Starting phenix.real_space_refine on Thu Mar 6 06:47:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhg_60102/03_2025/8zhg_60102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhg_60102/03_2025/8zhg_60102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zhg_60102/03_2025/8zhg_60102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhg_60102/03_2025/8zhg_60102.map" model { file = "/net/cci-nas-00/data/ceres_data/8zhg_60102/03_2025/8zhg_60102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhg_60102/03_2025/8zhg_60102.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2345 atoms to isotropic. 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 15 5.16 5 C 2100 2.51 5 N 556 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 926 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 820 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.67, per 1000 atoms: 0.80 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.1776, 88.972, 79.3904, 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 15 16.00 O 655 8.00 N 556 7.00 C 2100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN C 343 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 356.4 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 8.7% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.895A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.611A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.567A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.926A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.625A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.509A pdb=" N ASP L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 82 through 86' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 433 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE C 377 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.874A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.874A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 46 through 49 removed outlier: 3.965A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR L 90 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49 removed outlier: 3.965A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR L 90 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR L 89 " --> pdb=" O THR L 105 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 216 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: 0.82 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1070 1.35 - 1.47: 932 1.47 - 1.59: 1391 1.59 - 1.71: 0 1.71 - 1.84: 18 Bond restraints: 3411 Sorted by residual: bond pdb=" N TYR C 473 " pdb=" CA TYR C 473 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.27e-02 6.20e+03 5.42e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" C TYR C 473 " pdb=" O TYR C 473 " ideal model delta sigma weight residual 1.234 1.251 -0.017 1.27e-02 6.20e+03 1.88e+00 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 4447 1.40 - 2.80: 153 2.80 - 4.20: 26 4.20 - 5.61: 8 5.61 - 7.01: 5 Bond angle restraints: 4639 Sorted by residual: angle pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " pdb=" CD GLU L 86 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" CA LYS H 43 " pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.62e+00 angle pdb=" C CYS C 480 " pdb=" N ASN C 481 " pdb=" CA ASN C 481 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.68e+00 angle pdb=" CA GLU L 86 " pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.92e+00 angle pdb=" CA LYS L 16 " pdb=" CB LYS L 16 " pdb=" CG LYS L 16 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 ... (remaining 4634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1709 17.23 - 34.45: 227 34.45 - 51.68: 67 51.68 - 68.91: 13 68.91 - 86.14: 7 Dihedral angle restraints: 2023 sinusoidal: 803 harmonic: 1220 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.96 32.04 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" CA ASP L 68 " pdb=" CB ASP L 68 " pdb=" CG ASP L 68 " pdb=" OD1 ASP L 68 " ideal model delta sinusoidal sigma weight residual -30.00 -89.46 59.46 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 66.49 26.51 1 1.00e+01 1.00e-02 1.01e+01 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 303 0.033 - 0.067: 136 0.067 - 0.100: 36 0.100 - 0.133: 20 0.133 - 0.166: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CG LEU H 86 " pdb=" CB LEU H 86 " pdb=" CD1 LEU H 86 " pdb=" CD2 LEU H 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU C 452 " pdb=" CB LEU C 452 " pdb=" CD1 LEU C 452 " pdb=" CD2 LEU C 452 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 494 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 13 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO L 14 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO C 463 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO C 521 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.019 5.00e-02 4.00e+02 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 888 2.80 - 3.32: 2682 3.32 - 3.85: 5331 3.85 - 4.37: 5856 4.37 - 4.90: 10330 Nonbonded interactions: 25087 Sorted by model distance: nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR C 415 " pdb=" OD1 ASP C 420 " model vdw 2.323 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.339 3.040 nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.347 3.040 nonbonded pdb=" OE1 GLU H 57 " pdb=" OH TYR H 59 " model vdw 2.353 3.040 ... (remaining 25082 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 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 : 0.003 0.051 3411 Z= 0.221 Angle : 0.657 7.007 4639 Z= 0.335 Chirality : 0.044 0.166 497 Planarity : 0.007 0.090 602 Dihedral : 17.545 86.137 1235 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.11 % Allowed : 32.69 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.40), residues: 419 helix: -4.79 (0.32), residues: 19 sheet: 1.06 (0.51), residues: 119 loop : -1.75 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 110 HIS 0.002 0.001 HIS L 8 PHE 0.009 0.001 PHE C 456 TYR 0.019 0.001 TYR C 453 ARG 0.009 0.001 ARG L 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.336 Fit side-chains REVERT: C 465 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6116 (mt-10) REVERT: H 115 LEU cc_start: 0.8755 (tp) cc_final: 0.8505 (tt) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.2137 time to fit residues: 12.5687 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain H residue 77 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.172436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138901 restraints weight = 4003.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141933 restraints weight = 2733.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144104 restraints weight = 2165.600| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.223 Angle : 0.538 4.744 4639 Z= 0.287 Chirality : 0.043 0.143 497 Planarity : 0.006 0.070 602 Dihedral : 4.481 41.055 514 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.99 % Allowed : 26.87 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.39), residues: 419 helix: -4.54 (0.50), residues: 18 sheet: 0.54 (0.47), residues: 131 loop : -1.60 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.013 0.001 PHE C 429 TYR 0.016 0.001 TYR C 495 ARG 0.007 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.403 Fit side-chains REVERT: C 346 ARG cc_start: 0.7337 (mtp85) cc_final: 0.6932 (mtp85) REVERT: L 10 VAL cc_start: 0.4448 (OUTLIER) cc_final: 0.4247 (p) outliers start: 18 outliers final: 11 residues processed: 58 average time/residue: 0.1592 time to fit residues: 11.4281 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127185 restraints weight = 4043.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128091 restraints weight = 3183.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129391 restraints weight = 2835.788| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3411 Z= 0.344 Angle : 0.626 5.635 4639 Z= 0.331 Chirality : 0.045 0.136 497 Planarity : 0.006 0.072 602 Dihedral : 4.294 14.081 510 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.93 % Allowed : 28.25 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.39), residues: 419 helix: -4.66 (0.45), residues: 18 sheet: 0.51 (0.47), residues: 134 loop : -1.73 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS L 8 PHE 0.024 0.002 PHE C 429 TYR 0.032 0.002 TYR C 495 ARG 0.003 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.331 Fit side-chains REVERT: C 334 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7557 (p0) REVERT: C 346 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7134 (mtp85) REVERT: C 430 THR cc_start: 0.8713 (p) cc_final: 0.8478 (p) REVERT: C 516 GLU cc_start: 0.7886 (pm20) cc_final: 0.7206 (pt0) REVERT: H 100 GLN cc_start: 0.8234 (tt0) cc_final: 0.8001 (tt0) REVERT: L 53 ASN cc_start: 0.6493 (m-40) cc_final: 0.6223 (p0) REVERT: L 97 SER cc_start: 0.7685 (m) cc_final: 0.7318 (p) outliers start: 25 outliers final: 19 residues processed: 67 average time/residue: 0.1862 time to fit residues: 14.9255 Evaluate side-chains 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.159968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129278 restraints weight = 4113.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127353 restraints weight = 3051.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128342 restraints weight = 2865.296| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3411 Z= 0.253 Angle : 0.573 5.479 4639 Z= 0.302 Chirality : 0.044 0.137 497 Planarity : 0.005 0.066 602 Dihedral : 4.127 13.950 510 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.54 % Allowed : 29.09 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.39), residues: 419 helix: -4.60 (0.50), residues: 18 sheet: 0.47 (0.47), residues: 135 loop : -1.68 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.016 0.001 PHE C 429 TYR 0.025 0.002 TYR C 495 ARG 0.005 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.540 Fit side-chains REVERT: C 346 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7089 (mtp85) REVERT: C 430 THR cc_start: 0.8680 (p) cc_final: 0.8459 (p) REVERT: C 495 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.5818 (t80) REVERT: C 516 GLU cc_start: 0.7832 (pm20) cc_final: 0.7281 (pt0) REVERT: L 53 ASN cc_start: 0.6203 (m-40) cc_final: 0.5825 (p0) REVERT: L 97 SER cc_start: 0.7865 (m) cc_final: 0.7488 (p) outliers start: 20 outliers final: 16 residues processed: 59 average time/residue: 0.2460 time to fit residues: 17.8188 Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 2 optimal weight: 0.0570 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.161479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129003 restraints weight = 3985.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130317 restraints weight = 3965.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131559 restraints weight = 2807.280| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.205 Angle : 0.546 5.434 4639 Z= 0.288 Chirality : 0.043 0.135 497 Planarity : 0.005 0.061 602 Dihedral : 4.039 19.577 510 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.26 % Allowed : 29.64 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.39), residues: 419 helix: -4.51 (0.55), residues: 18 sheet: 0.81 (0.48), residues: 129 loop : -1.61 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.015 0.001 PHE C 429 TYR 0.021 0.001 TYR C 495 ARG 0.004 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.286 Fit side-chains REVERT: C 346 ARG cc_start: 0.7397 (mtp85) cc_final: 0.6980 (mtp85) REVERT: C 495 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6164 (t80) REVERT: C 516 GLU cc_start: 0.7823 (pm20) cc_final: 0.7362 (pt0) outliers start: 19 outliers final: 16 residues processed: 56 average time/residue: 0.3320 time to fit residues: 23.9017 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 chunk 29 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.160465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128391 restraints weight = 4116.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130087 restraints weight = 3275.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131233 restraints weight = 2682.901| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3411 Z= 0.200 Angle : 0.548 6.827 4639 Z= 0.286 Chirality : 0.043 0.137 497 Planarity : 0.005 0.059 602 Dihedral : 4.045 19.415 510 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.09 % Allowed : 27.15 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.40), residues: 419 helix: -4.48 (0.55), residues: 18 sheet: 0.84 (0.47), residues: 131 loop : -1.50 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.014 0.001 PHE C 429 TYR 0.021 0.001 TYR C 495 ARG 0.003 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.388 Fit side-chains REVERT: C 346 ARG cc_start: 0.7403 (mtp85) cc_final: 0.6992 (mtp85) REVERT: C 442 ASP cc_start: 0.8018 (m-30) cc_final: 0.7631 (m-30) REVERT: C 495 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6057 (t80) REVERT: C 516 GLU cc_start: 0.7919 (pm20) cc_final: 0.7529 (pt0) outliers start: 22 outliers final: 18 residues processed: 59 average time/residue: 0.2426 time to fit residues: 16.8767 Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.158542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124166 restraints weight = 4022.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126819 restraints weight = 2830.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128510 restraints weight = 2286.623| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3411 Z= 0.251 Angle : 0.581 6.350 4639 Z= 0.307 Chirality : 0.044 0.139 497 Planarity : 0.005 0.059 602 Dihedral : 4.269 18.963 510 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.93 % Allowed : 26.59 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.40), residues: 419 helix: -4.43 (0.52), residues: 19 sheet: 0.56 (0.45), residues: 137 loop : -1.40 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS L 8 PHE 0.014 0.002 PHE C 429 TYR 0.027 0.002 TYR C 495 ARG 0.008 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.366 Fit side-chains REVERT: C 346 ARG cc_start: 0.7439 (mtp85) cc_final: 0.7110 (mtp85) REVERT: C 442 ASP cc_start: 0.8099 (m-30) cc_final: 0.7734 (m-30) REVERT: C 454 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: C 495 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.5927 (t80) REVERT: C 516 GLU cc_start: 0.7990 (pm20) cc_final: 0.7711 (pt0) outliers start: 25 outliers final: 18 residues processed: 64 average time/residue: 0.2283 time to fit residues: 17.4007 Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.158864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126836 restraints weight = 4057.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128085 restraints weight = 3702.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129250 restraints weight = 2743.032| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.208 Angle : 0.563 5.941 4639 Z= 0.296 Chirality : 0.043 0.165 497 Planarity : 0.005 0.057 602 Dihedral : 4.177 18.595 510 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.54 % Allowed : 27.70 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.40), residues: 419 helix: -4.28 (0.58), residues: 18 sheet: 0.61 (0.46), residues: 137 loop : -1.42 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 PHE 0.013 0.001 PHE C 429 TYR 0.022 0.001 TYR C 495 ARG 0.007 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.477 Fit side-chains REVERT: C 346 ARG cc_start: 0.7428 (mtp85) cc_final: 0.7100 (mtp85) REVERT: C 442 ASP cc_start: 0.8040 (m-30) cc_final: 0.7664 (m-30) REVERT: C 495 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.6213 (t80) outliers start: 20 outliers final: 17 residues processed: 54 average time/residue: 0.1985 time to fit residues: 12.9740 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.703 > 50: distance: 72 - 78: 7.168 distance: 78 - 79: 13.582 distance: 79 - 80: 12.356 distance: 79 - 82: 12.834 distance: 80 - 81: 12.358 distance: 80 - 87: 6.531 distance: 82 - 83: 6.725 distance: 83 - 84: 14.675 distance: 84 - 85: 13.118 distance: 85 - 86: 15.955 distance: 87 - 88: 10.290 distance: 87 - 93: 47.817 distance: 88 - 89: 15.477 distance: 88 - 91: 14.159 distance: 89 - 90: 53.075 distance: 89 - 94: 7.090 distance: 91 - 92: 31.618 distance: 92 - 93: 22.330 distance: 94 - 95: 12.301 distance: 95 - 96: 15.325 distance: 95 - 98: 11.135 distance: 96 - 97: 26.643 distance: 96 - 105: 22.039 distance: 98 - 99: 14.261 distance: 99 - 100: 13.655 distance: 99 - 101: 14.109 distance: 100 - 102: 41.788 distance: 101 - 103: 34.212 distance: 102 - 104: 4.716 distance: 103 - 104: 47.953 distance: 105 - 106: 15.121 distance: 106 - 107: 17.190 distance: 106 - 109: 30.502 distance: 107 - 108: 36.166 distance: 107 - 114: 19.427 distance: 109 - 110: 31.452 distance: 110 - 111: 10.809 distance: 111 - 112: 9.426 distance: 111 - 113: 6.761 distance: 114 - 115: 14.353 distance: 115 - 116: 6.860 distance: 115 - 118: 29.473 distance: 116 - 117: 26.061 distance: 116 - 125: 19.434 distance: 118 - 119: 37.337 distance: 119 - 120: 7.468 distance: 120 - 121: 13.971 distance: 121 - 122: 6.241 distance: 122 - 123: 10.599 distance: 126 - 127: 9.229 distance: 126 - 129: 38.017 distance: 127 - 128: 8.825 distance: 127 - 133: 24.285 distance: 129 - 130: 25.025 distance: 130 - 131: 17.568 distance: 130 - 132: 22.744 distance: 133 - 134: 26.982 distance: 134 - 135: 3.410 distance: 134 - 137: 28.379 distance: 135 - 136: 9.428 distance: 135 - 141: 21.846 distance: 137 - 138: 18.668 distance: 137 - 139: 22.406 distance: 138 - 140: 9.465 distance: 141 - 142: 15.278 distance: 142 - 143: 24.685 distance: 142 - 145: 22.155 distance: 143 - 144: 47.571 distance: 143 - 147: 12.866 distance: 145 - 146: 27.174 distance: 147 - 148: 25.810 distance: 148 - 149: 3.034 distance: 148 - 151: 17.897 distance: 149 - 150: 23.893 distance: 149 - 154: 18.729 distance: 151 - 152: 17.935 distance: 151 - 153: 19.930 distance: 154 - 155: 21.011 distance: 155 - 156: 34.791 distance: 155 - 158: 15.488 distance: 156 - 157: 6.100 distance: 156 - 163: 15.731 distance: 158 - 159: 18.790 distance: 159 - 160: 12.017 distance: 160 - 161: 22.894 distance: 160 - 162: 26.156