Starting phenix.real_space_refine on Fri Feb 14 00:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkd_12438/02_2025/7nkd_12438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkd_12438/02_2025/7nkd_12438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nkd_12438/02_2025/7nkd_12438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkd_12438/02_2025/7nkd_12438.map" model { file = "/net/cci-nas-00/data/ceres_data/7nkd_12438/02_2025/7nkd_12438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkd_12438/02_2025/7nkd_12438.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 S 5 5.16 5 C 2952 2.51 5 N 852 2.21 5 O 978 1.98 5 H 4768 0.53 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-5592/modules/chem_data/mon_lib" Total number of atoms: 9555 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1346 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 6 Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 652 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 4 Chain: "C" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 448 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 2 Chain: "D" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 601 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain breaks: 3 Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 620 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain breaks: 3 Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 277 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain breaks: 3 Chain: "d" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5084 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 10, 'TRANS': 325} Chain: "b" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 527 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 6.43, per 1000 atoms: 0.67 Number of scatterers: 9555 At special positions: 0 Unit cell: (111.22, 73.04, 83, 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 5 16.00 O 978 8.00 N 852 7.00 C 2952 6.00 H 4768 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 712.3 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 51.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.529A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.593A pdb=" N ALA B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'd' and resid 110 through 138 Processing helix chain 'd' and resid 139 through 157 removed outlier: 3.559A pdb=" N GLN d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 192 removed outlier: 3.729A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 225 Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.577A pdb=" N ASN d 259 " --> pdb=" O THR d 255 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 286 removed outlier: 3.882A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 Processing helix chain 'd' and resid 306 through 314 Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 3.742A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 412 through 416 Processing helix chain 'd' and resid 431 through 442 Processing helix chain 'b' and resid 131 through 145 Processing helix chain 'b' and resid 147 through 161 removed outlier: 3.557A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 5.782A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 5.926A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.476A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.466A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY D 58 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG D 63 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS D 56 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.268A pdb=" N HIS E 56 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 63 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 804 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: 3.73 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4766 1.03 - 1.23: 2 1.23 - 1.42: 1901 1.42 - 1.61: 2901 1.61 - 1.81: 8 Bond restraints: 9578 Sorted by residual: bond pdb=" N THR d 166 " pdb=" CA THR d 166 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N ILE d 164 " pdb=" CA ILE d 164 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.13e+00 bond pdb=" CA ILE d 164 " pdb=" CB ILE d 164 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.42e-02 4.96e+03 6.61e-01 bond pdb=" C LEU d 416 " pdb=" N GLY d 417 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.46e-01 bond pdb=" C ASP d 412 " pdb=" O ASP d 412 " ideal model delta sigma weight residual 1.238 1.247 -0.009 1.28e-02 6.10e+03 5.13e-01 ... (remaining 9573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 16447 1.05 - 2.11: 831 2.11 - 3.16: 24 3.16 - 4.22: 16 4.22 - 5.27: 1 Bond angle restraints: 17319 Sorted by residual: angle pdb=" N ILE d 164 " pdb=" CA ILE d 164 " pdb=" C ILE d 164 " ideal model delta sigma weight residual 106.21 109.21 -3.00 1.07e+00 8.73e-01 7.87e+00 angle pdb=" C THR d 166 " pdb=" CA THR d 166 " pdb=" CB THR d 166 " ideal model delta sigma weight residual 110.42 115.69 -5.27 1.99e+00 2.53e-01 7.01e+00 angle pdb=" C SER C 21 " pdb=" N PHE C 22 " pdb=" CA PHE C 22 " ideal model delta sigma weight residual 122.56 118.63 3.93 1.72e+00 3.38e-01 5.21e+00 angle pdb=" CA GLY d 417 " pdb=" C GLY d 417 " pdb=" N GLY d 418 " ideal model delta sigma weight residual 115.34 116.84 -1.50 8.40e-01 1.42e+00 3.17e+00 angle pdb=" C ASP d 165 " pdb=" N THR d 166 " pdb=" CA THR d 166 " ideal model delta sigma weight residual 121.54 124.61 -3.07 1.91e+00 2.74e-01 2.58e+00 ... (remaining 17314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 3993 17.50 - 34.99: 301 34.99 - 52.49: 95 52.49 - 69.99: 22 69.99 - 87.48: 10 Dihedral angle restraints: 4421 sinusoidal: 2498 harmonic: 1923 Sorted by residual: dihedral pdb=" CB GLU C 12 " pdb=" CG GLU C 12 " pdb=" CD GLU C 12 " pdb=" OE1 GLU C 12 " ideal model delta sinusoidal sigma weight residual 0.00 -87.48 87.48 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP D 59 " pdb=" CB ASP D 59 " pdb=" CG ASP D 59 " pdb=" OD1 ASP D 59 " ideal model delta sinusoidal sigma weight residual -30.00 -84.12 54.12 1 2.00e+01 2.50e-03 9.93e+00 dihedral pdb=" CG ARG D 26 " pdb=" CD ARG D 26 " pdb=" NE ARG D 26 " pdb=" CZ ARG D 26 " ideal model delta sinusoidal sigma weight residual 180.00 138.41 41.59 2 1.50e+01 4.44e-03 9.40e+00 ... (remaining 4418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 535 0.026 - 0.053: 158 0.053 - 0.079: 53 0.079 - 0.105: 38 0.105 - 0.132: 18 Chirality restraints: 802 Sorted by residual: chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA VAL D 29 " pdb=" N VAL D 29 " pdb=" C VAL D 29 " pdb=" CB VAL D 29 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE d 428 " pdb=" N ILE d 428 " pdb=" C ILE d 428 " pdb=" CB ILE d 428 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 799 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 29 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" CD GLU A 29 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU A 29 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 29 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN b 136 " -0.005 2.00e-02 2.50e+03 9.30e-03 1.30e+00 pdb=" CD GLN b 136 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN b 136 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN b 136 " -0.009 2.00e-02 2.50e+03 pdb="HE21 GLN b 136 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN b 136 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 152 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.11e+00 pdb=" C SER b 152 " 0.018 2.00e-02 2.50e+03 pdb=" O SER b 152 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA b 153 " -0.006 2.00e-02 2.50e+03 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 651 2.20 - 2.80: 20245 2.80 - 3.40: 26639 3.40 - 4.00: 33554 4.00 - 4.60: 51795 Nonbonded interactions: 132884 Sorted by model distance: nonbonded pdb=" OE1 GLU B 71 " pdb=" H GLU B 71 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLU A 71 " pdb=" H GLU A 71 " model vdw 1.611 2.450 nonbonded pdb=" HG1 THR d 263 " pdb=" OD1 ASN d 266 " model vdw 1.616 2.450 nonbonded pdb=" HG SER d 179 " pdb=" O ARG d 260 " model vdw 1.638 2.450 nonbonded pdb=" O ARG F 11 " pdb=" H GLU F 23 " model vdw 1.647 2.450 ... (remaining 132879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 30 or resid 55 through 81)) selection = (chain 'E' and (resid 8 through 15 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 21 \ through 30 or (resid 55 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HE21 or name HE22)) or resid 56 through 81)) } 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: 13.810 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: 0.190 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.950 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4810 Z= 0.172 Angle : 0.452 5.270 6490 Z= 0.252 Chirality : 0.037 0.132 802 Planarity : 0.003 0.032 848 Dihedral : 14.504 87.484 1754 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 2.45 (0.37), residues: 585 helix: 2.72 (0.30), residues: 314 sheet: -1.17 (0.70), residues: 57 loop : 0.90 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.001 0.000 HIS A 43 PHE 0.009 0.001 PHE d 187 TYR 0.006 0.001 TYR A 18 ARG 0.004 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2574 time to fit residues: 21.4616 Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.073150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057598 restraints weight = 41498.130| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.37 r_work: 0.2965 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4810 Z= 0.280 Angle : 0.508 8.294 6490 Z= 0.273 Chirality : 0.039 0.137 802 Planarity : 0.003 0.030 848 Dihedral : 3.516 13.181 665 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.58 % Allowed : 3.86 % Favored : 95.56 % 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: 2.38 (0.35), residues: 585 helix: 2.87 (0.28), residues: 317 sheet: -1.11 (0.67), residues: 57 loop : 0.41 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.001 0.000 HIS C 72 PHE 0.014 0.001 PHE C 22 TYR 0.007 0.001 TYR B 18 ARG 0.003 0.000 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.2060 time to fit residues: 16.3188 Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.073195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058012 restraints weight = 41919.470| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.33 r_work: 0.2964 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4810 Z= 0.261 Angle : 0.481 6.480 6490 Z= 0.258 Chirality : 0.039 0.136 802 Planarity : 0.003 0.027 848 Dihedral : 3.528 13.524 665 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.58 % Allowed : 5.79 % Favored : 93.63 % 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 (0.36), residues: 585 helix: 3.04 (0.28), residues: 317 sheet: -1.08 (0.64), residues: 57 loop : 0.30 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.002 0.001 HIS d 410 PHE 0.015 0.001 PHE C 22 TYR 0.008 0.001 TYR B 18 ARG 0.003 0.000 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8421 (tp30) cc_final: 0.8115 (tp30) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.2044 time to fit residues: 15.3792 Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.072826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057719 restraints weight = 41807.522| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.30 r_work: 0.2955 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4810 Z= 0.263 Angle : 0.476 5.977 6490 Z= 0.254 Chirality : 0.039 0.136 802 Planarity : 0.003 0.034 848 Dihedral : 3.516 13.428 665 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.39 % Allowed : 7.14 % Favored : 92.47 % 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: 2.51 (0.35), residues: 585 helix: 3.08 (0.29), residues: 317 sheet: -1.05 (0.64), residues: 57 loop : 0.27 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP d 261 HIS 0.002 0.001 HIS d 378 PHE 0.014 0.001 PHE C 22 TYR 0.008 0.001 TYR B 18 ARG 0.003 0.000 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8432 (tp30) cc_final: 0.8117 (tp30) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.2042 time to fit residues: 15.0147 Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.073558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058450 restraints weight = 41379.948| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.29 r_work: 0.2977 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4810 Z= 0.142 Angle : 0.440 5.934 6490 Z= 0.232 Chirality : 0.039 0.139 802 Planarity : 0.003 0.036 848 Dihedral : 3.368 12.625 665 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.39 % Allowed : 7.34 % Favored : 92.28 % 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: 2.81 (0.36), residues: 585 helix: 3.29 (0.29), residues: 317 sheet: -0.93 (0.64), residues: 57 loop : 0.49 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.001 0.000 HIS d 378 PHE 0.014 0.001 PHE C 22 TYR 0.006 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8429 (tp30) cc_final: 0.8121 (tp30) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.2030 time to fit residues: 14.7743 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.073275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057717 restraints weight = 41230.022| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.35 r_work: 0.2967 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4810 Z= 0.198 Angle : 0.452 5.378 6490 Z= 0.239 Chirality : 0.039 0.137 802 Planarity : 0.003 0.036 848 Dihedral : 3.344 13.003 665 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.39 % Allowed : 8.88 % Favored : 90.73 % 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 (0.36), residues: 585 helix: 3.25 (0.29), residues: 317 sheet: -0.83 (0.65), residues: 57 loop : 0.46 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.002 0.000 HIS d 378 PHE 0.014 0.001 PHE C 22 TYR 0.007 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8632 (p0) cc_final: 0.8382 (p0) REVERT: A 43 HIS cc_start: 0.8547 (m90) cc_final: 0.8276 (m90) REVERT: F 23 GLU cc_start: 0.8421 (tp30) cc_final: 0.8114 (tp30) outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.1801 time to fit residues: 12.8206 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.072808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057405 restraints weight = 41639.813| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.30 r_work: 0.2966 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4810 Z= 0.231 Angle : 0.458 5.011 6490 Z= 0.243 Chirality : 0.039 0.136 802 Planarity : 0.003 0.036 848 Dihedral : 3.381 13.153 665 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.39 % Allowed : 8.88 % Favored : 90.73 % 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: 2.77 (0.36), residues: 585 helix: 3.24 (0.29), residues: 317 sheet: -0.77 (0.66), residues: 57 loop : 0.43 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 261 HIS 0.002 0.001 HIS d 378 PHE 0.014 0.001 PHE C 22 TYR 0.007 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8607 (p0) cc_final: 0.8355 (p0) REVERT: A 43 HIS cc_start: 0.8571 (m90) cc_final: 0.8311 (m90) REVERT: F 23 GLU cc_start: 0.8385 (tp30) cc_final: 0.8080 (tp30) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.1970 time to fit residues: 13.9102 Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.073152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057392 restraints weight = 42213.772| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.43 r_work: 0.2960 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4810 Z= 0.199 Angle : 0.457 8.657 6490 Z= 0.239 Chirality : 0.038 0.134 802 Planarity : 0.003 0.035 848 Dihedral : 3.349 12.965 665 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % 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: 2.86 (0.36), residues: 585 helix: 3.32 (0.29), residues: 317 sheet: -0.70 (0.66), residues: 57 loop : 0.46 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 261 HIS 0.001 0.000 HIS d 378 PHE 0.009 0.001 PHE d 187 TYR 0.006 0.001 TYR B 18 ARG 0.002 0.000 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8618 (p0) cc_final: 0.8333 (p0) REVERT: A 43 HIS cc_start: 0.8582 (m90) cc_final: 0.8309 (m90) REVERT: F 23 GLU cc_start: 0.8407 (tp30) cc_final: 0.7745 (tp30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2090 time to fit residues: 14.7804 Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.3980 chunk 47 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 33 optimal weight: 0.0870 overall best weight: 0.1686 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.073864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058282 restraints weight = 41338.770| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.39 r_work: 0.2981 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4810 Z= 0.120 Angle : 0.432 8.452 6490 Z= 0.221 Chirality : 0.039 0.136 802 Planarity : 0.003 0.035 848 Dihedral : 3.210 12.122 665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % 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: 3.09 (0.36), residues: 585 helix: 3.48 (0.29), residues: 317 sheet: -0.57 (0.67), residues: 57 loop : 0.60 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.001 0.000 HIS d 222 PHE 0.007 0.001 PHE d 187 TYR 0.004 0.001 TYR A 18 ARG 0.002 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8586 (p0) cc_final: 0.8290 (p0) REVERT: A 43 HIS cc_start: 0.8561 (m90) cc_final: 0.8307 (m90) REVERT: F 23 GLU cc_start: 0.8392 (tp30) cc_final: 0.7758 (tp30) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2202 time to fit residues: 16.8944 Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 0.0060 chunk 41 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.073463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.057839 restraints weight = 41749.514| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.38 r_work: 0.2969 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4810 Z= 0.194 Angle : 0.453 8.111 6490 Z= 0.236 Chirality : 0.038 0.134 802 Planarity : 0.003 0.035 848 Dihedral : 3.221 12.646 665 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.06 (0.36), residues: 585 helix: 3.44 (0.29), residues: 317 sheet: -0.55 (0.67), residues: 57 loop : 0.59 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.002 0.000 HIS d 378 PHE 0.009 0.001 PHE d 187 TYR 0.006 0.001 TYR B 18 ARG 0.002 0.000 ARG D 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8572 (p0) cc_final: 0.8274 (p0) REVERT: A 43 HIS cc_start: 0.8558 (m90) cc_final: 0.8304 (m90) REVERT: F 23 GLU cc_start: 0.8398 (tp30) cc_final: 0.7767 (tp30) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2000 time to fit residues: 14.7625 Evaluate side-chains 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 51.2348 > 50: distance: 43 - 183: 14.636 distance: 46 - 180: 6.157 distance: 80 - 155: 6.484 distance: 138 - 141: 3.606 distance: 138 - 144: 3.611 distance: 139 - 140: 4.333 distance: 152 - 160: 7.185 distance: 153 - 156: 3.344 distance: 153 - 161: 8.076 distance: 154 - 155: 10.064 distance: 154 - 164: 3.845 distance: 156 - 157: 7.421 distance: 156 - 162: 9.390 distance: 156 - 163: 8.362 distance: 157 - 158: 4.817 distance: 164 - 165: 4.349 distance: 164 - 171: 6.513 distance: 164 - 360: 4.062 distance: 165 - 166: 5.697 distance: 165 - 168: 6.776 distance: 165 - 172: 16.005 distance: 166 - 167: 15.074 distance: 166 - 180: 5.437 distance: 167 - 357: 15.355 distance: 168 - 169: 7.840 distance: 168 - 170: 9.877 distance: 168 - 173: 16.678 distance: 169 - 174: 7.822 distance: 169 - 175: 5.947 distance: 169 - 176: 4.597 distance: 170 - 177: 8.178 distance: 170 - 179: 4.569 distance: 180 - 181: 5.422 distance: 180 - 189: 10.065 distance: 181 - 182: 18.264 distance: 181 - 184: 3.957 distance: 181 - 190: 15.618 distance: 182 - 183: 22.065 distance: 182 - 195: 14.600 distance: 184 - 185: 4.291 distance: 184 - 191: 8.562 distance: 184 - 192: 8.558 distance: 185 - 193: 3.408 distance: 185 - 194: 5.260 distance: 186 - 187: 4.361 distance: 186 - 188: 6.981 distance: 195 - 196: 8.939 distance: 195 - 206: 16.466 distance: 196 - 197: 11.783 distance: 196 - 199: 18.525 distance: 196 - 207: 3.696 distance: 197 - 198: 17.374 distance: 197 - 215: 8.256 distance: 199 - 200: 14.659 distance: 199 - 208: 8.465 distance: 199 - 209: 8.072 distance: 200 - 201: 5.495 distance: 200 - 202: 3.286 distance: 201 - 203: 3.175 distance: 202 - 204: 5.446 distance: 202 - 211: 5.995 distance: 215 - 216: 4.876 distance: 215 - 221: 4.510 distance: 216 - 217: 9.819 distance: 216 - 219: 4.046 distance: 216 - 222: 3.769 distance: 217 - 218: 20.695 distance: 217 - 229: 12.216 distance: 219 - 220: 3.712 distance: 219 - 223: 5.592 distance: 219 - 224: 7.230 distance: 220 - 221: 5.520 distance: 220 - 225: 3.681 distance: 221 - 227: 5.506 distance: 221 - 228: 5.820 distance: 229 - 230: 7.558 distance: 229 - 240: 21.038 distance: 230 - 233: 8.141 distance: 230 - 241: 5.393 distance: 231 - 253: 4.738 distance: 233 - 234: 6.947 distance: 233 - 242: 3.050 distance: 233 - 243: 4.189 distance: 234 - 235: 4.402 distance: 234 - 244: 3.869 distance: 234 - 245: 4.813 distance: 235 - 236: 4.309 distance: 253 - 254: 4.590 distance: 253 - 257: 9.230 distance: 254 - 255: 4.536 distance: 255 - 260: 3.616 distance: 260 - 266: 13.955 distance: 261 - 262: 5.283 distance: 261 - 264: 6.753 distance: 261 - 267: 4.297 distance: 262 - 263: 20.314 distance: 262 - 271: 9.649 distance: 264 - 265: 10.758 distance: 264 - 268: 4.051 distance: 264 - 269: 7.401 distance: 265 - 270: 9.471 distance: 271 - 272: 3.495 distance: 271 - 278: 22.989 distance: 272 - 273: 4.662 distance: 272 - 275: 5.802 distance: 272 - 279: 8.216 distance: 273 - 274: 6.628 distance: 275 - 276: 8.310 distance: 275 - 277: 5.451 distance: 275 - 280: 12.960 distance: 276 - 281: 3.999 distance: 276 - 282: 6.312 distance: 277 - 284: 4.314 distance: 277 - 286: 3.064