Starting phenix.real_space_refine on Fri May 9 22:37:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uuy_26806/05_2025/7uuy_26806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uuy_26806/05_2025/7uuy_26806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uuy_26806/05_2025/7uuy_26806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uuy_26806/05_2025/7uuy_26806.map" model { file = "/net/cci-nas-00/data/ceres_data/7uuy_26806/05_2025/7uuy_26806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uuy_26806/05_2025/7uuy_26806.cif" } resolution = 3.3 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= 0.003 sd= 0.062 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 2512 2.51 5 N 601 2.21 5 O 668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3809 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3767 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 24, 'TRANS': 478} Chain breaks: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 3.08, per 1000 atoms: 0.81 Number of scatterers: 3809 At special positions: 0 Unit cell: (66.216, 85.44, 85.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 668 8.00 N 601 7.00 C 2512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 487.0 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 4.277A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 69 through 84 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 101 removed outlier: 4.034A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.624A pdb=" N LEU A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.710A pdb=" N GLU A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 161 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 164 through 180 Processing helix chain 'A' and resid 190 through 213 removed outlier: 4.173A pdb=" N VAL A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.559A pdb=" N LEU A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 removed outlier: 4.036A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 307 Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.855A pdb=" N LEU A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 370 removed outlier: 3.643A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.145A pdb=" N ARG A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 409 removed outlier: 4.294A pdb=" N LYS A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.624A pdb=" N GLY A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 4.118A pdb=" N LEU A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.568A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.509A pdb=" N GLY A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.327A pdb=" N GLY A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.645A pdb=" N LEU A 553 " --> pdb=" O ARG A 550 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 615 1.33 - 1.45: 1036 1.45 - 1.57: 2202 1.57 - 1.69: 2 1.69 - 1.82: 42 Bond restraints: 3897 Sorted by residual: bond pdb=" O14 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.527 1.654 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" O11 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.703 1.645 0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.526 1.491 0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" O13 3PH A 701 " pdb=" P 3PH A 701 " ideal model delta sigma weight residual 1.522 1.491 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 3PH A 701 " pdb=" O11 3PH A 701 " ideal model delta sigma weight residual 1.385 1.409 -0.024 2.00e-02 2.50e+03 1.47e+00 ... (remaining 3892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 5237 1.85 - 3.69: 59 3.69 - 5.54: 14 5.54 - 7.39: 1 7.39 - 9.23: 2 Bond angle restraints: 5313 Sorted by residual: angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 112.29 108.82 3.47 9.40e-01 1.13e+00 1.36e+01 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O14 3PH A 701 " ideal model delta sigma weight residual 113.84 104.61 9.23 3.00e+00 1.11e-01 9.48e+00 angle pdb=" O12 3PH A 701 " pdb=" P 3PH A 701 " pdb=" O13 3PH A 701 " ideal model delta sigma weight residual 115.12 123.51 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 118.57 -5.87 3.00e+00 1.11e-01 3.82e+00 angle pdb=" N GLY A 93 " pdb=" CA GLY A 93 " pdb=" C GLY A 93 " ideal model delta sigma weight residual 112.49 110.13 2.36 1.21e+00 6.83e-01 3.81e+00 ... (remaining 5308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2041 15.79 - 31.58: 162 31.58 - 47.37: 39 47.37 - 63.16: 10 63.16 - 78.96: 6 Dihedral angle restraints: 2258 sinusoidal: 838 harmonic: 1420 Sorted by residual: dihedral pdb=" CA LEU A 558 " pdb=" CB LEU A 558 " pdb=" CG LEU A 558 " pdb=" CD1 LEU A 558 " ideal model delta sinusoidal sigma weight residual 180.00 123.13 56.87 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN A 136 " pdb=" CA GLN A 136 " pdb=" CB GLN A 136 " pdb=" CG GLN A 136 " ideal model delta sinusoidal sigma weight residual -180.00 -123.34 -56.66 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N ASN A 97 " pdb=" CA ASN A 97 " pdb=" CB ASN A 97 " pdb=" CG ASN A 97 " ideal model delta sinusoidal sigma weight residual 60.00 116.64 -56.64 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 489 0.039 - 0.078: 122 0.078 - 0.117: 24 0.117 - 0.156: 0 0.156 - 0.195: 1 Chirality restraints: 636 Sorted by residual: chirality pdb=" C2 3PH A 701 " pdb=" C1 3PH A 701 " pdb=" C3 3PH A 701 " pdb=" O21 3PH A 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CA PRO A 312 " pdb=" N PRO A 312 " pdb=" C PRO A 312 " pdb=" CB PRO A 312 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" C PRO A 337 " pdb=" CB PRO A 337 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.20e-01 ... (remaining 633 not shown) Planarity restraints: 644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 195 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C VAL A 195 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 195 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 311 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 312 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 247 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C PHE A 247 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 247 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 248 " 0.009 2.00e-02 2.50e+03 ... (remaining 641 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 42 2.63 - 3.20: 3759 3.20 - 3.77: 5984 3.77 - 4.33: 8119 4.33 - 4.90: 13789 Nonbonded interactions: 31693 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLN A 265 " model vdw 2.067 3.120 nonbonded pdb=" O HIS A 273 " pdb=" OG1 THR A 274 " model vdw 2.097 3.040 nonbonded pdb=" ND2 ASN A 441 " pdb=" O GLY A 546 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP A 311 " pdb=" OH TYR A 324 " model vdw 2.228 3.040 nonbonded pdb=" O HIS A 226 " pdb=" OG SER A 227 " model vdw 2.332 3.040 ... (remaining 31688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.600 Find NCS groups from input model: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.004 0.127 3898 Z= 0.188 Angle : 0.580 9.235 5315 Z= 0.291 Chirality : 0.035 0.195 636 Planarity : 0.004 0.045 644 Dihedral : 13.503 78.955 1357 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.25 % Allowed : 10.83 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.41), residues: 495 helix: 1.24 (0.30), residues: 359 sheet: None (None), residues: 0 loop : -1.54 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 15 HIS 0.001 0.000 HIS A 273 PHE 0.010 0.001 PHE A 304 TYR 0.023 0.001 TYR A 17 ARG 0.006 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.14916 ( 265) hydrogen bonds : angle 6.88579 ( 792) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.20382 ( 2) covalent geometry : bond 0.00400 ( 3897) covalent geometry : angle 0.58049 ( 5313) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.6749 (mtm) cc_final: 0.6330 (mtp) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1345 time to fit residues: 10.1499 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108829 restraints weight = 5211.033| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.67 r_work: 0.3149 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3898 Z= 0.162 Angle : 0.592 8.792 5315 Z= 0.297 Chirality : 0.040 0.160 636 Planarity : 0.005 0.047 644 Dihedral : 8.066 88.125 579 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.02 % Allowed : 9.82 % Favored : 88.16 % 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: 1.34 (0.41), residues: 495 helix: 1.65 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.30 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 559 HIS 0.001 0.001 HIS A 226 PHE 0.014 0.002 PHE A 12 TYR 0.016 0.002 TYR A 17 ARG 0.004 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 265) hydrogen bonds : angle 4.55601 ( 792) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.70031 ( 2) covalent geometry : bond 0.00379 ( 3897) covalent geometry : angle 0.59152 ( 5313) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.399 Fit side-chains REVERT: A 516 ASP cc_start: 0.8294 (t0) cc_final: 0.8021 (t0) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1257 time to fit residues: 10.4748 Evaluate side-chains 56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 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 = 0.3563 r_free = 0.3563 target = 0.132502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109922 restraints weight = 5235.717| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.62 r_work: 0.3161 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3898 Z= 0.135 Angle : 0.551 6.819 5315 Z= 0.275 Chirality : 0.039 0.171 636 Planarity : 0.004 0.046 644 Dihedral : 7.834 89.979 579 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.02 % Allowed : 13.10 % Favored : 84.89 % 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: 1.67 (0.41), residues: 495 helix: 1.90 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.20 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.002 0.001 HIS A 226 PHE 0.026 0.002 PHE A 12 TYR 0.013 0.001 TYR A 17 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 265) hydrogen bonds : angle 4.33758 ( 792) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.51161 ( 2) covalent geometry : bond 0.00318 ( 3897) covalent geometry : angle 0.55054 ( 5313) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.425 Fit side-chains REVERT: A 68 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7366 (tpp) REVERT: A 97 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.7690 (t0) REVERT: A 198 MET cc_start: 0.7054 (mtm) cc_final: 0.6618 (mtm) REVERT: A 516 ASP cc_start: 0.8297 (t0) cc_final: 0.7952 (t0) outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.1327 time to fit residues: 10.5304 Evaluate side-chains 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 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 = 0.3560 r_free = 0.3560 target = 0.132284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109580 restraints weight = 5230.473| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.63 r_work: 0.3153 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3898 Z= 0.152 Angle : 0.561 7.905 5315 Z= 0.277 Chirality : 0.040 0.199 636 Planarity : 0.004 0.046 644 Dihedral : 7.667 87.087 579 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.52 % Allowed : 14.86 % Favored : 82.62 % 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: 1.72 (0.41), residues: 495 helix: 1.93 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.15 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.041 0.002 PHE A 12 TYR 0.014 0.002 TYR A 269 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 265) hydrogen bonds : angle 4.28167 ( 792) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.49533 ( 2) covalent geometry : bond 0.00374 ( 3897) covalent geometry : angle 0.56140 ( 5313) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.412 Fit side-chains REVERT: A 11 THR cc_start: 0.8345 (m) cc_final: 0.8011 (p) REVERT: A 67 PHE cc_start: 0.8236 (t80) cc_final: 0.8024 (t80) REVERT: A 516 ASP cc_start: 0.8295 (t0) cc_final: 0.7922 (t0) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1343 time to fit residues: 10.3679 Evaluate side-chains 56 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 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 = 0.3584 r_free = 0.3584 target = 0.134264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111412 restraints weight = 5367.083| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.66 r_work: 0.3173 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3898 Z= 0.120 Angle : 0.535 6.809 5315 Z= 0.265 Chirality : 0.038 0.174 636 Planarity : 0.004 0.043 644 Dihedral : 7.487 84.927 579 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.02 % Allowed : 16.37 % Favored : 81.61 % 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: 1.86 (0.41), residues: 495 helix: 2.07 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.26 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.000 0.000 HIS A 273 PHE 0.022 0.002 PHE A 12 TYR 0.011 0.001 TYR A 348 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 265) hydrogen bonds : angle 4.15537 ( 792) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.39104 ( 2) covalent geometry : bond 0.00287 ( 3897) covalent geometry : angle 0.53472 ( 5313) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.483 Fit side-chains REVERT: A 17 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: A 67 PHE cc_start: 0.8191 (t80) cc_final: 0.7841 (t80) REVERT: A 516 ASP cc_start: 0.8273 (t0) cc_final: 0.7867 (t0) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.1410 time to fit residues: 10.5717 Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 0.0370 chunk 6 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 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 = 0.3581 r_free = 0.3581 target = 0.133956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110954 restraints weight = 5355.666| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.68 r_work: 0.3172 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3898 Z= 0.130 Angle : 0.533 6.400 5315 Z= 0.263 Chirality : 0.038 0.162 636 Planarity : 0.004 0.043 644 Dihedral : 7.350 83.196 579 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.52 % Allowed : 15.62 % Favored : 81.86 % 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: 1.78 (0.40), residues: 495 helix: 2.13 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.50 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.000 0.000 HIS A 226 PHE 0.019 0.002 PHE A 12 TYR 0.010 0.001 TYR A 348 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 265) hydrogen bonds : angle 4.12032 ( 792) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.37533 ( 2) covalent geometry : bond 0.00317 ( 3897) covalent geometry : angle 0.53346 ( 5313) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.412 Fit side-chains REVERT: A 12 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: A 17 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: A 516 ASP cc_start: 0.8285 (t0) cc_final: 0.7874 (t0) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1446 time to fit residues: 11.0453 Evaluate side-chains 59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 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 = 0.3583 r_free = 0.3583 target = 0.133975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111249 restraints weight = 5210.843| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.65 r_work: 0.3181 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3898 Z= 0.130 Angle : 0.535 6.031 5315 Z= 0.266 Chirality : 0.038 0.160 636 Planarity : 0.004 0.042 644 Dihedral : 7.304 81.497 579 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.27 % Allowed : 16.62 % Favored : 81.11 % 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: 1.87 (0.41), residues: 495 helix: 2.19 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.46 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 PHE 0.019 0.002 PHE A 12 TYR 0.011 0.001 TYR A 348 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 265) hydrogen bonds : angle 4.11780 ( 792) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.35833 ( 2) covalent geometry : bond 0.00315 ( 3897) covalent geometry : angle 0.53512 ( 5313) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.407 Fit side-chains REVERT: A 12 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: A 17 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: A 516 ASP cc_start: 0.8293 (t0) cc_final: 0.7906 (t0) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.1339 time to fit residues: 9.9938 Evaluate side-chains 55 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 0.0060 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114870 restraints weight = 5311.557| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.67 r_work: 0.3230 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 3898 Z= 0.106 Angle : 0.528 5.950 5315 Z= 0.263 Chirality : 0.037 0.151 636 Planarity : 0.004 0.040 644 Dihedral : 6.837 79.936 579 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.52 % Allowed : 17.13 % Favored : 80.35 % 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: 1.95 (0.41), residues: 495 helix: 2.16 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.36 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.001 0.000 HIS A 226 PHE 0.017 0.001 PHE A 12 TYR 0.012 0.001 TYR A 348 ARG 0.004 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 265) hydrogen bonds : angle 3.99128 ( 792) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.27898 ( 2) covalent geometry : bond 0.00242 ( 3897) covalent geometry : angle 0.52803 ( 5313) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.364 Fit side-chains REVERT: A 12 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: A 17 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: A 23 MET cc_start: 0.7464 (tpp) cc_final: 0.7211 (ttm) REVERT: A 178 TYR cc_start: 0.7943 (m-80) cc_final: 0.7525 (m-10) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.1258 time to fit residues: 10.3655 Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.0050 chunk 14 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.134444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111366 restraints weight = 5199.625| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.66 r_work: 0.3185 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3898 Z= 0.147 Angle : 0.589 15.395 5315 Z= 0.281 Chirality : 0.039 0.151 636 Planarity : 0.004 0.041 644 Dihedral : 6.666 79.093 579 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 17.38 % Favored : 80.35 % 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: 1.81 (0.40), residues: 495 helix: 2.06 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -1.39 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.000 0.000 HIS A 226 PHE 0.018 0.002 PHE A 12 TYR 0.010 0.001 TYR A 118 ARG 0.006 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 265) hydrogen bonds : angle 4.11933 ( 792) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.38276 ( 2) covalent geometry : bond 0.00358 ( 3897) covalent geometry : angle 0.58908 ( 5313) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.399 Fit side-chains REVERT: A 12 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: A 17 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.6594 (m-80) REVERT: A 23 MET cc_start: 0.7603 (tpp) cc_final: 0.7336 (ttm) REVERT: A 178 TYR cc_start: 0.8033 (m-80) cc_final: 0.7591 (m-10) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.1313 time to fit residues: 9.0596 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 548 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 57.7263 > 50: distance: 74 - 92: 9.020 distance: 82 - 100: 6.472 distance: 85 - 87: 4.572 distance: 86 - 104: 8.542 distance: 87 - 88: 7.694 distance: 88 - 89: 4.608 distance: 88 - 91: 9.955 distance: 89 - 92: 5.036 distance: 90 - 111: 11.604 distance: 92 - 93: 7.416 distance: 93 - 94: 6.050 distance: 93 - 96: 7.133 distance: 94 - 95: 6.858 distance: 95 - 119: 19.676 distance: 96 - 97: 9.044 distance: 97 - 98: 5.917 distance: 97 - 99: 20.044 distance: 100 - 101: 6.489 distance: 101 - 102: 5.453 distance: 102 - 103: 8.388 distance: 102 - 104: 4.575 distance: 103 - 126: 16.472 distance: 104 - 105: 9.473 distance: 105 - 106: 11.554 distance: 105 - 108: 6.490 distance: 106 - 107: 11.750 distance: 106 - 111: 9.051 distance: 107 - 133: 21.065 distance: 108 - 109: 7.534 distance: 108 - 110: 11.529 distance: 111 - 112: 7.186 distance: 112 - 113: 3.585 distance: 112 - 115: 7.177 distance: 113 - 114: 4.019 distance: 113 - 119: 9.379 distance: 115 - 116: 9.944 distance: 116 - 117: 3.352 distance: 116 - 118: 8.647 distance: 119 - 120: 8.800 distance: 120 - 121: 10.026 distance: 120 - 123: 9.381 distance: 121 - 122: 10.009 distance: 121 - 126: 7.797 distance: 122 - 149: 44.393 distance: 123 - 124: 13.556 distance: 123 - 125: 6.971 distance: 126 - 127: 8.019 distance: 127 - 128: 5.201 distance: 127 - 130: 5.308 distance: 128 - 129: 4.875 distance: 128 - 133: 7.188 distance: 129 - 155: 25.222 distance: 130 - 131: 11.580 distance: 130 - 132: 4.664 distance: 133 - 134: 6.651 distance: 134 - 135: 7.968 distance: 134 - 137: 4.697 distance: 135 - 136: 5.007 distance: 135 - 141: 5.255 distance: 136 - 159: 17.488 distance: 137 - 138: 17.857 distance: 138 - 139: 13.410 distance: 139 - 140: 27.135 distance: 141 - 142: 9.048 distance: 142 - 143: 18.371 distance: 142 - 145: 13.825 distance: 143 - 144: 8.554 distance: 143 - 149: 34.445 distance: 144 - 164: 9.251 distance: 145 - 146: 7.662 distance: 146 - 147: 11.693 distance: 146 - 148: 4.250 distance: 149 - 150: 43.330 distance: 150 - 151: 17.687 distance: 150 - 153: 33.424 distance: 151 - 152: 10.443 distance: 151 - 155: 11.731 distance: 152 - 172: 21.375 distance: 153 - 154: 36.351 distance: 158 - 180: 3.597