Starting phenix.real_space_refine on Tue Jan 14 20:26:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iu0_35713/01_2025/8iu0_35713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iu0_35713/01_2025/8iu0_35713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iu0_35713/01_2025/8iu0_35713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iu0_35713/01_2025/8iu0_35713.map" model { file = "/net/cci-nas-00/data/ceres_data/8iu0_35713/01_2025/8iu0_35713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iu0_35713/01_2025/8iu0_35713.cif" } resolution = 2.66 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= 0.004 sd= 0.125 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 9 5.49 5 S 60 5.16 5 C 4863 2.51 5 N 954 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Restraints were copied for chains: C, B Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE A 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 35 " occ=0.50 residue: pdb=" N APHE A 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 144 " occ=0.50 residue: pdb=" N APHE B 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 35 " occ=0.50 residue: pdb=" N APHE B 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 144 " occ=0.50 residue: pdb=" N APHE C 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 35 " occ=0.50 residue: pdb=" N APHE C 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 144 " occ=0.50 Time building chain proxies: 5.28, per 1000 atoms: 0.75 Number of scatterers: 7062 At special positions: 0 Unit cell: (77.19, 77.19, 84.66, 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 60 16.00 P 9 15.00 O 1176 8.00 N 954 7.00 C 4863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 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 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 426 hydrogen bonds defined for protein. 1281 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: 1.81 Time building geometry restraints manager: 2.14 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: 1226 1.33 - 1.46: 2621 1.46 - 1.59: 3260 1.59 - 1.72: 15 1.72 - 1.85: 81 Bond restraints: 7203 Sorted by residual: bond pdb=" C7 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC A 311 " pdb=" C4 PSC A 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC B 311 " pdb=" C4 PSC B 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC C 311 " pdb=" C4 PSC C 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C7 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 1.530 1.320 0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 7198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 9164 3.02 - 6.03: 409 6.03 - 9.05: 18 9.05 - 12.07: 21 12.07 - 15.08: 18 Bond angle restraints: 9630 Sorted by residual: angle pdb=" C10 PSC B 310 " pdb=" C9 PSC B 310 " pdb=" C8 PSC B 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC A 310 " pdb=" C9 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC C 310 " pdb=" C9 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 127.68 112.61 15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC B 310 " pdb=" C11 PSC B 310 " pdb=" C12 PSC B 310 " ideal model delta sigma weight residual 111.07 126.14 -15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC A 310 " pdb=" C11 PSC A 310 " pdb=" C12 PSC A 310 " ideal model delta sigma weight residual 111.07 126.12 -15.05 3.00e+00 1.11e-01 2.52e+01 ... (remaining 9625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 3708 23.98 - 47.95: 324 47.95 - 71.93: 108 71.93 - 95.90: 0 95.90 - 119.88: 3 Dihedral angle restraints: 4143 sinusoidal: 1890 harmonic: 2253 Sorted by residual: dihedral pdb=" C03 PSC C 302 " pdb=" O11 PSC C 302 " pdb=" P PSC C 302 " pdb=" O12 PSC C 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.58 119.88 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC A 302 " pdb=" O11 PSC A 302 " pdb=" P PSC A 302 " pdb=" O12 PSC A 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.59 119.87 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC B 302 " pdb=" O11 PSC B 302 " pdb=" P PSC B 302 " pdb=" O12 PSC B 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.60 119.86 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 457 0.051 - 0.102: 326 0.102 - 0.153: 113 0.153 - 0.204: 31 0.204 - 0.255: 9 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA PRO A 147 " pdb=" N PRO A 147 " pdb=" C PRO A 147 " pdb=" CB PRO A 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO C 147 " pdb=" N PRO C 147 " pdb=" C PRO C 147 " pdb=" CB PRO C 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO B 147 " pdb=" N PRO B 147 " pdb=" C PRO B 147 " pdb=" CB PRO B 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 933 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" C11 PSC B 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC B 312 " -0.100 2.00e-02 2.50e+03 pdb=" C9 PSC B 312 " 0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC A 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC A 312 " -0.099 2.00e-02 2.50e+03 pdb=" C9 PSC A 312 " 0.307 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 312 " 0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC C 312 " -0.102 2.00e-02 2.50e+03 pdb=" C8 PSC C 312 " 0.099 2.00e-02 2.50e+03 pdb=" C9 PSC C 312 " -0.307 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1588 2.79 - 3.32: 6677 3.32 - 3.84: 12411 3.84 - 4.37: 15914 4.37 - 4.90: 25235 Nonbonded interactions: 61825 Sorted by model distance: nonbonded pdb=" OH TYR A 103 " pdb=" O HOH A 401 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 103 " pdb=" O HOH C 401 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 103 " pdb=" O HOH B 401 " model vdw 2.259 3.040 nonbonded pdb=" NH2 ARG C 171 " pdb=" O13 PSC C 309 " model vdw 2.306 3.120 nonbonded pdb=" NH2 ARG A 171 " pdb=" O13 PSC A 309 " model vdw 2.306 3.120 ... (remaining 61820 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.620 Find NCS groups from input model: 0.140 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.014 0.211 7203 Z= 0.870 Angle : 1.596 15.084 9630 Z= 0.937 Chirality : 0.077 0.255 936 Planarity : 0.023 0.230 1158 Dihedral : 18.616 119.879 2715 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.90 % Allowed : 4.95 % Favored : 94.14 % 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: -1.94 (0.27), residues: 780 helix: -1.30 (0.19), residues: 543 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.011 TRP B 187 HIS 0.011 0.006 HIS C 215 PHE 0.035 0.008 PHE B 243 TYR 0.044 0.009 TYR A 150 ARG 0.016 0.003 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.669 Fit side-chains REVERT: A 207 ILE cc_start: 0.7232 (mt) cc_final: 0.7024 (mm) REVERT: A 230 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6532 (tp) REVERT: B 207 ILE cc_start: 0.7118 (mt) cc_final: 0.6911 (mm) REVERT: C 207 ILE cc_start: 0.7298 (mt) cc_final: 0.7051 (mm) outliers start: 6 outliers final: 0 residues processed: 79 average time/residue: 1.3548 time to fit residues: 112.6060 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105412 restraints weight = 26485.409| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.22 r_work: 0.3107 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7203 Z= 0.300 Angle : 0.974 11.623 9630 Z= 0.508 Chirality : 0.058 0.485 936 Planarity : 0.011 0.112 1158 Dihedral : 19.500 106.056 1334 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.48 % Favored : 94.99 % Rotamer: Outliers : 1.95 % Allowed : 7.66 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.28 (0.28), residues: 780 helix: -0.68 (0.20), residues: 549 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.010 TRP B 138 HIS 0.017 0.004 HIS C 215 PHE 0.103 0.006 PHE C 134 TYR 0.109 0.005 TYR B 155 ARG 0.029 0.002 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.724 Fit side-chains REVERT: A 87 ASP cc_start: 0.8614 (t70) cc_final: 0.8321 (t70) REVERT: A 248 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 171 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7481 (ttm110) REVERT: C 174 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7966 (mttm) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 1.3506 time to fit residues: 120.8298 Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099013 restraints weight = 34773.411| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.43 r_work: 0.3015 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7203 Z= 0.264 Angle : 0.623 6.019 9630 Z= 0.304 Chirality : 0.044 0.130 936 Planarity : 0.005 0.059 1158 Dihedral : 17.492 91.788 1332 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.80 % Allowed : 8.71 % Favored : 89.49 % 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: 0.99 (0.29), residues: 780 helix: 1.09 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.22 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 42 HIS 0.003 0.001 HIS C 125 PHE 0.017 0.002 PHE A 134 TYR 0.013 0.002 TYR C 81 ARG 0.003 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.836 Fit side-chains REVERT: A 87 ASP cc_start: 0.8742 (t70) cc_final: 0.8417 (t70) REVERT: C 76 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8221 (tt) REVERT: C 121 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8150 (mp) REVERT: C 174 LYS cc_start: 0.8303 (mtpp) cc_final: 0.8103 (mttm) outliers start: 9 outliers final: 2 residues processed: 72 average time/residue: 1.3029 time to fit residues: 99.1355 Evaluate side-chains 66 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 121 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.124379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101234 restraints weight = 36538.141| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.48 r_work: 0.3051 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7203 Z= 0.199 Angle : 0.549 6.719 9630 Z= 0.264 Chirality : 0.041 0.124 936 Planarity : 0.005 0.047 1158 Dihedral : 15.477 71.275 1332 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.20 % Allowed : 8.86 % Favored : 89.94 % 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: 2.09 (0.29), residues: 780 helix: 1.95 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.09 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 42 HIS 0.003 0.001 HIS B 125 PHE 0.017 0.001 PHE A 134 TYR 0.010 0.001 TYR C 81 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.685 Fit side-chains REVERT: A 87 ASP cc_start: 0.8705 (t70) cc_final: 0.8377 (t70) REVERT: C 76 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 244 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8312 (mtp180) outliers start: 5 outliers final: 0 residues processed: 67 average time/residue: 1.1808 time to fit residues: 83.9738 Evaluate side-chains 57 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.122716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099819 restraints weight = 33694.688| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.37 r_work: 0.3034 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7203 Z= 0.236 Angle : 0.586 6.434 9630 Z= 0.279 Chirality : 0.042 0.128 936 Planarity : 0.005 0.042 1158 Dihedral : 14.805 59.952 1332 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.35 % Allowed : 9.31 % Favored : 89.34 % 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: 2.22 (0.29), residues: 780 helix: 2.03 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.18 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 42 HIS 0.003 0.001 HIS B 125 PHE 0.017 0.002 PHE A 134 TYR 0.011 0.002 TYR A 81 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.683 Fit side-chains REVERT: A 87 ASP cc_start: 0.8738 (t70) cc_final: 0.8435 (t70) REVERT: B 80 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8616 (mtm) REVERT: C 244 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8292 (mtp180) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 1.1914 time to fit residues: 81.1086 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106487 restraints weight = 34142.979| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.47 r_work: 0.3122 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7203 Z= 0.125 Angle : 0.475 6.290 9630 Z= 0.226 Chirality : 0.038 0.122 936 Planarity : 0.004 0.037 1158 Dihedral : 12.965 59.973 1332 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.20 % Allowed : 9.76 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.79 (0.30), residues: 780 helix: 2.51 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.25 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 42 HIS 0.003 0.001 HIS C 125 PHE 0.014 0.001 PHE C 134 TYR 0.009 0.001 TYR A 81 ARG 0.002 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.687 Fit side-chains REVERT: A 87 ASP cc_start: 0.8638 (t70) cc_final: 0.8358 (t70) REVERT: B 80 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8558 (mtt) REVERT: B 176 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7874 (mtp180) REVERT: C 76 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8209 (tt) REVERT: C 244 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8233 (mtm-85) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 1.2298 time to fit residues: 92.5563 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.121977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098974 restraints weight = 34218.920| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.40 r_work: 0.3016 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7203 Z= 0.282 Angle : 0.621 6.715 9630 Z= 0.293 Chirality : 0.044 0.132 936 Planarity : 0.005 0.039 1158 Dihedral : 14.208 59.907 1332 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.90 % Allowed : 10.36 % Favored : 88.74 % 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: 2.37 (0.29), residues: 780 helix: 2.14 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.24 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 190 HIS 0.003 0.001 HIS C 125 PHE 0.016 0.002 PHE A 134 TYR 0.012 0.002 TYR A 81 ARG 0.005 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.683 Fit side-chains REVERT: A 87 ASP cc_start: 0.8739 (t70) cc_final: 0.8447 (t70) REVERT: B 80 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8620 (mtm) REVERT: C 244 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8289 (mtp180) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 1.2666 time to fit residues: 85.8905 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.124231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101192 restraints weight = 33432.129| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.39 r_work: 0.3037 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7203 Z= 0.205 Angle : 0.551 6.604 9630 Z= 0.261 Chirality : 0.041 0.121 936 Planarity : 0.005 0.038 1158 Dihedral : 13.534 59.444 1332 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.50 % Allowed : 9.46 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.48 (0.29), residues: 780 helix: 2.25 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 102 HIS 0.003 0.001 HIS C 125 PHE 0.016 0.001 PHE A 134 TYR 0.011 0.001 TYR A 81 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.669 Fit side-chains REVERT: A 87 ASP cc_start: 0.8761 (t70) cc_final: 0.8461 (t70) REVERT: B 80 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8630 (mtm) REVERT: C 121 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8077 (tp) REVERT: C 244 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8250 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 1.3048 time to fit residues: 84.4469 Evaluate side-chains 61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.128889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105823 restraints weight = 33622.465| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.42 r_work: 0.3100 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7203 Z= 0.136 Angle : 0.483 6.912 9630 Z= 0.230 Chirality : 0.038 0.119 936 Planarity : 0.004 0.036 1158 Dihedral : 12.310 59.913 1332 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.35 % Allowed : 9.91 % Favored : 88.74 % 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: 2.83 (0.30), residues: 780 helix: 2.55 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.24 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 42 HIS 0.002 0.001 HIS A 125 PHE 0.014 0.001 PHE A 134 TYR 0.009 0.001 TYR A 81 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.613 Fit side-chains REVERT: A 87 ASP cc_start: 0.8675 (t70) cc_final: 0.8391 (t70) REVERT: B 80 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8586 (mtt) REVERT: C 121 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7931 (tp) REVERT: C 244 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8255 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 1.3839 time to fit residues: 88.9431 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 59.116 > 50: distance: 90 - 115: 3.406 distance: 101 - 126: 3.862 distance: 105 - 131: 7.690 distance: 115 - 116: 5.019 distance: 116 - 119: 5.766 distance: 117 - 118: 5.597 distance: 117 - 126: 3.074 distance: 118 - 158: 7.980 distance: 119 - 120: 7.481 distance: 120 - 121: 7.552 distance: 120 - 122: 6.117 distance: 121 - 123: 3.116 distance: 122 - 124: 4.708 distance: 123 - 125: 4.300 distance: 124 - 125: 4.851 distance: 126 - 127: 6.779 distance: 127 - 128: 3.615 distance: 127 - 130: 12.349 distance: 128 - 129: 7.160 distance: 128 - 131: 4.710 distance: 129 - 166: 10.707 distance: 131 - 134: 5.947 distance: 131 - 142: 5.916 distance: 132 - 134: 5.752 distance: 132 - 142: 4.830 distance: 132 - 150: 5.200 distance: 133 - 174: 7.139 distance: 134 - 135: 3.003 distance: 135 - 136: 4.371 distance: 136 - 138: 3.701 distance: 137 - 139: 7.249 distance: 138 - 140: 6.969 distance: 139 - 141: 7.089 distance: 140 - 141: 3.048 distance: 142 - 143: 9.887 distance: 143 - 144: 6.943 distance: 144 - 145: 5.510 distance: 144 - 146: 10.719 distance: 145 - 147: 6.773 distance: 146 - 148: 7.082 distance: 147 - 149: 9.723 distance: 148 - 149: 3.841 distance: 150 - 151: 7.873 distance: 151 - 152: 3.871 distance: 151 - 154: 6.851 distance: 152 - 153: 7.073 distance: 152 - 158: 4.174 distance: 153 - 181: 8.646 distance: 154 - 155: 4.801 distance: 155 - 156: 3.073 distance: 155 - 157: 4.351 distance: 158 - 159: 7.177 distance: 159 - 160: 7.356 distance: 159 - 162: 12.308 distance: 160 - 161: 6.670 distance: 160 - 166: 5.269 distance: 161 - 187: 27.359 distance: 162 - 163: 9.601 distance: 163 - 164: 13.085 distance: 163 - 165: 13.688 distance: 166 - 167: 7.889 distance: 167 - 168: 7.718 distance: 167 - 170: 14.318 distance: 168 - 169: 8.168 distance: 171 - 172: 17.522 distance: 171 - 173: 8.702 distance: 175 - 178: 3.783 distance: 176 - 177: 7.904 distance: 176 - 181: 4.160 distance: 178 - 179: 6.991 distance: 178 - 180: 10.181 distance: 181 - 182: 17.373 distance: 182 - 183: 7.188 distance: 182 - 185: 17.202 distance: 183 - 184: 12.489 distance: 183 - 187: 5.072 distance: 185 - 186: 17.296 distance: 187 - 188: 13.246 distance: 188 - 189: 10.772 distance: 188 - 191: 7.404 distance: 189 - 190: 21.156 distance: 189 - 196: 22.904 distance: 190 - 217: 26.883 distance: 191 - 192: 10.741 distance: 192 - 193: 15.459 distance: 193 - 194: 9.989 distance: 194 - 195: 20.684 distance: 195 - 232: 9.948 distance: 196 - 197: 30.597 distance: 197 - 198: 6.331 distance: 197 - 200: 23.005 distance: 198 - 199: 4.192 distance: 198 - 202: 6.606 distance: 199 - 221: 8.719 distance: 200 - 201: 35.506