple way. whole: 0.87 (0.47), residues: 313 helix: 1.84 (0.43), residues: 140 sheet: -0.86 (0.59), residues: 63 loop : -0.04 (0.59), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.018 0.002 TYR A 482 PHE 0.008 0.001 PHE A 348 TRP 0.011 0.001 TRP A 442 HIS 0.003 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 ( 3762) covalent geometry : angle 0.60347 / 0.35 ( 5306) hydrogen bonds : bond 0.04385 / 2.94 ( 185) hydrogen bonds : angle 3.87590 / 3.15 ( 466) metal coordination : bond 0.00846 / 0.42 ( 4) metal coordination : angle 2.96658 / 2.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.114 Fit side-chains REVERT: A 155 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7934 (ptm-80) REVERT: A 226 GLN cc_start: 0.7676 (mp10) cc_final: 0.7448 (mp10) REVERT: A 272 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7364 (ttm-80) REVERT: A 371 SER cc_start: 0.7525 (t) cc_final: 0.7009 (m) REVERT: A 434 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7594 (mm-30) REVERT: A 463 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7385 (t) outliers start: 4 outliers final: 1 residues processed: 26 average time/residue: 0.0709 time to fit residues: 2.2995 Evaluate side-chains 25 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.223036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.157049 restraints weight = 3873.322| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.09 r_work: 0.3425 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3766 Z= 0.189 Angle : 0.623 8.946 5312 Z= 0.352 Chirality : 0.040 0.236 573 Planarity : 0.004 0.034 516 Dihedral : 26.119 87.117 896 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.02 % Allowed : 9.81 % Favored : 87.17 % 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 are not related in a simple way. whole: 1.12 (0.47), residues: 313 helix: 2.01 (0.43), residues: 140 sheet: -0.82 (0.61), residues: 63 loop : 0.19 (0.60), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 223 TYR 0.016 0.002 TYR A 482 PHE 0.010 0.002 PHE A 464 TRP 0.009 0.001 TRP A 345 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 ( 3762) covalent geometry : angle 0.61498 / 0.35 ( 5306) hydrogen bonds : bond 0.04563 / 2.97 ( 185) hydrogen bonds : angle 3.88265 / 3.15 ( 466) metal coordination : bond 0.00952 / 0.48 ( 4) metal coordination : angle 3.01398 / 2.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.115 Fit side-chains REVERT: A 155 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7492 (ttp80) REVERT: A 226 GLN cc_start: 0.7688 (mp10) cc_final: 0.7485 (mp10) REVERT: A 272 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7362 (ttm-80) REVERT: A 283 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7478 (t) REVERT: A 371 SER cc_start: 0.7554 (t) cc_final: 0.7014 (m) REVERT: A 434 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7610 (mm-30) REVERT: A 463 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7558 (t) outliers start: 8 outliers final: 4 residues processed: 31 average time/residue: 0.0912 time to fit residues: 3.4139 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.224869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159905 restraints weight = 3936.008| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.08 r_work: 0.3546 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3766 Z= 0.148 Angle : 0.574 9.675 5312 Z= 0.329 Chirality : 0.038 0.207 573 Planarity : 0.004 0.025 516 Dihedral : 25.978 85.867 896 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.40 % Allowed : 9.43 % Favored : 87.17 % 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 are not related in a simple way. whole: 1.62 (0.47), residues: 313 helix: 2.37 (0.43), residues: 140 sheet: -0.87 (0.67), residues: 49 loop : 0.54 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.014 0.002 TYR A 482 PHE 0.008 0.001 PHE A 314 TRP 0.011 0.001 TRP A 345 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 ( 3762) covalent geometry : angle 0.56970 / 0.33 ( 5306) hydrogen bonds : bond 0.03859 / 2.51 ( 185) hydrogen bonds : angle 3.76354 / 3.04 ( 466) metal coordination : bond 0.00601 / 0.30 ( 4) metal coordination : angle 2.26482 / 1.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.106 Fit side-chains REVERT: A 155 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7594 (ptt90) REVERT: A 272 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7210 (ttm-80) REVERT: A 283 VAL cc_start: 0.7672 (OUTLIER) cc_final: 0.7421 (t) REVERT: A 371 SER cc_start: 0.7488 (t) cc_final: 0.7013 (m) REVERT: A 434 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7647 (mm-30) outliers start: 9 outliers final: 3 residues processed: 34 average time/residue: 0.0861 time to fit residues: 3.5840 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.220755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.186017 restraints weight = 3952.446| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.00 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 3766 Z= 0.279 Angle : 0.694 10.813 5312 Z= 0.380 Chirality : 0.043 0.237 573 Planarity : 0.005 0.045 516 Dihedral : 26.252 89.234 895 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.02 % Allowed : 9.81 % Favored : 87.17 % 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 are not related in a simple way. whole: 1.40 (0.48), residues: 313 helix: 2.19 (0.42), residues: 140 sheet: -1.02 (0.68), residues: 51 loop : 0.47 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.014 0.003 TYR A 154 PHE 0.014 0.002 PHE A 464 TRP 0.009 0.002 TRP A 345 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 ( 3762) covalent geometry : angle 0.68780 / 0.38 ( 5306) hydrogen bonds : bond 0.04936 / 3.13 ( 185) hydrogen bonds : angle 3.88868 / 3.13 ( 466) metal coordination : bond 0.01044 / 0.53 ( 4) metal coordination : angle 2.90764 / 2.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.110 Fit side-chains REVERT: A 155 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7499 (ptt90) REVERT: A 226 GLN cc_start: 0.7548 (mp10) cc_final: 0.7229 (mp10) REVERT: A 272 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7497 (ttm-80) REVERT: A 283 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7630 (t) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.0681 time to fit residues: 2.7982 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.222786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156524 restraints weight = 4022.732| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.94 r_work: 0.3533 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3766 Z= 0.171 Angle : 0.625 11.616 5312 Z= 0.350 Chirality : 0.040 0.222 573 Planarity : 0.004 0.028 516 Dihedral : 26.151 87.422 895 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.40 % Allowed : 9.81 % Favored : 86.79 % 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 are not related in a simple way. whole: 1.74 (0.47), residues: 313 helix: 2.47 (0.43), residues: 140 sheet: -0.72 (0.80), residues: 37 loop : 0.41 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.017 0.002 TYR A 154 PHE 0.009 0.001 PHE A 464 TRP 0.012 0.001 TRP A 345 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 3762) covalent geometry : angle 0.61928 / 0.35 ( 5306) hydrogen bonds : bond 0.04055 / 2.62 ( 185) hydrogen bonds : angle 3.79687 / 3.06 ( 466) metal coordination : bond 0.00755 / 0.38 ( 4) metal coordination : angle 2.51582 / 2.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.106 Fit side-chains REVERT: A 155 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7548 (ptm-80) REVERT: A 226 GLN cc_start: 0.7612 (mp10) cc_final: 0.7235 (mp10) REVERT: A 272 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7248 (ttm-80) REVERT: A 283 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7502 (t) outliers start: 9 outliers final: 5 residues processed: 33 average time/residue: 0.0816 time to fit residues: 3.3204 Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.223145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176428 restraints weight = 3995.095| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.74 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3766 Z= 0.184 Angle : 0.623 12.523 5312 Z= 0.346 Chirality : 0.040 0.224 573 Planarity : 0.005 0.037 516 Dihedral : 26.225 87.530 895 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.02 % Allowed : 10.94 % Favored : 86.04 % 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 are not related in a simple way. whole: 1.85 (0.48), residues: 313 helix: 2.40 (0.43), residues: 143 sheet: -0.69 (0.80), residues: 37 loop : 0.63 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.015 0.002 TYR A 154 PHE 0.009 0.002 PHE A 464 TRP 0.011 0.001 TRP A 345 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 3762) covalent geometry : angle 0.61804 / 0.35 ( 5306) hydrogen bonds : bond 0.04089 / 2.63 ( 185) hydrogen bonds : angle 3.77930 / 3.05 ( 466) metal coordination : bond 0.00799 / 0.40 ( 4) metal coordination : angle 2.35492 / 1.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.109 Fit side-chains REVERT: A 155 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7720 (ptm-80) REVERT: A 226 GLN cc_start: 0.7774 (mp10) cc_final: 0.7497 (mp10) REVERT: A 272 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7304 (ttm-80) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.0871 time to fit residues: 3.5007 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.224139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162144 restraints weight = 3961.463| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.90 r_work: 0.3524 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3766 Z= 0.164 Angle : 0.608 13.170 5312 Z= 0.338 Chirality : 0.039 0.218 573 Planarity : 0.004 0.030 516 Dihedral : 26.100 87.386 895 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.64 % Allowed : 10.94 % Favored : 86.42 % 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 are not related in a simple way. whole: 2.01 (0.48), residues: 313 helix: 2.56 (0.43), residues: 143 sheet: -0.60 (0.80), residues: 37 loop : 0.66 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.015 0.002 TYR A 154 PHE 0.008 0.001 PHE A 314 TRP 0.011 0.001 TRP A 345 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 3762) covalent geometry : angle 0.60344 / 0.34 ( 5306) hydrogen bonds : bond 0.03842 / 2.48 ( 185) hydrogen bonds : angle 3.74799 / 3.02 ( 466) metal coordination : bond 0.00670 / 0.34 ( 4) metal coordination : angle 2.27523 / 1.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.104 Fit side-chains REVERT: A 155 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7491 (ptt90) REVERT: A 226 GLN cc_start: 0.7716 (mp10) cc_final: 0.7372 (mp10) REVERT: A 272 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7353 (ttm-80) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.0827 time to fit residues: 3.1511 Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8818 > 50: distance: 10 - 18: 3.483 distance: 59 - 76: 4.197 distance: 72 - 76: 5.456 distance: 76 - 77: 3.448 distance: 77 - 78: 6.074 distance: 78 - 79: 8.212 distance: 78 - 80: 5.887 distance: 80 - 81: 15.247 distance: 81 - 82: 45.753 distance: 81 - 84: 8.721 distance: 82 - 83: 54.831 distance: 82 - 91: 58.882 distance: 84 - 85: 9.561 distance: 85 - 86: 22.926 distance: 86 - 87: 13.090 distance: 87 - 88: 3.522 distance: 88 - 89: 10.090 distance: 88 - 90: 7.234 distance: 91 - 92: 44.774 distance: 92 - 93: 34.629 distance: 92 - 95: 34.949 distance: 93 - 94: 21.995 distance: 93 - 100: 12.168 distance: 95 - 96: 18.445 distance: 96 - 97: 3.791 distance: 97 - 98: 15.397 distance: 97 - 99: 8.563 distance: 100 - 101: 8.192 distance: 100 - 106: 5.227 distance: 101 - 102: 3.500 distance: 101 - 104: 7.762 distance: 102 - 103: 8.016 distance: 102 - 107: 10.560 distance: 104 - 105: 16.561 distance: 105 - 106: 9.520 distance: 107 - 108: 6.650 distance: 108 - 109: 5.804 distance: 108 - 111: 13.045 distance: 109 - 110: 11.527 distance: 109 - 116: 12.901 distance: 111 - 112: 27.510 distance: 112 - 113: 13.713 distance: 113 - 114: 11.203 distance: 113 - 115: 11.552 distance: 116 - 117: 10.078 distance: 117 - 118: 5.751 distance: 118 - 119: 17.762 distance: 118 - 120: 9.406 distance: 120 - 121: 13.717 distance: 121 - 122: 6.355 distance: 121 - 124: 10.941 distance: 122 - 123: 15.439 distance: 122 - 131: 6.175 distance: 124 - 125: 26.066 distance: 125 - 126: 11.576 distance: 126 - 127: 4.538 distance: 127 - 128: 6.249 distance: 128 - 129: 9.198 distance: 128 - 130: 9.394 distance: 132 - 133: 3.597 distance: 132 - 135: 5.259 distance: 133 - 134: 5.676 distance: 133 - 140: 5.293 distance: 135 - 136: 7.759 distance: 136 - 137: 15.879 distance: 137 - 138: 10.751 distance: 137 - 139: 6.312 distance: 140 - 141: 8.484 distance: 141 - 144: 4.508 distance: 142 - 143: 14.823 distance: 142 - 154: 6.608 distance: 144 - 145: 7.350 distance: 145 - 146: 5.423 distance: 145 - 147: 6.173 distance: 146 - 148: 12.623 distance: 147 - 149: 5.338 distance: 147 - 150: 5.440 distance: 148 - 149: 14.193 distance: 149 - 151: 7.752 distance: 150 - 152: 17.148 distance: 151 - 153: 7.487 distance: 152 - 153: 17.203 distance: 154 - 155: 5.079 distance: 155 - 156: 8.262 distance: 155 - 158: 4.724 distance: 156 - 157: 19.230 distance: 156 - 160: 8.842 distance: 157 - 173: 16.136 distance: 158 - 159: 5.874