Starting phenix.real_space_refine on Sat Apr 26 21:16:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lx5_23566/04_2025/7lx5_23566.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lx5_23566/04_2025/7lx5_23566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lx5_23566/04_2025/7lx5_23566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lx5_23566/04_2025/7lx5_23566.map" model { file = "/net/cci-nas-00/data/ceres_data/7lx5_23566/04_2025/7lx5_23566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lx5_23566/04_2025/7lx5_23566.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2206 2.51 5 N 591 2.21 5 O 669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3485 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 951 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Time building chain proxies: 2.55, per 1000 atoms: 0.73 Number of scatterers: 3485 At special positions: 0 Unit cell: (61.92, 80.84, 99.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 669 8.00 N 591 7.00 C 2206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 112 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " 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: 0.83 Conformation dependent library (CDL) restraints added in 640.3 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 14.1% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.526A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.313A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.330A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.776A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.577A pdb=" N MET C 117 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.971A pdb=" N ARG A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.537A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 375 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 110 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 112 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 117 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.537A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 375 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 110 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 112 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 92 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.521A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 34 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR C 32 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR C 119 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.521A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 34 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR C 32 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 23 " --> pdb=" O GLN A 5 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 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: 0.97 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1125 1.34 - 1.46: 961 1.46 - 1.58: 1465 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 3575 Sorted by residual: bond pdb=" CB VAL B 350 " pdb=" CG1 VAL B 350 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.76e-01 bond pdb=" CB TRP C 120 " pdb=" CG TRP C 120 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 7.91e-01 bond pdb=" CG LEU B 461 " pdb=" CD2 LEU B 461 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.71e-01 bond pdb=" CB TRP C 36 " pdb=" CG TRP C 36 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.65e-01 bond pdb=" CB PRO A 106 " pdb=" CG PRO A 106 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.53e-01 ... (remaining 3570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 4753 1.85 - 3.70: 87 3.70 - 5.54: 6 5.54 - 7.39: 1 7.39 - 9.24: 1 Bond angle restraints: 4848 Sorted by residual: angle pdb=" CA LEU B 461 " pdb=" CB LEU B 461 " pdb=" CG LEU B 461 " ideal model delta sigma weight residual 116.30 125.54 -9.24 3.50e+00 8.16e-02 6.97e+00 angle pdb=" CA ARG A 30 " pdb=" CB ARG A 30 " pdb=" CG ARG A 30 " ideal model delta sigma weight residual 114.10 108.92 5.18 2.00e+00 2.50e-01 6.70e+00 angle pdb=" N GLY B 485 " pdb=" CA GLY B 485 " pdb=" C GLY B 485 " ideal model delta sigma weight residual 113.18 108.49 4.69 2.37e+00 1.78e-01 3.92e+00 angle pdb=" C ARG A 30 " pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 123.24 120.36 2.88 1.54e+00 4.22e-01 3.49e+00 angle pdb=" N GLY A 15 " pdb=" CA GLY A 15 " pdb=" C GLY A 15 " ideal model delta sigma weight residual 115.36 112.93 2.43 1.33e+00 5.65e-01 3.34e+00 ... (remaining 4843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1968 16.02 - 32.04: 101 32.04 - 48.06: 16 48.06 - 64.07: 2 64.07 - 80.09: 3 Dihedral angle restraints: 2090 sinusoidal: 810 harmonic: 1280 Sorted by residual: dihedral pdb=" CA SER B 366 " pdb=" C SER B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR B 489 " pdb=" C TYR B 489 " pdb=" N PHE B 490 " pdb=" CA PHE B 490 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " pdb=" OE1 GLU B 471 " ideal model delta sinusoidal sigma weight residual 0.00 80.09 -80.09 1 3.00e+01 1.11e-03 8.83e+00 ... (remaining 2087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 311 0.031 - 0.063: 112 0.063 - 0.094: 48 0.094 - 0.126: 23 0.126 - 0.157: 7 Chirality restraints: 501 Sorted by residual: chirality pdb=" CG LEU B 461 " pdb=" CB LEU B 461 " pdb=" CD1 LEU B 461 " pdb=" CD2 LEU B 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ARG A 30 " pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CB ARG A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 498 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 110 " -0.010 2.00e-02 2.50e+03 8.62e-03 1.30e+00 pdb=" CG PHE A 110 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 110 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 80 " 0.007 2.00e-02 2.50e+03 6.42e-03 8.25e-01 pdb=" CG TYR C 80 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 80 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 80 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 80 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 80 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 80 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 467 " -0.004 2.00e-02 2.50e+03 8.40e-03 7.06e-01 pdb=" C ASP B 467 " 0.015 2.00e-02 2.50e+03 pdb=" O ASP B 467 " -0.005 2.00e-02 2.50e+03 pdb=" N ILE B 468 " -0.005 2.00e-02 2.50e+03 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 268 2.74 - 3.28: 3134 3.28 - 3.82: 5333 3.82 - 4.36: 6330 4.36 - 4.90: 11179 Nonbonded interactions: 26244 Sorted by model distance: nonbonded pdb=" OE1 GLN B 498 " pdb=" OG1 THR C 28 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" O TRP A 105 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.258 3.040 nonbonded pdb=" O PHE A 29 " pdb=" NH2 ARG A 71 " model vdw 2.268 3.120 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.292 3.040 ... (remaining 26239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.005 0.043 3582 Z= 0.211 Angle : 0.617 9.238 4862 Z= 0.337 Chirality : 0.045 0.157 501 Planarity : 0.003 0.021 633 Dihedral : 10.099 80.092 1267 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.38), residues: 442 helix: -4.06 (0.60), residues: 27 sheet: 0.79 (0.46), residues: 132 loop : -0.43 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.002 0.001 HIS B 519 PHE 0.020 0.002 PHE A 110 TYR 0.016 0.001 TYR C 80 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.25654 ( 115) hydrogen bonds : angle 9.50671 ( 399) SS BOND : bond 0.00341 ( 7) SS BOND : angle 0.87374 ( 14) covalent geometry : bond 0.00479 ( 3575) covalent geometry : angle 0.61584 ( 4848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 357 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7165 (tmm-80) REVERT: B 469 SER cc_start: 0.8965 (t) cc_final: 0.8593 (p) REVERT: B 501 ASN cc_start: 0.8483 (m110) cc_final: 0.8133 (m110) REVERT: C 59 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8191 (mtpt) REVERT: C 73 ASP cc_start: 0.8733 (m-30) cc_final: 0.7297 (m-30) REVERT: C 76 LYS cc_start: 0.8240 (mmmt) cc_final: 0.8016 (mtmm) REVERT: C 80 TYR cc_start: 0.7863 (m-80) cc_final: 0.7638 (m-80) REVERT: C 87 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7734 (mmmt) REVERT: A 3 GLN cc_start: 0.8205 (pt0) cc_final: 0.7772 (pm20) REVERT: A 36 TRP cc_start: 0.8333 (m100) cc_final: 0.7580 (m100) REVERT: A 75 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7687 (mtpt) REVERT: A 84 SER cc_start: 0.7257 (m) cc_final: 0.6808 (p) REVERT: A 121 VAL cc_start: 0.8394 (t) cc_final: 0.8149 (t) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2119 time to fit residues: 35.4737 Evaluate side-chains 115 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108014 restraints weight = 5634.550| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.50 r_work: 0.3181 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3582 Z= 0.121 Angle : 0.621 8.356 4862 Z= 0.326 Chirality : 0.045 0.140 501 Planarity : 0.004 0.029 633 Dihedral : 4.268 20.873 500 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.50 % Allowed : 13.21 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.38), residues: 442 helix: -3.13 (0.67), residues: 33 sheet: 1.59 (0.45), residues: 131 loop : -0.38 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 113 HIS 0.000 0.000 HIS C 114 PHE 0.014 0.001 PHE B 392 TYR 0.016 0.001 TYR C 32 ARG 0.003 0.001 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 115) hydrogen bonds : angle 5.13124 ( 399) SS BOND : bond 0.00448 ( 7) SS BOND : angle 3.04699 ( 14) covalent geometry : bond 0.00266 ( 3575) covalent geometry : angle 0.59956 ( 4848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8178 (mp0) REVERT: B 357 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7676 (tmm-80) REVERT: B 465 GLU cc_start: 0.8305 (tt0) cc_final: 0.8028 (tt0) REVERT: B 469 SER cc_start: 0.9150 (t) cc_final: 0.8806 (p) REVERT: B 472 ILE cc_start: 0.8768 (mm) cc_final: 0.8354 (tp) REVERT: B 498 GLN cc_start: 0.8414 (mt0) cc_final: 0.8039 (mt0) REVERT: B 501 ASN cc_start: 0.8528 (m110) cc_final: 0.7992 (m110) REVERT: C 2 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.6865 (m) REVERT: C 27 PHE cc_start: 0.8960 (m-80) cc_final: 0.8319 (m-80) REVERT: C 31 TYR cc_start: 0.8373 (m-80) cc_final: 0.8163 (m-80) REVERT: C 73 ASP cc_start: 0.8679 (m-30) cc_final: 0.7373 (m-30) REVERT: C 76 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7877 (mtmm) REVERT: C 80 TYR cc_start: 0.7959 (m-80) cc_final: 0.7660 (m-80) REVERT: C 87 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7699 (mmmt) REVERT: C 91 THR cc_start: 0.8429 (p) cc_final: 0.8025 (p) REVERT: C 124 THR cc_start: 0.8100 (p) cc_final: 0.7797 (p) REVERT: A 3 GLN cc_start: 0.8128 (pt0) cc_final: 0.7839 (pm20) REVERT: A 100 MET cc_start: 0.8193 (mmm) cc_final: 0.7255 (mtm) outliers start: 13 outliers final: 4 residues processed: 134 average time/residue: 0.2100 time to fit residues: 32.5399 Evaluate side-chains 122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 50 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.0040 chunk 41 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN A 39 GLN A 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107795 restraints weight = 5574.028| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.62 r_work: 0.3170 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3582 Z= 0.105 Angle : 0.594 7.434 4862 Z= 0.305 Chirality : 0.043 0.149 501 Planarity : 0.003 0.029 633 Dihedral : 3.949 16.875 500 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.16 % Allowed : 14.02 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.39), residues: 442 helix: -3.71 (0.87), residues: 20 sheet: 1.79 (0.44), residues: 130 loop : -0.35 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS C 114 PHE 0.006 0.001 PHE B 392 TYR 0.018 0.001 TYR C 32 ARG 0.003 0.001 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 115) hydrogen bonds : angle 4.53645 ( 399) SS BOND : bond 0.00253 ( 7) SS BOND : angle 2.87300 ( 14) covalent geometry : bond 0.00241 ( 3575) covalent geometry : angle 0.57417 ( 4848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8216 (mp0) REVERT: B 357 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7789 (tmm160) REVERT: B 465 GLU cc_start: 0.8297 (tt0) cc_final: 0.8019 (tt0) REVERT: B 469 SER cc_start: 0.9195 (t) cc_final: 0.8897 (p) REVERT: B 498 GLN cc_start: 0.8437 (mt0) cc_final: 0.8009 (mt0) REVERT: B 501 ASN cc_start: 0.8583 (m110) cc_final: 0.8062 (m110) REVERT: C 67 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8293 (mtm-85) REVERT: C 73 ASP cc_start: 0.8579 (m-30) cc_final: 0.7243 (m-30) REVERT: C 76 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7853 (mtmm) REVERT: C 80 TYR cc_start: 0.7981 (m-80) cc_final: 0.7674 (m-80) REVERT: C 87 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7680 (mmmt) REVERT: C 91 THR cc_start: 0.8393 (p) cc_final: 0.8054 (p) REVERT: C 108 TYR cc_start: 0.8273 (m-80) cc_final: 0.8010 (m-80) REVERT: A 3 GLN cc_start: 0.8142 (pt0) cc_final: 0.7882 (pm20) REVERT: A 89 ASP cc_start: 0.8455 (m-30) cc_final: 0.7690 (t0) outliers start: 8 outliers final: 7 residues processed: 124 average time/residue: 0.1956 time to fit residues: 28.2216 Evaluate side-chains 120 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103811 restraints weight = 5709.942| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.60 r_work: 0.3117 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3582 Z= 0.148 Angle : 0.610 9.015 4862 Z= 0.313 Chirality : 0.044 0.183 501 Planarity : 0.003 0.027 633 Dihedral : 3.975 16.911 500 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.96 % Allowed : 16.17 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.39), residues: 442 helix: -3.27 (1.08), residues: 21 sheet: 1.83 (0.44), residues: 128 loop : -0.42 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.007 0.001 PHE B 392 TYR 0.016 0.001 TYR C 32 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 115) hydrogen bonds : angle 4.49456 ( 399) SS BOND : bond 0.00252 ( 7) SS BOND : angle 3.07792 ( 14) covalent geometry : bond 0.00338 ( 3575) covalent geometry : angle 0.58857 ( 4848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8220 (mp0) REVERT: B 357 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7730 (tmm160) REVERT: B 406 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8299 (mt-10) REVERT: B 466 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7766 (ptm160) REVERT: B 469 SER cc_start: 0.9206 (t) cc_final: 0.8991 (p) REVERT: B 472 ILE cc_start: 0.8697 (mm) cc_final: 0.8337 (tp) REVERT: B 498 GLN cc_start: 0.8415 (mt0) cc_final: 0.8073 (mt0) REVERT: B 501 ASN cc_start: 0.8618 (m110) cc_final: 0.8115 (m110) REVERT: C 59 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7480 (mtpt) REVERT: C 67 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8364 (mtm-85) REVERT: C 73 ASP cc_start: 0.8593 (m-30) cc_final: 0.7351 (m-30) REVERT: C 76 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7918 (mtmm) REVERT: C 80 TYR cc_start: 0.8061 (m-80) cc_final: 0.7783 (m-80) REVERT: C 87 LYS cc_start: 0.8021 (mmtp) cc_final: 0.7709 (mmmt) REVERT: C 91 THR cc_start: 0.8513 (p) cc_final: 0.8220 (p) REVERT: C 125 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 3 GLN cc_start: 0.8179 (pt0) cc_final: 0.7673 (pm20) REVERT: A 5 GLN cc_start: 0.7608 (mp10) cc_final: 0.7090 (mp10) REVERT: A 19 ARG cc_start: 0.8553 (mpp80) cc_final: 0.8219 (mpp80) REVERT: A 89 ASP cc_start: 0.8560 (m-30) cc_final: 0.7817 (t0) REVERT: A 100 MET cc_start: 0.8316 (mmm) cc_final: 0.7234 (mtm) outliers start: 11 outliers final: 11 residues processed: 124 average time/residue: 0.2177 time to fit residues: 31.2904 Evaluate side-chains 122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN C 3 GLN A 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107483 restraints weight = 5699.931| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.59 r_work: 0.3154 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3582 Z= 0.107 Angle : 0.566 7.870 4862 Z= 0.287 Chirality : 0.042 0.148 501 Planarity : 0.003 0.028 633 Dihedral : 3.752 14.726 500 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.77 % Allowed : 15.90 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.39), residues: 442 helix: -3.00 (1.05), residues: 21 sheet: 1.87 (0.43), residues: 128 loop : -0.39 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.001 PHE C 68 TYR 0.018 0.001 TYR C 32 ARG 0.002 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 115) hydrogen bonds : angle 4.35395 ( 399) SS BOND : bond 0.00343 ( 7) SS BOND : angle 2.43178 ( 14) covalent geometry : bond 0.00247 ( 3575) covalent geometry : angle 0.55171 ( 4848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8220 (mp0) REVERT: B 357 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7753 (tmm160) REVERT: B 457 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7814 (ttt-90) REVERT: B 466 ARG cc_start: 0.8039 (ptm160) cc_final: 0.7782 (ptm160) REVERT: B 469 SER cc_start: 0.9184 (t) cc_final: 0.8960 (p) REVERT: B 472 ILE cc_start: 0.8660 (mm) cc_final: 0.8308 (tp) REVERT: B 498 GLN cc_start: 0.8385 (mt0) cc_final: 0.8055 (mt0) REVERT: B 501 ASN cc_start: 0.8569 (m110) cc_final: 0.8048 (m110) REVERT: C 27 PHE cc_start: 0.8964 (m-80) cc_final: 0.8719 (m-80) REVERT: C 67 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8344 (mtm-85) REVERT: C 73 ASP cc_start: 0.8478 (m-30) cc_final: 0.7298 (m-30) REVERT: C 76 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7855 (mtmm) REVERT: C 80 TYR cc_start: 0.8019 (m-10) cc_final: 0.7774 (m-80) REVERT: C 87 LYS cc_start: 0.7995 (mmtp) cc_final: 0.7657 (mmmt) REVERT: C 91 THR cc_start: 0.8545 (p) cc_final: 0.8282 (p) REVERT: C 125 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 3 GLN cc_start: 0.8227 (pt0) cc_final: 0.7745 (pm20) REVERT: A 19 ARG cc_start: 0.8500 (mpp80) cc_final: 0.8222 (mpp80) REVERT: A 89 ASP cc_start: 0.8512 (m-30) cc_final: 0.7824 (t0) REVERT: A 100 MET cc_start: 0.8214 (mmm) cc_final: 0.7090 (mtm) outliers start: 14 outliers final: 10 residues processed: 125 average time/residue: 0.2103 time to fit residues: 30.6289 Evaluate side-chains 123 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain A residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101975 restraints weight = 5818.143| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.59 r_work: 0.3073 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3582 Z= 0.183 Angle : 0.618 8.376 4862 Z= 0.317 Chirality : 0.043 0.158 501 Planarity : 0.003 0.023 633 Dihedral : 4.089 14.225 500 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.85 % Allowed : 15.90 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.39), residues: 442 helix: -2.95 (1.09), residues: 21 sheet: 1.77 (0.44), residues: 128 loop : -0.47 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.001 0.000 HIS B 519 PHE 0.007 0.001 PHE A 29 TYR 0.016 0.001 TYR C 32 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 115) hydrogen bonds : angle 4.61996 ( 399) SS BOND : bond 0.00261 ( 7) SS BOND : angle 2.84057 ( 14) covalent geometry : bond 0.00419 ( 3575) covalent geometry : angle 0.59993 ( 4848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8268 (mp0) REVERT: B 357 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7772 (tmm160) REVERT: B 406 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8301 (mt-10) REVERT: B 420 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: B 457 ARG cc_start: 0.8229 (ttt180) cc_final: 0.7572 (ttt-90) REVERT: B 498 GLN cc_start: 0.8347 (mt0) cc_final: 0.8097 (mt0) REVERT: B 501 ASN cc_start: 0.8606 (m110) cc_final: 0.8201 (m110) REVERT: C 73 ASP cc_start: 0.8584 (m-30) cc_final: 0.7862 (m-30) REVERT: C 76 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7985 (mtmm) REVERT: C 87 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7786 (mmmt) REVERT: C 91 THR cc_start: 0.8696 (p) cc_final: 0.8451 (p) REVERT: C 125 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 5 GLN cc_start: 0.7626 (mp10) cc_final: 0.7150 (mp10) REVERT: A 64 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8809 (mtpt) REVERT: A 89 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.7862 (t0) outliers start: 18 outliers final: 13 residues processed: 128 average time/residue: 0.1975 time to fit residues: 29.5728 Evaluate side-chains 135 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103671 restraints weight = 5740.242| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.52 r_work: 0.3096 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3582 Z= 0.156 Angle : 0.673 12.355 4862 Z= 0.340 Chirality : 0.043 0.146 501 Planarity : 0.004 0.046 633 Dihedral : 4.179 23.899 500 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.12 % Allowed : 17.52 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.39), residues: 442 helix: -2.92 (1.09), residues: 21 sheet: 1.81 (0.45), residues: 127 loop : -0.52 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 105 HIS 0.001 0.001 HIS C 114 PHE 0.007 0.001 PHE B 392 TYR 0.018 0.001 TYR C 32 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 115) hydrogen bonds : angle 4.52934 ( 399) SS BOND : bond 0.00215 ( 7) SS BOND : angle 3.18520 ( 14) covalent geometry : bond 0.00367 ( 3575) covalent geometry : angle 0.65160 ( 4848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8251 (mp0) REVERT: B 357 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7741 (tmm160) REVERT: B 406 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8266 (mt-10) REVERT: B 498 GLN cc_start: 0.8328 (mt0) cc_final: 0.8065 (mt0) REVERT: B 501 ASN cc_start: 0.8707 (m110) cc_final: 0.8225 (m110) REVERT: C 27 PHE cc_start: 0.8973 (m-80) cc_final: 0.8603 (m-80) REVERT: C 67 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: C 73 ASP cc_start: 0.8573 (m-30) cc_final: 0.7507 (m-30) REVERT: C 76 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7937 (mtmm) REVERT: C 80 TYR cc_start: 0.8177 (m-80) cc_final: 0.7937 (m-80) REVERT: C 87 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7745 (mmmt) REVERT: C 91 THR cc_start: 0.8723 (p) cc_final: 0.8487 (p) REVERT: C 125 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8639 (tm-30) REVERT: A 3 GLN cc_start: 0.8451 (pt0) cc_final: 0.8237 (pt0) REVERT: A 5 GLN cc_start: 0.7659 (mp10) cc_final: 0.7181 (mp10) REVERT: A 19 ARG cc_start: 0.8543 (mpp80) cc_final: 0.8270 (mpp80) REVERT: A 64 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8807 (mtpt) REVERT: A 89 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.7929 (t0) REVERT: A 100 MET cc_start: 0.8373 (mmm) cc_final: 0.7238 (mtm) outliers start: 19 outliers final: 15 residues processed: 130 average time/residue: 0.1916 time to fit residues: 29.0732 Evaluate side-chains 135 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104458 restraints weight = 5725.937| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.61 r_work: 0.3129 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3582 Z= 0.118 Angle : 0.619 7.985 4862 Z= 0.312 Chirality : 0.042 0.148 501 Planarity : 0.003 0.034 633 Dihedral : 3.984 24.245 500 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.12 % Allowed : 17.79 % 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: 0.13 (0.39), residues: 442 helix: -2.85 (1.09), residues: 21 sheet: 1.72 (0.46), residues: 127 loop : -0.45 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 105 HIS 0.001 0.001 HIS C 114 PHE 0.009 0.001 PHE B 392 TYR 0.017 0.001 TYR C 32 ARG 0.005 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 115) hydrogen bonds : angle 4.39375 ( 399) SS BOND : bond 0.00272 ( 7) SS BOND : angle 2.69924 ( 14) covalent geometry : bond 0.00280 ( 3575) covalent geometry : angle 0.60258 ( 4848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8296 (mp0) REVERT: B 357 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7771 (tmm160) REVERT: B 466 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7686 (ptm160) REVERT: B 498 GLN cc_start: 0.8331 (mt0) cc_final: 0.8014 (mt0) REVERT: B 501 ASN cc_start: 0.8655 (m110) cc_final: 0.8146 (m110) REVERT: C 27 PHE cc_start: 0.9021 (m-80) cc_final: 0.8695 (m-80) REVERT: C 67 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8452 (mtm-85) REVERT: C 73 ASP cc_start: 0.8562 (m-30) cc_final: 0.7592 (m-30) REVERT: C 76 LYS cc_start: 0.8351 (mmmt) cc_final: 0.7935 (mtmm) REVERT: C 87 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7677 (mmmt) REVERT: C 91 THR cc_start: 0.8707 (p) cc_final: 0.8480 (p) REVERT: C 125 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 3 GLN cc_start: 0.8474 (pt0) cc_final: 0.8256 (pt0) REVERT: A 5 GLN cc_start: 0.7687 (mp10) cc_final: 0.7189 (mp10) REVERT: A 19 ARG cc_start: 0.8516 (mpp80) cc_final: 0.8211 (mpp80) REVERT: A 89 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7884 (t0) REVERT: A 100 MET cc_start: 0.8377 (mmm) cc_final: 0.7228 (mtm) outliers start: 19 outliers final: 16 residues processed: 127 average time/residue: 0.1918 time to fit residues: 28.4251 Evaluate side-chains 128 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105112 restraints weight = 5765.152| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.58 r_work: 0.3118 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3582 Z= 0.113 Angle : 0.625 10.760 4862 Z= 0.309 Chirality : 0.043 0.149 501 Planarity : 0.003 0.025 633 Dihedral : 3.731 14.985 500 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.12 % Allowed : 18.87 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.39), residues: 442 helix: -3.24 (0.86), residues: 27 sheet: 1.69 (0.46), residues: 128 loop : -0.42 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 105 HIS 0.001 0.000 HIS C 114 PHE 0.012 0.001 PHE C 68 TYR 0.015 0.001 TYR C 32 ARG 0.007 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 115) hydrogen bonds : angle 4.32216 ( 399) SS BOND : bond 0.00184 ( 7) SS BOND : angle 2.43861 ( 14) covalent geometry : bond 0.00269 ( 3575) covalent geometry : angle 0.61222 ( 4848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8276 (mp0) REVERT: B 357 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7631 (ttp80) REVERT: B 420 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: B 466 ARG cc_start: 0.8004 (ptm160) cc_final: 0.7640 (ptm160) REVERT: B 498 GLN cc_start: 0.8335 (mt0) cc_final: 0.8028 (mt0) REVERT: B 501 ASN cc_start: 0.8631 (m110) cc_final: 0.8123 (m110) REVERT: C 27 PHE cc_start: 0.9001 (m-80) cc_final: 0.8711 (m-80) REVERT: C 60 TYR cc_start: 0.8334 (m-80) cc_final: 0.8011 (m-80) REVERT: C 67 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8432 (mtm-85) REVERT: C 68 PHE cc_start: 0.9111 (m-10) cc_final: 0.8766 (m-10) REVERT: C 73 ASP cc_start: 0.8431 (m-30) cc_final: 0.8148 (m-30) REVERT: C 87 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7677 (mmmt) REVERT: C 91 THR cc_start: 0.8735 (p) cc_final: 0.8520 (p) REVERT: C 125 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8660 (tm-30) REVERT: A 3 GLN cc_start: 0.8489 (pt0) cc_final: 0.8255 (pt0) REVERT: A 5 GLN cc_start: 0.7751 (mp10) cc_final: 0.7258 (mp10) REVERT: A 19 ARG cc_start: 0.8510 (mpp80) cc_final: 0.8205 (mpp80) REVERT: A 64 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8802 (mtpt) REVERT: A 89 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.7883 (t0) REVERT: A 100 MET cc_start: 0.8315 (mmm) cc_final: 0.7202 (mtm) outliers start: 19 outliers final: 16 residues processed: 124 average time/residue: 0.2035 time to fit residues: 29.6247 Evaluate side-chains 129 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100559 restraints weight = 5878.706| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.51 r_work: 0.3053 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3582 Z= 0.189 Angle : 0.662 9.876 4862 Z= 0.337 Chirality : 0.044 0.154 501 Planarity : 0.003 0.027 633 Dihedral : 4.130 15.136 500 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.39 % Allowed : 18.06 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.39), residues: 442 helix: -2.99 (1.07), residues: 21 sheet: 1.65 (0.46), residues: 128 loop : -0.50 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 105 HIS 0.001 0.001 HIS C 114 PHE 0.013 0.001 PHE C 68 TYR 0.016 0.001 TYR C 32 ARG 0.008 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 115) hydrogen bonds : angle 4.58715 ( 399) SS BOND : bond 0.00228 ( 7) SS BOND : angle 2.88809 ( 14) covalent geometry : bond 0.00435 ( 3575) covalent geometry : angle 0.64483 ( 4848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.361 Fit side-chains REVERT: B 340 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8284 (mp0) REVERT: B 357 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7721 (tmm160) REVERT: B 406 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 420 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: B 466 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7904 (ptm160) REVERT: B 498 GLN cc_start: 0.8289 (mt0) cc_final: 0.8056 (mt0) REVERT: B 501 ASN cc_start: 0.8675 (m110) cc_final: 0.8300 (m110) REVERT: C 27 PHE cc_start: 0.9062 (m-80) cc_final: 0.8741 (m-80) REVERT: C 73 ASP cc_start: 0.8566 (m-30) cc_final: 0.7498 (m-30) REVERT: C 76 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7908 (mtmm) REVERT: C 87 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7799 (mmmt) REVERT: C 91 THR cc_start: 0.8791 (p) cc_final: 0.8584 (p) REVERT: C 125 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8715 (tm-30) REVERT: A 5 GLN cc_start: 0.7820 (mp10) cc_final: 0.7499 (mp10) REVERT: A 19 ARG cc_start: 0.8567 (mpp80) cc_final: 0.8297 (mpp80) REVERT: A 64 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8824 (mtpt) REVERT: A 89 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.7941 (t0) REVERT: A 98 ASP cc_start: 0.8612 (t70) cc_final: 0.8397 (t0) REVERT: A 100 MET cc_start: 0.8414 (mmm) cc_final: 0.7227 (mtm) REVERT: A 121 VAL cc_start: 0.8882 (t) cc_final: 0.8680 (p) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.1962 time to fit residues: 28.4561 Evaluate side-chains 127 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 67.7617 > 50: distance: 26 - 167: 21.737 distance: 29 - 164: 6.618 distance: 66 - 86: 11.966 distance: 82 - 86: 12.787 distance: 86 - 87: 32.037 distance: 87 - 88: 44.717 distance: 87 - 90: 40.338 distance: 88 - 94: 30.327 distance: 90 - 91: 12.966 distance: 91 - 93: 8.410 distance: 94 - 95: 17.611 distance: 95 - 96: 21.060 distance: 95 - 98: 19.666 distance: 96 - 97: 40.120 distance: 96 - 106: 22.546 distance: 98 - 99: 6.983 distance: 99 - 100: 18.785 distance: 99 - 101: 13.219 distance: 100 - 102: 33.269 distance: 101 - 103: 21.896 distance: 102 - 104: 18.428 distance: 103 - 104: 19.625 distance: 104 - 105: 15.084 distance: 106 - 107: 39.811 distance: 107 - 108: 45.057 distance: 107 - 110: 32.413 distance: 108 - 109: 45.539 distance: 108 - 115: 29.330 distance: 110 - 111: 18.876 distance: 111 - 112: 43.659 distance: 112 - 113: 38.549 distance: 113 - 114: 56.544 distance: 115 - 116: 3.764 distance: 116 - 117: 20.583 distance: 116 - 119: 53.356 distance: 117 - 118: 20.699 distance: 117 - 123: 41.620 distance: 119 - 120: 25.843 distance: 120 - 121: 18.788 distance: 120 - 122: 41.477 distance: 123 - 124: 6.888 distance: 123 - 129: 40.171 distance: 124 - 125: 55.123 distance: 124 - 127: 40.991 distance: 125 - 126: 13.063 distance: 125 - 130: 9.988 distance: 127 - 128: 4.664 distance: 130 - 131: 14.396 distance: 131 - 132: 7.871 distance: 131 - 134: 22.081 distance: 132 - 133: 27.459 distance: 132 - 138: 10.130 distance: 134 - 135: 12.054 distance: 135 - 136: 14.483 distance: 135 - 137: 6.011 distance: 138 - 139: 28.625 distance: 139 - 140: 22.584 distance: 139 - 142: 14.163 distance: 140 - 141: 15.458 distance: 140 - 146: 8.159 distance: 142 - 143: 9.155 distance: 143 - 144: 9.356 distance: 143 - 145: 22.817 distance: 146 - 147: 25.163 distance: 147 - 148: 26.801 distance: 147 - 150: 20.045 distance: 148 - 149: 22.701 distance: 148 - 157: 40.468 distance: 150 - 151: 22.030 distance: 151 - 152: 20.674 distance: 151 - 153: 9.116 distance: 152 - 154: 10.810 distance: 153 - 155: 7.343 distance: 154 - 156: 15.145 distance: 155 - 156: 10.276 distance: 158 - 159: 27.225 distance: 158 - 161: 23.568 distance: 159 - 160: 20.184 distance: 159 - 164: 30.496 distance: 161 - 162: 24.744 distance: 161 - 163: 20.834 distance: 164 - 165: 24.608 distance: 165 - 166: 30.911 distance: 166 - 167: 16.637 distance: 166 - 168: 6.052