Starting phenix.real_space_refine on Tue Mar 11 16:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrv_32736/03_2025/7wrv_32736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrv_32736/03_2025/7wrv_32736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2025/7wrv_32736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2025/7wrv_32736.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2025/7wrv_32736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrv_32736/03_2025/7wrv_32736_neut.cif" } resolution = 2.47 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= -0.001 sd= 0.060 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 16 5.16 5 C 2087 2.51 5 N 543 2.21 5 O 621 1.98 5 H 3092 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6359 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 2966 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 186} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "U" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1814 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "V" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1579 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 7.78, per 1000 atoms: 1.22 Number of scatterers: 6359 At special positions: 0 Unit cell: (80.752, 60.976, 90.64, 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 16 16.00 O 621 8.00 N 543 7.00 C 2087 6.00 H 3092 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 290 " - pdb=" SG CYS V 355 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 690.6 milliseconds 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: 786 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 13.3% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.704A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.105A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.859A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'V' and resid 346 through 350 Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'U' and resid 10 through 12 removed outlier: 7.093A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.163A pdb=" N ILE U 112 " --> pdb=" O SER U 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 271 through 274 removed outlier: 5.298A pdb=" N THR V 336 " --> pdb=" O ALA V 292 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N GLN V 294 " --> pdb=" O SER V 334 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N SER V 334 " --> pdb=" O GLN V 294 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE V 296 " --> pdb=" O SER V 332 " (cutoff:3.500A) removed outlier: 11.711A pdb=" N SER V 332 " --> pdb=" O ILE V 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 277 through 279 removed outlier: 6.729A pdb=" N TRP V 302 " --> pdb=" O LEU V 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 277 through 279 removed outlier: 3.513A pdb=" N THR V 364 " --> pdb=" O GLN V 357 " (cutoff:3.500A) 118 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: 2.30 Time building geometry restraints manager: 2.00 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: 3092 1.03 - 1.23: 0 1.23 - 1.42: 1483 1.42 - 1.62: 1849 1.62 - 1.81: 20 Bond restraints: 6444 Sorted by residual: bond pdb=" N GLU U 107 " pdb=" H GLU U 107 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.82e+00 bond pdb=" N GLU U 107 " pdb=" CA GLU U 107 " ideal model delta sigma weight residual 1.456 1.482 -0.027 1.44e-02 4.82e+03 3.44e+00 bond pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ASN C 331 " pdb=" H ASN C 331 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CB MET U 81 " pdb=" CG MET U 81 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 6439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11474 2.03 - 4.07: 77 4.07 - 6.10: 3 6.10 - 8.14: 1 8.14 - 10.17: 1 Bond angle restraints: 11556 Sorted by residual: angle pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " pdb=" CD GLU U 107 " ideal model delta sigma weight residual 112.60 122.77 -10.17 1.70e+00 3.46e-01 3.58e+01 angle pdb=" CA GLU U 107 " pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " ideal model delta sigma weight residual 114.10 108.35 5.75 2.00e+00 2.50e-01 8.25e+00 angle pdb=" CA GLU U 107 " pdb=" C GLU U 107 " pdb=" O GLU U 107 " ideal model delta sigma weight residual 121.49 118.50 2.99 1.16e+00 7.43e-01 6.64e+00 angle pdb=" CB MET U 81 " pdb=" CG MET U 81 " pdb=" SD MET U 81 " ideal model delta sigma weight residual 112.70 119.95 -7.25 3.00e+00 1.11e-01 5.84e+00 angle pdb=" N ILE C 410 " pdb=" CA ILE C 410 " pdb=" C ILE C 410 " ideal model delta sigma weight residual 106.21 108.78 -2.57 1.07e+00 8.73e-01 5.78e+00 ... (remaining 11551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.08: 2848 19.08 - 38.16: 187 38.16 - 57.24: 81 57.24 - 76.33: 5 76.33 - 95.41: 5 Dihedral angle restraints: 3126 sinusoidal: 1617 harmonic: 1509 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -161.72 75.72 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS U 22 " pdb=" SG CYS U 22 " pdb=" SG CYS U 96 " pdb=" CB CYS U 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.92 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " pdb=" CD GLU U 107 " pdb=" OE1 GLU U 107 " ideal model delta sinusoidal sigma weight residual 0.00 95.41 -95.41 1 3.00e+01 1.11e-03 1.17e+01 ... (remaining 3123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 375 0.040 - 0.079: 71 0.079 - 0.119: 42 0.119 - 0.159: 8 0.159 - 0.198: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA GLU U 107 " pdb=" N GLU U 107 " pdb=" C GLU U 107 " pdb=" CB GLU U 107 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CA ILE U 52 " pdb=" N ILE U 52 " pdb=" C ILE U 52 " pdb=" CB ILE U 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE V 342 " pdb=" N ILE V 342 " pdb=" C ILE V 342 " pdb=" CB ILE V 342 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 494 not shown) Planarity restraints: 991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU U 107 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CD GLU U 107 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU U 107 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU U 107 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 285 " -0.135 9.50e-02 1.11e+02 4.55e-02 2.89e+00 pdb=" NE ARG V 285 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG V 285 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG V 285 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG V 285 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG V 285 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG V 285 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG V 285 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG V 285 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP U 106 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C TRP U 106 " -0.022 2.00e-02 2.50e+03 pdb=" O TRP U 106 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU U 107 " 0.007 2.00e-02 2.50e+03 ... (remaining 988 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 453 2.21 - 2.81: 12881 2.81 - 3.40: 16507 3.40 - 4.00: 22758 4.00 - 4.60: 34243 Nonbonded interactions: 86842 Sorted by model distance: nonbonded pdb=" O GLY U 26 " pdb=" HH TYR U 32 " model vdw 1.611 2.450 nonbonded pdb=" OD1 ASP C 442 " pdb=" HH TYR C 451 " model vdw 1.644 2.450 nonbonded pdb=" HG2 GLU U 10 " pdb=" HE2 LYS U 12 " model vdw 1.682 2.440 nonbonded pdb="HH22 ARG C 454 " pdb=" O SER C 469 " model vdw 1.725 2.450 nonbonded pdb=" HG1 THR C 376 " pdb=" O ALA C 435 " model vdw 1.737 2.450 ... (remaining 86837 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: 7.710 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 3352 Z= 0.161 Angle : 0.601 10.169 4564 Z= 0.338 Chirality : 0.044 0.198 497 Planarity : 0.004 0.061 588 Dihedral : 14.423 95.407 1165 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.58 % Allowed : 10.14 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.41), residues: 421 helix: -2.90 (1.06), residues: 21 sheet: 1.01 (0.43), residues: 164 loop : -0.07 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 299 HIS 0.001 0.000 HIS C 519 PHE 0.007 0.001 PHE C 490 TYR 0.021 0.001 TYR V 316 ARG 0.014 0.001 ARG V 285 *********************** 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 **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4841 (tttt) cc_final: 0.3259 (ttpt) REVERT: V 349 ASP cc_start: 0.6610 (m-30) cc_final: 0.6350 (m-30) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 2.5719 time to fit residues: 195.5880 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 ASN C 505 HIS U 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.176681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.160870 restraints weight = 14255.103| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.88 r_work: 0.4058 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3352 Z= 0.226 Angle : 0.556 4.349 4564 Z= 0.302 Chirality : 0.046 0.149 497 Planarity : 0.004 0.031 588 Dihedral : 4.639 16.547 467 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.32 % Allowed : 14.78 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.41), residues: 421 helix: -3.17 (0.94), residues: 21 sheet: 0.94 (0.42), residues: 164 loop : -0.25 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.011 0.001 PHE V 340 TYR 0.013 0.002 TYR V 316 ARG 0.003 0.001 ARG C 403 *********************** 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 **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.5020 (OUTLIER) cc_final: 0.3291 (ttpt) REVERT: U 12 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6681 (mmmm) REVERT: U 87 ARG cc_start: 0.6985 (ptt90) cc_final: 0.6772 (mtm-85) REVERT: U 112 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8147 (mp) REVERT: V 349 ASP cc_start: 0.7023 (m-30) cc_final: 0.6799 (m-30) REVERT: V 372 GLU cc_start: 0.4955 (tp30) cc_final: 0.4696 (tm-30) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 2.7348 time to fit residues: 171.3761 Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN U 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.174518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158812 restraints weight = 14371.969| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.88 r_work: 0.4037 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3352 Z= 0.203 Angle : 0.530 4.000 4564 Z= 0.285 Chirality : 0.045 0.140 497 Planarity : 0.004 0.025 588 Dihedral : 4.729 17.655 467 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.32 % Allowed : 16.23 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.41), residues: 421 helix: -3.59 (1.24), residues: 14 sheet: 0.74 (0.42), residues: 164 loop : -0.58 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.012 0.001 PHE C 377 TYR 0.014 0.002 TYR V 316 ARG 0.002 0.000 ARG C 403 *********************** 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 **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4944 (tttt) cc_final: 0.3040 (ttmt) REVERT: U 48 MET cc_start: 0.7223 (mtp) cc_final: 0.7015 (mtp) REVERT: U 87 ARG cc_start: 0.6968 (ptt90) cc_final: 0.6764 (mtm-85) REVERT: U 112 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8110 (mp) REVERT: V 349 ASP cc_start: 0.7075 (m-30) cc_final: 0.6848 (m-30) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 2.2602 time to fit residues: 137.7385 Evaluate side-chains 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.172073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.157235 restraints weight = 14718.279| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.79 r_work: 0.4034 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3352 Z= 0.242 Angle : 0.547 4.101 4564 Z= 0.295 Chirality : 0.046 0.140 497 Planarity : 0.004 0.026 588 Dihedral : 4.923 17.767 467 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.90 % Allowed : 17.10 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.40), residues: 421 helix: -3.61 (1.21), residues: 14 sheet: 0.66 (0.42), residues: 159 loop : -0.79 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.012 0.002 PHE C 490 TYR 0.018 0.002 TYR V 316 ARG 0.002 0.000 ARG C 457 *********************** 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 **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4992 (tttt) cc_final: 0.3057 (ttpt) REVERT: U 48 MET cc_start: 0.7456 (mtp) cc_final: 0.7159 (mtp) REVERT: U 65 GLN cc_start: 0.6566 (tp-100) cc_final: 0.6330 (tp40) REVERT: U 81 MET cc_start: 0.7863 (tmm) cc_final: 0.7652 (tmm) REVERT: U 112 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7954 (mp) REVERT: V 349 ASP cc_start: 0.7215 (m-30) cc_final: 0.6942 (m-30) REVERT: V 372 GLU cc_start: 0.5057 (OUTLIER) cc_final: 0.4509 (tm-30) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 2.2590 time to fit residues: 130.6756 Evaluate side-chains 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 297 SER Chi-restraints excluded: chain V residue 372 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7554 > 50: distance: 136 - 181: 26.493 distance: 143 - 193: 29.347 distance: 155 - 214: 26.211 distance: 173 - 181: 25.234 distance: 181 - 182: 13.741 distance: 181 - 189: 26.212 distance: 182 - 183: 30.212 distance: 182 - 185: 23.461 distance: 182 - 190: 9.843 distance: 183 - 184: 5.313 distance: 183 - 193: 63.643 distance: 185 - 186: 26.736 distance: 185 - 191: 31.592 distance: 185 - 192: 15.753 distance: 186 - 187: 40.189 distance: 186 - 188: 35.925 distance: 194 - 195: 15.020 distance: 194 - 197: 14.456 distance: 194 - 206: 5.074 distance: 195 - 196: 45.967 distance: 195 - 214: 16.015 distance: 197 - 198: 7.371 distance: 197 - 207: 19.837 distance: 197 - 208: 16.840 distance: 198 - 199: 26.783 distance: 198 - 200: 7.562 distance: 199 - 201: 9.890 distance: 199 - 209: 7.724 distance: 200 - 202: 15.881 distance: 200 - 210: 9.360 distance: 201 - 203: 12.546 distance: 201 - 211: 16.841 distance: 202 - 203: 11.447 distance: 202 - 212: 5.318 distance: 203 - 204: 16.097 distance: 204 - 213: 23.236 distance: 214 - 215: 16.024 distance: 214 - 222: 28.229 distance: 215 - 216: 15.934 distance: 215 - 218: 23.755 distance: 215 - 223: 32.170 distance: 216 - 217: 20.498 distance: 216 - 228: 24.424 distance: 218 - 219: 18.539 distance: 218 - 224: 14.118 distance: 218 - 225: 12.818 distance: 219 - 220: 11.695 distance: 219 - 221: 16.204 distance: 221 - 226: 9.044 distance: 221 - 227: 3.170 distance: 228 - 229: 20.207 distance: 228 - 240: 35.373 distance: 229 - 230: 16.235 distance: 229 - 232: 24.722 distance: 229 - 241: 32.672 distance: 230 - 231: 13.211 distance: 230 - 249: 16.066 distance: 232 - 233: 17.799 distance: 232 - 242: 22.572 distance: 232 - 243: 18.587 distance: 233 - 234: 8.295 distance: 233 - 235: 16.833 distance: 234 - 236: 6.677 distance: 234 - 244: 12.837 distance: 235 - 245: 7.854 distance: 236 - 238: 10.955 distance: 236 - 246: 5.703 distance: 237 - 238: 9.092 distance: 237 - 247: 5.832 distance: 238 - 239: 11.195 distance: 239 - 248: 7.469 distance: 249 - 250: 29.529 distance: 249 - 258: 11.873 distance: 250 - 251: 44.704 distance: 250 - 253: 44.920 distance: 250 - 259: 15.724 distance: 251 - 252: 24.617 distance: 253 - 254: 12.972 distance: 253 - 261: 31.545 distance: 254 - 255: 24.639 distance: 254 - 262: 6.863 distance: 254 - 263: 13.792 distance: 255 - 256: 8.308 distance: 255 - 264: 11.244 distance: 255 - 265: 5.413 distance: 256 - 257: 4.906 distance: 256 - 266: 7.426 distance: 257 - 268: 14.442 distance: 257 - 269: 7.928 distance: 257 - 270: 5.207 distance: 271 - 272: 24.447 distance: 271 - 279: 60.534 distance: 272 - 273: 32.018 distance: 272 - 275: 9.093 distance: 272 - 280: 55.475 distance: 273 - 274: 39.837 distance: 273 - 290: 46.840 distance: 275 - 276: 6.898 distance: 275 - 282: 38.784 distance: 276 - 277: 12.728 distance: 276 - 278: 34.962 distance: 276 - 283: 15.557 distance: 277 - 284: 23.277 distance: 277 - 285: 10.581 distance: 277 - 286: 4.033 distance: 278 - 287: 8.880 distance: 278 - 288: 8.946 distance: 278 - 289: 5.583 distance: 290 - 291: 19.619 distance: 290 - 296: 9.647 distance: 291 - 292: 25.538 distance: 291 - 294: 26.376 distance: 291 - 297: 21.821 distance: 292 - 293: 29.161 distance: 292 - 304: 56.361 distance: 294 - 295: 17.706 distance: 294 - 298: 28.637 distance: 294 - 299: 9.110 distance: 295 - 296: 31.418 distance: 295 - 300: 36.133 distance: 296 - 303: 5.430 distance: 304 - 305: 20.197 distance: 305 - 306: 23.097 distance: 305 - 308: 33.770 distance: 305 - 310: 14.930 distance: 306 - 307: 20.803 distance: 306 - 311: 24.490 distance: 311 - 312: 20.721 distance: 311 - 319: 16.857 distance: 312 - 313: 6.616 distance: 312 - 315: 10.902 distance: 312 - 320: 14.303 distance: 313 - 314: 6.814 distance: 313 - 323: 61.585 distance: 315 - 316: 35.090 distance: 315 - 321: 14.059 distance: 315 - 322: 11.532 distance: 316 - 317: 9.366 distance: 316 - 318: 30.974 distance: 323 - 324: 17.453 distance: 323 - 334: 5.704 distance: 324 - 325: 15.891 distance: 324 - 327: 22.526 distance: 324 - 335: 11.162 distance: 325 - 343: 34.837 distance: 327 - 328: 17.401 distance: 327 - 336: 19.780 distance: 328 - 329: 20.506 distance: 328 - 330: 8.184 distance: 329 - 331: 17.037 distance: 329 - 338: 14.524 distance: 330 - 332: 21.535 distance: 330 - 339: 10.783 distance: 331 - 333: 11.480 distance: 331 - 340: 20.472 distance: 332 - 333: 5.134 distance: 332 - 341: 8.214 distance: 333 - 342: 5.406