Starting phenix.real_space_refine on Tue Apr 29 14:37:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc1_15959/04_2025/8bc1_15959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc1_15959/04_2025/8bc1_15959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bc1_15959/04_2025/8bc1_15959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc1_15959/04_2025/8bc1_15959.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc1_15959/04_2025/8bc1_15959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc1_15959/04_2025/8bc1_15959.cif" } resolution = 2.93 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= 0.019 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 Ca 6 9.91 5 S 62 5.16 5 C 5758 2.51 5 N 1366 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8684 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4339 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 7.62, per 1000 atoms: 0.88 Number of scatterers: 8684 At special positions: 0 Unit cell: (123.69, 79.422, 98.952, 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) Ca 6 19.99 S 62 16.00 O 1492 8.00 N 1366 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " 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: 2.16 Conformation dependent library (CDL) restraints added in 941.7 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.612A pdb=" N TYR A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.648A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.671A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.697A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 487 removed outlier: 4.235A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 539 removed outlier: 3.924A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 639 Proline residue: A 628 - end of helix removed outlier: 3.687A pdb=" N ARG A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.659A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.416A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.553A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 276 through 281 removed outlier: 4.614A pdb=" N TYR B 280 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.647A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.672A pdb=" N LEU B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.696A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 487 removed outlier: 4.234A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 539 removed outlier: 3.923A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 639 Proline residue: B 628 - end of helix removed outlier: 3.687A pdb=" N ARG B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.660A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.417A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.552A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1713 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: 2.36 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2590 1.35 - 1.46: 2389 1.46 - 1.58: 3853 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 8928 Sorted by residual: bond pdb=" CA VAL B 411 " pdb=" CB VAL B 411 " ideal model delta sigma weight residual 1.530 1.541 -0.010 1.05e-02 9.07e+03 9.92e-01 bond pdb=" CA VAL A 411 " pdb=" CB VAL A 411 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 8.51e-01 bond pdb=" CA ILE B 751 " pdb=" CB ILE B 751 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.43e-01 bond pdb=" CA ILE A 700 " pdb=" C ILE A 700 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.22e-02 6.72e+03 6.40e-01 bond pdb=" CA PHE A 685 " pdb=" CB PHE A 685 " ideal model delta sigma weight residual 1.532 1.544 -0.013 1.67e-02 3.59e+03 6.00e-01 ... (remaining 8923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 11780 1.11 - 2.22: 263 2.22 - 3.32: 71 3.32 - 4.43: 8 4.43 - 5.54: 8 Bond angle restraints: 12130 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 113.26 -2.56 1.22e+00 6.72e-01 4.40e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 113.23 -2.53 1.22e+00 6.72e-01 4.29e+00 angle pdb=" C TYR B 580 " pdb=" CA TYR B 580 " pdb=" CB TYR B 580 " ideal model delta sigma weight residual 109.22 112.23 -3.01 1.52e+00 4.33e-01 3.92e+00 angle pdb=" C TYR A 580 " pdb=" CA TYR A 580 " pdb=" CB TYR A 580 " ideal model delta sigma weight residual 109.22 112.20 -2.98 1.52e+00 4.33e-01 3.85e+00 angle pdb=" CA PRO B 763 " pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 117.93 120.18 -2.25 1.20e+00 6.94e-01 3.51e+00 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 4748 12.66 - 25.33: 336 25.33 - 37.99: 96 37.99 - 50.65: 32 50.65 - 63.31: 8 Dihedral angle restraints: 5220 sinusoidal: 2106 harmonic: 3114 Sorted by residual: dihedral pdb=" CA VAL A 625 " pdb=" C VAL A 625 " pdb=" N LEU A 626 " pdb=" CA LEU A 626 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA VAL B 625 " pdb=" C VAL B 625 " pdb=" N LEU B 626 " pdb=" CA LEU B 626 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N GLU B 395 " pdb=" CA GLU B 395 " pdb=" CB GLU B 395 " pdb=" CG GLU B 395 " ideal model delta sinusoidal sigma weight residual -60.00 -117.63 57.63 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 812 0.025 - 0.050: 276 0.050 - 0.075: 173 0.075 - 0.100: 63 0.100 - 0.125: 8 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO A 689 " pdb=" N PRO A 689 " pdb=" C PRO A 689 " pdb=" CB PRO A 689 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 1329 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 700 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ILE A 700 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 700 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG A 701 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 697 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C ILE B 697 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 697 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 698 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 697 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ILE A 697 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 697 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 698 " -0.008 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2201 2.79 - 3.32: 9052 3.32 - 3.85: 14674 3.85 - 4.37: 16711 4.37 - 4.90: 28388 Nonbonded interactions: 71026 Sorted by model distance: nonbonded pdb=" O LEU B 626 " pdb=" N VAL B 630 " model vdw 2.265 3.120 nonbonded pdb=" O LEU A 626 " pdb=" N VAL A 630 " model vdw 2.265 3.120 nonbonded pdb=" O THR B 364 " pdb=" OG SER B 367 " model vdw 2.273 3.040 nonbonded pdb=" O THR A 364 " pdb=" OG SER A 367 " model vdw 2.273 3.040 nonbonded pdb=" O SER A 376 " pdb=" OG1 THR A 379 " model vdw 2.281 3.040 ... (remaining 71021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Normalize map: mean=0, sd=1: 24.190 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.260 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 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 : 0.002 0.018 8936 Z= 0.112 Angle : 0.458 5.542 12146 Z= 0.261 Chirality : 0.036 0.125 1332 Planarity : 0.004 0.032 1486 Dihedral : 10.381 63.314 3196 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.43 % Allowed : 5.25 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1026 helix: 1.62 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.011 0.001 PHE B 393 TYR 0.011 0.001 TYR A 580 ARG 0.002 0.000 ARG B 592 Details of bonding type rmsd hydrogen bonds : bond 0.10487 ( 579) hydrogen bonds : angle 5.31130 ( 1713) SS BOND : bond 0.00181 ( 8) SS BOND : angle 0.74170 ( 16) covalent geometry : bond 0.00194 ( 8928) covalent geometry : angle 0.45784 (12130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8370 (mt) cc_final: 0.8006 (tp) REVERT: A 381 ILE cc_start: 0.6080 (mt) cc_final: 0.5828 (mt) REVERT: A 386 MET cc_start: 0.5095 (mmp) cc_final: 0.4500 (mmp) REVERT: A 530 LYS cc_start: 0.6932 (mmtm) cc_final: 0.6593 (mmmm) REVERT: A 595 GLU cc_start: 0.5110 (mp0) cc_final: 0.3651 (tm-30) REVERT: A 613 MET cc_start: 0.6979 (mtp) cc_final: 0.6312 (mtp) REVERT: A 638 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7104 (tmmt) REVERT: A 813 ARG cc_start: 0.4596 (mtt90) cc_final: 0.3334 (ppt170) REVERT: B 285 LEU cc_start: 0.8377 (mt) cc_final: 0.8019 (tp) REVERT: B 381 ILE cc_start: 0.6065 (mt) cc_final: 0.5805 (mt) REVERT: B 386 MET cc_start: 0.5120 (mmp) cc_final: 0.4486 (mmp) REVERT: B 507 MET cc_start: 0.5033 (ttm) cc_final: 0.4176 (tpp) REVERT: B 530 LYS cc_start: 0.6927 (mmtm) cc_final: 0.6587 (mmmm) REVERT: B 595 GLU cc_start: 0.5123 (mp0) cc_final: 0.3668 (tm-30) REVERT: B 613 MET cc_start: 0.6980 (mtp) cc_final: 0.6311 (mtp) REVERT: B 638 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7140 (tmmt) REVERT: B 813 ARG cc_start: 0.4723 (mtt90) cc_final: 0.3329 (ppt170) outliers start: 32 outliers final: 3 residues processed: 280 average time/residue: 0.9521 time to fit residues: 289.6850 Evaluate side-chains 170 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.0020 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 730 GLN A 814 ASN A 830 HIS B 401 GLN B 559 GLN B 632 ASN B 730 GLN B 814 ASN B 830 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.269961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.248916 restraints weight = 14181.110| |-----------------------------------------------------------------------------| r_work (start): 0.5064 rms_B_bonded: 2.53 r_work: 0.4976 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8936 Z= 0.161 Angle : 0.654 10.985 12146 Z= 0.338 Chirality : 0.042 0.163 1332 Planarity : 0.005 0.045 1486 Dihedral : 4.291 42.945 1172 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.64 % Allowed : 14.99 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1026 helix: 1.61 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.41 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 408 HIS 0.020 0.002 HIS B 844 PHE 0.013 0.001 PHE B 558 TYR 0.015 0.001 TYR A 668 ARG 0.004 0.001 ARG B 592 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 579) hydrogen bonds : angle 4.66450 ( 1713) SS BOND : bond 0.00425 ( 8) SS BOND : angle 2.72050 ( 16) covalent geometry : bond 0.00367 ( 8928) covalent geometry : angle 0.64673 (12130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6319 (mt) cc_final: 0.6032 (mt) REVERT: A 553 MET cc_start: 0.6826 (tmt) cc_final: 0.6372 (tmm) REVERT: A 595 GLU cc_start: 0.4783 (mp0) cc_final: 0.3307 (tm-30) REVERT: A 613 MET cc_start: 0.6999 (mtp) cc_final: 0.6279 (ttm) REVERT: A 638 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7065 (tmmt) REVERT: A 813 ARG cc_start: 0.4741 (mtt90) cc_final: 0.3251 (ppt170) REVERT: B 381 ILE cc_start: 0.6359 (mt) cc_final: 0.6068 (mt) REVERT: B 553 MET cc_start: 0.6807 (tmt) cc_final: 0.6355 (tmm) REVERT: B 595 GLU cc_start: 0.4800 (mp0) cc_final: 0.3322 (tm-30) REVERT: B 613 MET cc_start: 0.6988 (mtp) cc_final: 0.6296 (ttm) REVERT: B 638 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7087 (tmmt) REVERT: B 813 ARG cc_start: 0.4799 (mtt90) cc_final: 0.3311 (ppt170) outliers start: 34 outliers final: 8 residues processed: 205 average time/residue: 1.0012 time to fit residues: 221.6851 Evaluate side-chains 148 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.266862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.245935 restraints weight = 14141.493| |-----------------------------------------------------------------------------| r_work (start): 0.5020 rms_B_bonded: 2.63 r_work: 0.4930 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8936 Z= 0.164 Angle : 0.657 9.655 12146 Z= 0.334 Chirality : 0.041 0.150 1332 Planarity : 0.005 0.049 1486 Dihedral : 4.431 42.315 1172 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.18 % Allowed : 18.31 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1026 helix: 1.51 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 408 HIS 0.013 0.002 HIS A 844 PHE 0.026 0.001 PHE A 558 TYR 0.015 0.001 TYR B 528 ARG 0.013 0.001 ARG B 810 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 579) hydrogen bonds : angle 4.56301 ( 1713) SS BOND : bond 0.00188 ( 8) SS BOND : angle 2.72965 ( 16) covalent geometry : bond 0.00364 ( 8928) covalent geometry : angle 0.65033 (12130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.999 Fit side-chains REVERT: A 294 GLU cc_start: 0.4475 (mm-30) cc_final: 0.4141 (mp0) REVERT: A 381 ILE cc_start: 0.6364 (mt) cc_final: 0.6071 (mt) REVERT: A 553 MET cc_start: 0.6717 (tmt) cc_final: 0.6212 (tmm) REVERT: A 595 GLU cc_start: 0.5016 (mp0) cc_final: 0.3514 (tm-30) REVERT: A 604 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6957 (mt-10) REVERT: A 613 MET cc_start: 0.7174 (mtp) cc_final: 0.6465 (mtp) REVERT: A 638 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7234 (tmmt) REVERT: A 813 ARG cc_start: 0.4695 (mtt90) cc_final: 0.3272 (ppt170) REVERT: B 294 GLU cc_start: 0.4469 (mm-30) cc_final: 0.4136 (mp0) REVERT: B 310 LEU cc_start: 0.5076 (mt) cc_final: 0.4805 (mt) REVERT: B 381 ILE cc_start: 0.6363 (mt) cc_final: 0.6069 (mt) REVERT: B 553 MET cc_start: 0.6711 (tmt) cc_final: 0.6209 (tmm) REVERT: B 595 GLU cc_start: 0.4994 (mp0) cc_final: 0.3502 (tm-30) REVERT: B 604 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6806 (mt-10) REVERT: B 613 MET cc_start: 0.7177 (mtp) cc_final: 0.6605 (mtp) REVERT: B 638 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7268 (tmmt) REVERT: B 813 ARG cc_start: 0.4852 (mtt90) cc_final: 0.3302 (ppt170) outliers start: 39 outliers final: 17 residues processed: 193 average time/residue: 0.8909 time to fit residues: 187.4527 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.268501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.247288 restraints weight = 14123.561| |-----------------------------------------------------------------------------| r_work (start): 0.5034 rms_B_bonded: 2.70 r_work: 0.4938 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8936 Z= 0.149 Angle : 0.668 13.540 12146 Z= 0.328 Chirality : 0.041 0.144 1332 Planarity : 0.005 0.049 1486 Dihedral : 4.400 42.699 1172 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.14 % Allowed : 17.77 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1026 helix: 1.42 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.64 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 408 HIS 0.008 0.001 HIS A 844 PHE 0.027 0.001 PHE A 558 TYR 0.018 0.001 TYR A 306 ARG 0.008 0.000 ARG B 810 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 579) hydrogen bonds : angle 4.57839 ( 1713) SS BOND : bond 0.00394 ( 8) SS BOND : angle 3.26223 ( 16) covalent geometry : bond 0.00321 ( 8928) covalent geometry : angle 0.65814 (12130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6940 (tmt90) REVERT: A 306 TYR cc_start: 0.6707 (t80) cc_final: 0.6500 (t80) REVERT: A 381 ILE cc_start: 0.6341 (mt) cc_final: 0.6040 (mt) REVERT: A 553 MET cc_start: 0.6686 (tmt) cc_final: 0.6177 (tmm) REVERT: A 595 GLU cc_start: 0.5071 (mp0) cc_final: 0.3395 (tm-30) REVERT: A 604 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6889 (mt-10) REVERT: A 613 MET cc_start: 0.7202 (mtp) cc_final: 0.6616 (mtp) REVERT: A 638 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7134 (tmmt) REVERT: A 699 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: A 813 ARG cc_start: 0.4766 (mtt90) cc_final: 0.3237 (ppt170) REVERT: B 294 GLU cc_start: 0.4767 (mm-30) cc_final: 0.4277 (mp0) REVERT: B 381 ILE cc_start: 0.6340 (mt) cc_final: 0.6037 (mt) REVERT: B 408 TRP cc_start: 0.6552 (m-10) cc_final: 0.6347 (m-10) REVERT: B 553 MET cc_start: 0.6683 (tmt) cc_final: 0.6391 (tmt) REVERT: B 595 GLU cc_start: 0.4787 (mp0) cc_final: 0.3257 (tm-30) REVERT: B 604 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6841 (mt-10) REVERT: B 613 MET cc_start: 0.7204 (mtp) cc_final: 0.6608 (mtp) REVERT: B 638 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7170 (tmmt) REVERT: B 699 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: B 813 ARG cc_start: 0.5065 (mtt90) cc_final: 0.3381 (ppt170) outliers start: 48 outliers final: 13 residues processed: 205 average time/residue: 0.8466 time to fit residues: 189.8272 Evaluate side-chains 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.266353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.243964 restraints weight = 14151.584| |-----------------------------------------------------------------------------| r_work (start): 0.5018 rms_B_bonded: 2.78 r_work: 0.4916 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8936 Z= 0.159 Angle : 0.682 12.324 12146 Z= 0.339 Chirality : 0.042 0.153 1332 Planarity : 0.005 0.052 1486 Dihedral : 4.350 41.051 1170 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.28 % Allowed : 20.02 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1026 helix: 1.43 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 408 HIS 0.005 0.001 HIS B 844 PHE 0.032 0.002 PHE A 558 TYR 0.017 0.001 TYR B 306 ARG 0.004 0.001 ARG B 649 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 579) hydrogen bonds : angle 4.57524 ( 1713) SS BOND : bond 0.00309 ( 8) SS BOND : angle 1.53478 ( 16) covalent geometry : bond 0.00364 ( 8928) covalent geometry : angle 0.68058 (12130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6847 (tmt90) REVERT: A 294 GLU cc_start: 0.4644 (mm-30) cc_final: 0.4357 (mp0) REVERT: A 381 ILE cc_start: 0.6425 (mt) cc_final: 0.6118 (mt) REVERT: A 534 MET cc_start: 0.6749 (mmt) cc_final: 0.6512 (mmt) REVERT: A 553 MET cc_start: 0.6784 (tmt) cc_final: 0.6281 (tmm) REVERT: A 592 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.5318 (tmm-80) REVERT: A 595 GLU cc_start: 0.4486 (mp0) cc_final: 0.3151 (tm-30) REVERT: A 604 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6905 (mt-10) REVERT: A 611 ILE cc_start: 0.7523 (mm) cc_final: 0.7317 (mm) REVERT: A 613 MET cc_start: 0.6954 (mtp) cc_final: 0.6366 (mtp) REVERT: A 638 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7130 (tmmt) REVERT: A 699 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6697 (tp30) REVERT: A 813 ARG cc_start: 0.4718 (mtt90) cc_final: 0.3120 (ppt170) REVERT: B 289 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7246 (tmt90) REVERT: B 294 GLU cc_start: 0.4700 (mm-30) cc_final: 0.4449 (mp0) REVERT: B 381 ILE cc_start: 0.6381 (mt) cc_final: 0.6078 (mt) REVERT: B 534 MET cc_start: 0.6781 (mmt) cc_final: 0.6545 (mmt) REVERT: B 553 MET cc_start: 0.6740 (tmt) cc_final: 0.6231 (tmm) REVERT: B 592 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5394 (tmm-80) REVERT: B 595 GLU cc_start: 0.4800 (mp0) cc_final: 0.3080 (tm-30) REVERT: B 604 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6812 (mt-10) REVERT: B 613 MET cc_start: 0.7185 (mtp) cc_final: 0.6636 (mtp) REVERT: B 638 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7172 (tmmt) REVERT: B 699 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: B 813 ARG cc_start: 0.4833 (mtt90) cc_final: 0.3136 (ppt170) outliers start: 40 outliers final: 14 residues processed: 186 average time/residue: 0.9027 time to fit residues: 182.5534 Evaluate side-chains 166 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.264605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.243513 restraints weight = 13933.499| |-----------------------------------------------------------------------------| r_work (start): 0.5010 rms_B_bonded: 2.60 r_work: 0.4909 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8936 Z= 0.162 Angle : 0.709 15.666 12146 Z= 0.349 Chirality : 0.043 0.187 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.484 41.314 1170 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.64 % Allowed : 21.52 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1026 helix: 1.35 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.88 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 408 HIS 0.005 0.001 HIS B 844 PHE 0.031 0.002 PHE A 558 TYR 0.019 0.001 TYR A 528 ARG 0.007 0.001 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 579) hydrogen bonds : angle 4.63734 ( 1713) SS BOND : bond 0.00521 ( 8) SS BOND : angle 3.33313 ( 16) covalent geometry : bond 0.00373 ( 8928) covalent geometry : angle 0.69918 (12130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.467 Fit side-chains REVERT: A 294 GLU cc_start: 0.4630 (mm-30) cc_final: 0.4274 (mp0) REVERT: A 381 ILE cc_start: 0.6378 (mt) cc_final: 0.6076 (mt) REVERT: A 408 TRP cc_start: 0.6562 (m-10) cc_final: 0.6360 (m100) REVERT: A 553 MET cc_start: 0.6860 (tmt) cc_final: 0.6354 (tmm) REVERT: A 595 GLU cc_start: 0.4482 (mp0) cc_final: 0.3123 (tm-30) REVERT: A 604 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6904 (mt-10) REVERT: A 613 MET cc_start: 0.6841 (mtp) cc_final: 0.6318 (mtp) REVERT: A 638 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7133 (tmmt) REVERT: A 699 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: A 813 ARG cc_start: 0.4828 (mtt90) cc_final: 0.3159 (ppt170) REVERT: B 294 GLU cc_start: 0.4533 (mm-30) cc_final: 0.4101 (mp0) REVERT: B 381 ILE cc_start: 0.6410 (mt) cc_final: 0.6100 (mt) REVERT: B 408 TRP cc_start: 0.6625 (m-10) cc_final: 0.6400 (m100) REVERT: B 553 MET cc_start: 0.6865 (tmt) cc_final: 0.6323 (tmm) REVERT: B 595 GLU cc_start: 0.4477 (mp0) cc_final: 0.3081 (tm-30) REVERT: B 604 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6814 (mt-10) REVERT: B 613 MET cc_start: 0.6943 (mtp) cc_final: 0.6402 (mtp) REVERT: B 638 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7233 (tmmt) REVERT: B 699 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: B 813 ARG cc_start: 0.4804 (mtt90) cc_final: 0.3146 (ppt170) REVERT: B 842 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7333 (mpp) outliers start: 34 outliers final: 14 residues processed: 179 average time/residue: 1.1609 time to fit residues: 225.0692 Evaluate side-chains 166 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 60.6537 > 50: distance: 69 - 80: 3.122 distance: 117 - 134: 9.619 distance: 121 - 142: 26.005 distance: 127 - 149: 32.558 distance: 131 - 134: 12.747 distance: 132 - 157: 31.683 distance: 134 - 135: 33.558 distance: 135 - 136: 15.637 distance: 135 - 138: 30.236 distance: 136 - 137: 34.375 distance: 136 - 142: 18.405 distance: 137 - 165: 32.509 distance: 138 - 139: 11.697 distance: 139 - 140: 14.451 distance: 139 - 141: 50.353 distance: 142 - 143: 25.591 distance: 143 - 144: 40.332 distance: 143 - 146: 19.328 distance: 144 - 145: 28.427 distance: 144 - 149: 50.345 distance: 145 - 173: 10.017 distance: 146 - 147: 24.356 distance: 146 - 148: 26.287 distance: 149 - 150: 25.616 distance: 150 - 151: 16.369 distance: 150 - 153: 21.691 distance: 151 - 152: 12.673 distance: 151 - 157: 31.616 distance: 152 - 181: 38.133 distance: 153 - 154: 16.096 distance: 154 - 155: 7.453 distance: 154 - 156: 19.223 distance: 157 - 158: 37.872 distance: 158 - 159: 34.356 distance: 158 - 161: 25.407 distance: 159 - 160: 20.620 distance: 159 - 165: 34.193 distance: 160 - 190: 31.545 distance: 161 - 162: 5.723 distance: 162 - 163: 4.009 distance: 165 - 166: 37.142 distance: 166 - 167: 5.633 distance: 166 - 169: 19.405 distance: 167 - 168: 12.655 distance: 167 - 173: 13.738 distance: 169 - 170: 14.002 distance: 169 - 171: 27.116 distance: 170 - 172: 25.603 distance: 173 - 174: 10.179 distance: 174 - 175: 13.779 distance: 174 - 177: 7.517 distance: 175 - 176: 29.081 distance: 175 - 181: 11.797 distance: 176 - 209: 21.008 distance: 177 - 178: 23.710 distance: 178 - 179: 17.805 distance: 178 - 180: 14.981 distance: 181 - 182: 12.036 distance: 182 - 183: 18.449 distance: 182 - 185: 24.951 distance: 183 - 184: 28.302 distance: 183 - 190: 37.977 distance: 184 - 216: 20.979 distance: 185 - 186: 36.884 distance: 186 - 187: 11.307 distance: 187 - 188: 14.943 distance: 187 - 189: 18.024 distance: 190 - 191: 26.045 distance: 191 - 192: 22.064 distance: 191 - 194: 23.176 distance: 192 - 193: 15.375 distance: 192 - 198: 24.090 distance: 193 - 224: 25.036 distance: 194 - 195: 21.303 distance: 194 - 196: 24.350 distance: 195 - 197: 25.010 distance: 198 - 199: 27.792 distance: 199 - 200: 28.655 distance: 199 - 202: 29.521 distance: 200 - 201: 21.290 distance: 200 - 209: 17.006 distance: 201 - 229: 23.025 distance: 202 - 203: 23.365 distance: 203 - 204: 16.406 distance: 204 - 205: 16.961 distance: 205 - 206: 15.806 distance: 206 - 207: 10.559 distance: 206 - 208: 16.101 distance: 209 - 210: 25.125 distance: 210 - 211: 30.554 distance: 210 - 213: 23.576 distance: 211 - 212: 28.529 distance: 211 - 216: 21.375 distance: 212 - 235: 35.510 distance: 213 - 214: 44.724 distance: 213 - 215: 26.086