Starting phenix.real_space_refine on Fri Aug 22 18:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x96_33068/08_2025/7x96_33068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x96_33068/08_2025/7x96_33068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x96_33068/08_2025/7x96_33068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x96_33068/08_2025/7x96_33068_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x96_33068/08_2025/7x96_33068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x96_33068/08_2025/7x96_33068.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 17 5.16 5 C 2159 2.51 5 N 556 2.21 5 O 670 1.98 5 H 3184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6586 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3065 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1826 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1624 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.25, per 1000 atoms: 0.19 Number of scatterers: 6586 At special positions: 0 Unit cell: (72.123, 86.216, 92.848, 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 17 16.00 O 670 8.00 N 556 7.00 C 2159 6.00 H 3184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 253.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 14.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 364 through 371 removed outlier: 4.481A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 389 Processing helix chain 'G' and resid 403 through 408 removed outlier: 3.922A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.524A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.581A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.720A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.518A pdb=" N VAL H 116 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.677A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 1.10 Time building geometry restraints manager: 0.82 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: 3183 1.03 - 1.23: 20 1.23 - 1.43: 1514 1.43 - 1.62: 1934 1.62 - 1.82: 21 Bond restraints: 6672 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN A 5 " pdb=" C2 MAN A 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 6667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11726 1.51 - 3.03: 178 3.03 - 4.54: 26 4.54 - 6.06: 7 6.06 - 7.57: 4 Bond angle restraints: 11941 Sorted by residual: angle pdb=" CA ARG L 97 " pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N VAL H 102 " pdb=" CA VAL H 102 " pdb=" C VAL H 102 " ideal model delta sigma weight residual 110.21 106.93 3.28 1.13e+00 7.83e-01 8.43e+00 angle pdb=" C PRO L 96 " pdb=" N ARG L 97 " pdb=" CA ARG L 97 " ideal model delta sigma weight residual 122.30 125.62 -3.32 1.35e+00 5.49e-01 6.04e+00 angle pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " pdb=" CD ARG L 97 " ideal model delta sigma weight residual 111.30 116.67 -5.37 2.30e+00 1.89e-01 5.45e+00 angle pdb=" C3 MAN A 4 " pdb=" C2 MAN A 4 " pdb=" O2 MAN A 4 " ideal model delta sigma weight residual 111.77 105.58 6.19 3.00e+00 1.11e-01 4.25e+00 ... (remaining 11936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 3063 21.62 - 43.23: 166 43.23 - 64.85: 57 64.85 - 86.47: 13 86.47 - 108.08: 5 Dihedral angle restraints: 3304 sinusoidal: 1796 harmonic: 1508 Sorted by residual: dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.36 -88.64 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 146.29 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 454 0.054 - 0.107: 55 0.107 - 0.161: 25 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 535 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2 BMA A 3 " pdb=" C1 BMA A 3 " pdb=" C3 BMA A 3 " pdb=" O2 BMA A 3 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE G 402 " pdb=" N ILE G 402 " pdb=" C ILE G 402 " pdb=" CB ILE G 402 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 532 not shown) Planarity restraints: 1007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 97 " 0.199 9.50e-02 1.11e+02 6.65e-02 4.79e+00 pdb=" NE ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG L 97 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG L 97 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG L 97 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO G 521 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO L 96 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.015 5.00e-02 4.00e+02 ... (remaining 1004 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 288 2.17 - 2.78: 12644 2.78 - 3.38: 17363 3.38 - 3.99: 23147 3.99 - 4.60: 35239 Nonbonded interactions: 88681 Sorted by model distance: nonbonded pdb=" O TRP G 353 " pdb="HH12 ARG G 466 " model vdw 1.562 2.450 nonbonded pdb=" HG SER L 12 " pdb=" O ASP L 107 " model vdw 1.624 2.450 nonbonded pdb=" H LEU G 455 " pdb=" O PRO G 491 " model vdw 1.641 2.450 nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.643 2.450 nonbonded pdb=" OE1 GLU H 89 " pdb=" H GLU H 89 " model vdw 1.649 2.450 ... (remaining 88676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 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: 0.030 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 0.033 3500 Z= 0.158 Angle : 0.615 7.571 4777 Z= 0.301 Chirality : 0.045 0.268 535 Planarity : 0.005 0.086 603 Dihedral : 15.740 108.084 1322 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.42), residues: 421 helix: -1.99 (1.15), residues: 19 sheet: -0.82 (0.42), residues: 167 loop : -0.77 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 97 TYR 0.011 0.001 TYR H 80 PHE 0.005 0.001 PHE G 400 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3488) covalent geometry : angle 0.60890 ( 4747) SS BOND : bond 0.00201 ( 6) SS BOND : angle 0.82262 ( 12) hydrogen bonds : bond 0.19473 ( 99) hydrogen bonds : angle 7.60033 ( 264) link_ALPHA1-3 : bond 0.00427 ( 1) link_ALPHA1-3 : angle 1.55077 ( 3) link_ALPHA1-6 : bond 0.00442 ( 1) link_ALPHA1-6 : angle 1.51718 ( 3) link_BETA1-4 : bond 0.00288 ( 2) link_BETA1-4 : angle 1.16527 ( 6) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.55489 ( 3) link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 1.75245 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 493 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8639 (tp-100) REVERT: H 62 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1288 time to fit residues: 11.1509 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.057061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.046746 restraints weight = 35353.520| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 4.26 r_work: 0.2566 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.008 0.049 3500 Z= 0.356 Angle : 0.643 6.700 4777 Z= 0.337 Chirality : 0.043 0.209 535 Planarity : 0.005 0.039 603 Dihedral : 10.001 71.261 582 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.37 % Allowed : 8.74 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.40), residues: 421 helix: -2.45 (1.00), residues: 20 sheet: -1.04 (0.42), residues: 155 loop : -1.15 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 97 TYR 0.014 0.002 TYR L 49 PHE 0.011 0.001 PHE H 64 TRP 0.006 0.001 TRP G 353 HIS 0.005 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 3488) covalent geometry : angle 0.62297 ( 4747) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.99289 ( 12) hydrogen bonds : bond 0.03986 ( 99) hydrogen bonds : angle 6.10211 ( 264) link_ALPHA1-3 : bond 0.00410 ( 1) link_ALPHA1-3 : angle 4.42213 ( 3) link_ALPHA1-6 : bond 0.00696 ( 1) link_ALPHA1-6 : angle 2.03359 ( 3) link_BETA1-4 : bond 0.00560 ( 2) link_BETA1-4 : angle 1.89074 ( 6) link_BETA1-6 : bond 0.00354 ( 1) link_BETA1-6 : angle 1.78661 ( 3) link_NAG-ASN : bond 0.00261 ( 1) link_NAG-ASN : angle 2.65426 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8591 (tp-100) REVERT: H 62 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8677 (tm-30) REVERT: H 82 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7963 (tm-30) REVERT: L 38 GLN cc_start: 0.8800 (tp40) cc_final: 0.8532 (tp40) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.1262 time to fit residues: 9.2563 Evaluate side-chains 62 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.058866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.048451 restraints weight = 33853.756| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.26 r_work: 0.2606 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3500 Z= 0.123 Angle : 0.541 5.026 4777 Z= 0.279 Chirality : 0.043 0.153 535 Planarity : 0.004 0.029 603 Dihedral : 6.882 48.430 582 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.37 % Allowed : 9.56 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.41), residues: 421 helix: -2.13 (1.08), residues: 20 sheet: -0.71 (0.43), residues: 151 loop : -1.08 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 454 TYR 0.006 0.001 TYR G 380 PHE 0.008 0.001 PHE H 64 TRP 0.004 0.001 TRP G 436 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3488) covalent geometry : angle 0.53004 ( 4747) SS BOND : bond 0.00167 ( 6) SS BOND : angle 0.81044 ( 12) hydrogen bonds : bond 0.03299 ( 99) hydrogen bonds : angle 5.88791 ( 264) link_ALPHA1-3 : bond 0.01003 ( 1) link_ALPHA1-3 : angle 2.63865 ( 3) link_ALPHA1-6 : bond 0.00707 ( 1) link_ALPHA1-6 : angle 1.63170 ( 3) link_BETA1-4 : bond 0.00427 ( 2) link_BETA1-4 : angle 1.39501 ( 6) link_BETA1-6 : bond 0.00181 ( 1) link_BETA1-6 : angle 1.21189 ( 3) link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 2.03284 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8505 (tp-100) REVERT: H 62 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8654 (tm-30) REVERT: H 82 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7862 (tm-30) REVERT: L 38 GLN cc_start: 0.8705 (tp40) cc_final: 0.8434 (tp40) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.1316 time to fit residues: 10.4751 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.049517 restraints weight = 34112.681| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.18 r_work: 0.2633 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3500 Z= 0.120 Angle : 0.524 5.144 4777 Z= 0.268 Chirality : 0.042 0.156 535 Planarity : 0.004 0.028 603 Dihedral : 5.997 46.891 582 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.37 % Allowed : 10.11 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.41), residues: 421 helix: -2.06 (1.09), residues: 20 sheet: -0.61 (0.44), residues: 152 loop : -1.00 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 105 TYR 0.026 0.001 TYR L 49 PHE 0.007 0.001 PHE H 64 TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3488) covalent geometry : angle 0.51249 ( 4747) SS BOND : bond 0.00157 ( 6) SS BOND : angle 0.75632 ( 12) hydrogen bonds : bond 0.02854 ( 99) hydrogen bonds : angle 5.70578 ( 264) link_ALPHA1-3 : bond 0.01188 ( 1) link_ALPHA1-3 : angle 2.27971 ( 3) link_ALPHA1-6 : bond 0.00267 ( 1) link_ALPHA1-6 : angle 1.67795 ( 3) link_BETA1-4 : bond 0.00351 ( 2) link_BETA1-4 : angle 1.53431 ( 6) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 1.28843 ( 3) link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 2.16865 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8580 (tp-100) REVERT: G 427 ASP cc_start: 0.8815 (m-30) cc_final: 0.8512 (p0) REVERT: H 62 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8614 (tm-30) REVERT: H 82 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7931 (tm-30) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.1303 time to fit residues: 10.1198 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.5784 > 50: distance: 137 - 185: 13.911 distance: 152 - 206: 6.415 distance: 175 - 185: 11.302 distance: 185 - 186: 5.763 distance: 185 - 197: 14.438 distance: 186 - 187: 9.094 distance: 186 - 189: 16.257 distance: 186 - 198: 6.315 distance: 187 - 188: 13.800 distance: 187 - 206: 12.934 distance: 189 - 199: 22.742 distance: 189 - 200: 18.569 distance: 190 - 191: 4.007 distance: 190 - 192: 7.414 distance: 191 - 193: 5.437 distance: 191 - 201: 4.588 distance: 192 - 194: 5.520 distance: 192 - 202: 5.356 distance: 193 - 195: 5.838 distance: 193 - 203: 4.696 distance: 194 - 204: 5.704 distance: 195 - 196: 12.121 distance: 196 - 205: 5.980 distance: 206 - 207: 4.872 distance: 206 - 214: 20.402 distance: 207 - 208: 6.395 distance: 207 - 210: 14.021 distance: 207 - 215: 7.881 distance: 208 - 209: 4.933 distance: 208 - 220: 10.228 distance: 210 - 211: 9.391 distance: 210 - 216: 10.692 distance: 210 - 217: 8.694 distance: 211 - 212: 14.281 distance: 211 - 213: 17.592 distance: 213 - 218: 7.012 distance: 213 - 219: 7.883 distance: 220 - 221: 10.262 distance: 220 - 232: 15.909 distance: 221 - 222: 6.255 distance: 221 - 224: 15.553 distance: 222 - 223: 16.341 distance: 222 - 241: 18.515 distance: 224 - 225: 4.416 distance: 224 - 234: 4.323 distance: 224 - 235: 3.031 distance: 225 - 227: 3.719 distance: 226 - 228: 6.808 distance: 227 - 229: 5.405 distance: 227 - 237: 3.402 distance: 228 - 230: 3.038 distance: 228 - 238: 3.573 distance: 229 - 239: 3.754 distance: 230 - 231: 5.274 distance: 231 - 240: 6.511 distance: 241 - 242: 21.207 distance: 241 - 250: 17.083 distance: 242 - 243: 6.209 distance: 242 - 245: 17.223 distance: 242 - 251: 14.713 distance: 243 - 244: 13.785 distance: 243 - 263: 16.988 distance: 245 - 246: 8.427 distance: 245 - 252: 5.828 distance: 245 - 253: 17.512 distance: 246 - 247: 7.380 distance: 246 - 254: 6.816 distance: 246 - 255: 5.147 distance: 247 - 248: 6.260 distance: 247 - 256: 4.039 distance: 247 - 257: 5.405 distance: 248 - 249: 7.266 distance: 248 - 259: 3.444 distance: 249 - 261: 3.743 distance: 263 - 264: 18.695 distance: 263 - 271: 24.468 distance: 264 - 265: 28.575 distance: 264 - 267: 25.555 distance: 264 - 272: 38.133 distance: 265 - 266: 23.659 distance: 265 - 282: 8.172 distance: 267 - 268: 18.922 distance: 267 - 273: 17.736 distance: 267 - 274: 15.682 distance: 268 - 269: 14.037 distance: 268 - 270: 12.247 distance: 268 - 275: 12.485 distance: 269 - 276: 9.111 distance: 269 - 277: 8.883 distance: 269 - 278: 8.774 distance: 270 - 279: 4.062 distance: 270 - 280: 9.556 distance: 270 - 281: 4.444 distance: 282 - 283: 11.863 distance: 282 - 288: 9.437 distance: 283 - 284: 14.100 distance: 283 - 286: 22.841 distance: 283 - 289: 15.080 distance: 284 - 285: 16.947 distance: 284 - 296: 27.814 distance: 286 - 287: 15.268 distance: 286 - 290: 18.102 distance: 286 - 291: 14.167 distance: 287 - 288: 20.292 distance: 288 - 294: 24.538 distance: 288 - 295: 8.757 distance: 296 - 297: 8.603 distance: 296 - 304: 20.155 distance: 297 - 298: 4.039 distance: 297 - 300: 7.265 distance: 297 - 305: 6.984 distance: 298 - 299: 4.139 distance: 298 - 308: 4.326 distance: 300 - 301: 8.207 distance: 300 - 306: 19.095 distance: 300 - 307: 5.517 distance: 301 - 302: 19.021 distance: 301 - 303: 12.706 distance: 308 - 309: 6.273 distance: 309 - 310: 4.991 distance: 309 - 312: 5.376 distance: 309 - 317: 12.324 distance: 310 - 311: 8.118 distance: 310 - 320: 3.110 distance: 312 - 313: 10.356 distance: 312 - 319: 4.001 distance: 313 - 314: 9.536 distance: 313 - 315: 15.710 distance: 320 - 321: 6.381 distance: 320 - 331: 5.630 distance: 321 - 322: 4.268 distance: 321 - 324: 3.047 distance: 321 - 332: 3.277 distance: 322 - 323: 15.940 distance: 322 - 340: 11.971 distance: 324 - 325: 5.759 distance: 324 - 333: 4.109 distance: 324 - 334: 5.387 distance: 326 - 328: 4.170 distance: 340 - 341: 7.007 distance: 340 - 347: 16.502 distance: 341 - 342: 3.994 distance: 341 - 344: 7.951 distance: 341 - 348: 12.178 distance: 342 - 343: 16.216 distance: 342 - 354: 9.239 distance: 344 - 346: 3.179 distance: 344 - 349: 3.795 distance: 345 - 350: 5.451 distance: 346 - 351: 7.628 distance: 346 - 352: 4.036 distance: 346 - 353: 4.719