Starting phenix.real_space_refine on Wed Mar 12 16:35:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq6_38567/03_2025/8xq6_38567.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq6_38567/03_2025/8xq6_38567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xq6_38567/03_2025/8xq6_38567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq6_38567/03_2025/8xq6_38567.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq6_38567/03_2025/8xq6_38567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq6_38567/03_2025/8xq6_38567.cif" } resolution = 3.36 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= 0.023 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 43 5.16 5 C 5269 2.51 5 N 1335 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8063 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8063 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 29, 'TRANS': 990} Chain breaks: 5 Time building chain proxies: 5.38, per 1000 atoms: 0.67 Number of scatterers: 8063 At special positions: 0 Unit cell: (82.08, 112.32, 123.12, 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 43 16.00 O 1416 8.00 N 1335 7.00 C 5269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 958.6 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 76.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.137A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.018A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.613A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 188 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 291 Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 296 through 318 removed outlier: 4.076A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.705A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 412 removed outlier: 3.562A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.611A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.414A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.974A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.892A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 516 through 520' Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.590A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.936A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.270A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 4.288A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 679 through 705 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 754 Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 798 through 853 Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 853 through 858 removed outlier: 4.023A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 889 removed outlier: 3.524A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.589A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 967 through 977 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.790A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.424A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.677A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.426A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 3.861A pdb=" N ASN A1154 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A1159 " --> pdb=" O ASN A1154 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1815 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: 2.56 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2390 1.34 - 1.46: 1226 1.46 - 1.57: 4523 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8218 Sorted by residual: bond pdb=" C SER A 407 " pdb=" N PRO A 408 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.36e-02 5.41e+03 1.22e+01 bond pdb=" C ILE A 488 " pdb=" N PRO A 489 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.23e-02 6.61e+03 3.31e+00 bond pdb=" CA ILE A 742 " pdb=" CB ILE A 742 " ideal model delta sigma weight residual 1.540 1.563 -0.023 1.36e-02 5.41e+03 2.94e+00 bond pdb=" C ILE A 818 " pdb=" N PRO A 819 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.72e+00 bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.51e+00 ... (remaining 8213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10946 2.36 - 4.72: 160 4.72 - 7.08: 26 7.08 - 9.44: 11 9.44 - 11.81: 1 Bond angle restraints: 11144 Sorted by residual: angle pdb=" C GLY A 414 " pdb=" N TYR A 415 " pdb=" CA TYR A 415 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C HIS A1156 " pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 122.46 128.56 -6.10 1.41e+00 5.03e-01 1.87e+01 angle pdb=" C HIS A 677 " pdb=" N MET A 678 " pdb=" CA MET A 678 " ideal model delta sigma weight residual 122.08 128.20 -6.12 1.47e+00 4.63e-01 1.73e+01 angle pdb=" C VAL A 741 " pdb=" N ILE A 742 " pdb=" CA ILE A 742 " ideal model delta sigma weight residual 121.97 128.97 -7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" C LYS A 765 " pdb=" N PHE A 766 " pdb=" CA PHE A 766 " ideal model delta sigma weight residual 121.58 114.02 7.56 1.95e+00 2.63e-01 1.50e+01 ... (remaining 11139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 4355 15.36 - 30.73: 438 30.73 - 46.09: 87 46.09 - 61.45: 27 61.45 - 76.81: 2 Dihedral angle restraints: 4909 sinusoidal: 1942 harmonic: 2967 Sorted by residual: dihedral pdb=" CA LEU A 963 " pdb=" C LEU A 963 " pdb=" N ALA A 964 " pdb=" CA ALA A 964 " ideal model delta harmonic sigma weight residual -180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE A 254 " pdb=" C PHE A 254 " pdb=" N PRO A 255 " pdb=" CA PRO A 255 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1205 0.073 - 0.147: 121 0.147 - 0.220: 13 0.220 - 0.293: 1 0.293 - 0.366: 1 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA PHE A 766 " pdb=" N PHE A 766 " pdb=" C PHE A 766 " pdb=" CB PHE A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A 608 " pdb=" CB LEU A 608 " pdb=" CD1 LEU A 608 " pdb=" CD2 LEU A 608 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1338 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 415 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C TYR A 415 " 0.044 2.00e-02 2.50e+03 pdb=" O TYR A 415 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 416 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 467 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C LEU A 467 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 467 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 468 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 168 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ILE A 168 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 168 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 169 " -0.012 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2323 2.82 - 3.34: 7685 3.34 - 3.86: 13268 3.86 - 4.38: 14447 4.38 - 4.90: 26288 Nonbonded interactions: 64011 Sorted by model distance: nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR A1179 " pdb=" OE1 GLU A1182 " model vdw 2.309 3.040 nonbonded pdb=" O SER A 404 " pdb=" OG SER A 407 " model vdw 2.310 3.040 nonbonded pdb=" O ILE A 230 " pdb=" OG SER A 234 " model vdw 2.312 3.040 nonbonded pdb=" N ASP A 983 " pdb=" OD1 ASP A 983 " model vdw 2.345 3.120 ... (remaining 64006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 0.065 8218 Z= 0.302 Angle : 0.786 11.805 11144 Z= 0.437 Chirality : 0.049 0.366 1341 Planarity : 0.006 0.047 1371 Dihedral : 13.251 76.814 2985 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.56 % Allowed : 9.91 % Favored : 85.54 % 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 (0.23), residues: 1008 helix: -0.66 (0.16), residues: 750 sheet: -0.04 (0.97), residues: 30 loop : -1.84 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 635 HIS 0.003 0.001 HIS A 614 PHE 0.031 0.002 PHE A 766 TYR 0.012 0.002 TYR A 984 ARG 0.002 0.000 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7921 (mttp) cc_final: 0.7674 (ttpt) REVERT: A 112 ILE cc_start: 0.8228 (mm) cc_final: 0.7987 (mm) REVERT: A 180 LEU cc_start: 0.7993 (mt) cc_final: 0.7711 (mt) REVERT: A 200 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: A 225 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7951 (mm-40) REVERT: A 233 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 236 LEU cc_start: 0.8274 (mt) cc_final: 0.8054 (mp) REVERT: A 251 MET cc_start: 0.7367 (ttm) cc_final: 0.7139 (ttm) REVERT: A 263 GLN cc_start: 0.8183 (mt0) cc_final: 0.7881 (mt0) REVERT: A 264 ASN cc_start: 0.7992 (m-40) cc_final: 0.7454 (m110) REVERT: A 267 TYR cc_start: 0.8335 (t80) cc_final: 0.7935 (t80) REVERT: A 320 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 335 ASN cc_start: 0.8204 (t0) cc_final: 0.7959 (t0) REVERT: A 338 LYS cc_start: 0.8314 (mtmm) cc_final: 0.8012 (mtmm) REVERT: A 344 GLU cc_start: 0.7726 (pt0) cc_final: 0.7447 (tm-30) REVERT: A 355 MET cc_start: 0.8371 (ttp) cc_final: 0.7979 (ttp) REVERT: A 366 MET cc_start: 0.8477 (mmm) cc_final: 0.8222 (mmm) REVERT: A 383 MET cc_start: 0.7755 (mmt) cc_final: 0.6943 (mmt) REVERT: A 386 PHE cc_start: 0.8035 (t80) cc_final: 0.7676 (t80) REVERT: A 387 TYR cc_start: 0.8184 (m-10) cc_final: 0.7361 (m-10) REVERT: A 406 PHE cc_start: 0.7881 (m-80) cc_final: 0.7637 (m-80) REVERT: A 419 TRP cc_start: 0.8174 (p-90) cc_final: 0.7578 (p-90) REVERT: A 423 VAL cc_start: 0.8514 (t) cc_final: 0.8277 (t) REVERT: A 443 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7127 (tp30) REVERT: A 445 LEU cc_start: 0.8781 (mt) cc_final: 0.8440 (mt) REVERT: A 449 ASP cc_start: 0.8332 (t0) cc_final: 0.7963 (t0) REVERT: A 485 ASP cc_start: 0.7852 (p0) cc_final: 0.7525 (m-30) REVERT: A 500 ARG cc_start: 0.7172 (ptt180) cc_final: 0.4778 (ttp-110) REVERT: A 503 GLU cc_start: 0.8109 (tt0) cc_final: 0.7880 (tt0) REVERT: A 505 GLN cc_start: 0.8422 (mt0) cc_final: 0.8078 (mt0) REVERT: A 585 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7189 (mtm180) REVERT: A 587 LEU cc_start: 0.8777 (mt) cc_final: 0.8406 (mt) REVERT: A 588 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8161 (mmtt) REVERT: A 591 LYS cc_start: 0.8329 (mttt) cc_final: 0.8018 (mtpp) REVERT: A 592 ILE cc_start: 0.8473 (mt) cc_final: 0.8154 (mm) REVERT: A 621 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: A 628 VAL cc_start: 0.8507 (t) cc_final: 0.8161 (m) REVERT: A 632 LYS cc_start: 0.8585 (mttt) cc_final: 0.8313 (mttt) REVERT: A 641 TYR cc_start: 0.7893 (m-80) cc_final: 0.7362 (m-80) REVERT: A 670 LEU cc_start: 0.3115 (OUTLIER) cc_final: 0.1125 (mp) REVERT: A 681 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 697 MET cc_start: 0.7056 (tpt) cc_final: 0.6757 (tpt) REVERT: A 743 TYR cc_start: 0.7601 (t80) cc_final: 0.7178 (t80) REVERT: A 769 PHE cc_start: 0.7924 (t80) cc_final: 0.7486 (t80) REVERT: A 777 ASP cc_start: 0.7721 (m-30) cc_final: 0.7146 (m-30) REVERT: A 808 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 810 MET cc_start: 0.6063 (ptt) cc_final: 0.5577 (ptt) REVERT: A 821 LEU cc_start: 0.8487 (mt) cc_final: 0.8022 (mt) REVERT: A 824 VAL cc_start: 0.8801 (t) cc_final: 0.8565 (p) REVERT: A 828 LYS cc_start: 0.8330 (mttt) cc_final: 0.7874 (mttt) REVERT: A 837 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: A 848 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 857 MET cc_start: 0.7218 (mtt) cc_final: 0.6608 (mtt) REVERT: A 865 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7783 (ttp-170) REVERT: A 872 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8043 (tp30) REVERT: A 938 MET cc_start: 0.8388 (mmm) cc_final: 0.8166 (mmm) REVERT: A 967 MET cc_start: 0.8030 (mtp) cc_final: 0.7332 (mtp) REVERT: A 968 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7497 (mmmm) REVERT: A 971 ASP cc_start: 0.8136 (m-30) cc_final: 0.7739 (m-30) REVERT: A 981 HIS cc_start: 0.8723 (m-70) cc_final: 0.8521 (m90) REVERT: A 983 ASP cc_start: 0.8032 (p0) cc_final: 0.7531 (p0) REVERT: A 1009 TYR cc_start: 0.7952 (t80) cc_final: 0.7687 (t80) REVERT: A 1033 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 1045 MET cc_start: 0.8611 (mmm) cc_final: 0.8259 (mmm) REVERT: A 1048 LEU cc_start: 0.8578 (mt) cc_final: 0.8368 (mt) REVERT: A 1053 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7173 (mtt-85) REVERT: A 1063 VAL cc_start: 0.8014 (t) cc_final: 0.7798 (p) REVERT: A 1067 PHE cc_start: 0.8283 (t80) cc_final: 0.8017 (t80) REVERT: A 1104 MET cc_start: 0.8110 (mmm) cc_final: 0.7909 (mmm) REVERT: A 1110 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7668 (mm-40) REVERT: A 1116 LYS cc_start: 0.8666 (tttp) cc_final: 0.8437 (tttm) REVERT: A 1134 PHE cc_start: 0.8239 (m-80) cc_final: 0.7528 (m-80) REVERT: A 1136 PHE cc_start: 0.8499 (t80) cc_final: 0.8185 (t80) REVERT: A 1139 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: A 1144 ASP cc_start: 0.8097 (p0) cc_final: 0.7773 (p0) REVERT: A 1178 TYR cc_start: 0.6524 (t80) cc_final: 0.6072 (t80) outliers start: 40 outliers final: 11 residues processed: 331 average time/residue: 0.2205 time to fit residues: 97.3101 Evaluate side-chains 292 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 0.0060 chunk 41 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1064 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112606 restraints weight = 12796.620| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.00 r_work: 0.3272 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8218 Z= 0.188 Angle : 0.570 8.712 11144 Z= 0.300 Chirality : 0.040 0.201 1341 Planarity : 0.004 0.037 1371 Dihedral : 6.633 53.322 1126 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.99 % Allowed : 18.22 % Favored : 77.79 % 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: 0.31 (0.26), residues: 1008 helix: 0.80 (0.19), residues: 745 sheet: 0.20 (0.95), residues: 33 loop : -1.59 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1112 HIS 0.003 0.001 HIS A1120 PHE 0.027 0.001 PHE A 766 TYR 0.008 0.001 TYR A 672 ARG 0.005 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8382 (mm) cc_final: 0.8150 (mm) REVERT: A 176 VAL cc_start: 0.8656 (p) cc_final: 0.8415 (p) REVERT: A 180 LEU cc_start: 0.8064 (mt) cc_final: 0.7768 (mt) REVERT: A 183 VAL cc_start: 0.8033 (t) cc_final: 0.7665 (m) REVERT: A 200 MET cc_start: 0.8391 (mtm) cc_final: 0.8137 (ttp) REVERT: A 217 LEU cc_start: 0.8103 (mt) cc_final: 0.7888 (mt) REVERT: A 233 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7389 (tp30) REVERT: A 236 LEU cc_start: 0.8272 (mt) cc_final: 0.8029 (mp) REVERT: A 250 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7411 (mmmt) REVERT: A 263 GLN cc_start: 0.8260 (mt0) cc_final: 0.7907 (mt0) REVERT: A 264 ASN cc_start: 0.8028 (m-40) cc_final: 0.7461 (m110) REVERT: A 267 TYR cc_start: 0.8355 (t80) cc_final: 0.7997 (t80) REVERT: A 284 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8275 (mmmm) REVERT: A 335 ASN cc_start: 0.7895 (t0) cc_final: 0.7577 (t0) REVERT: A 337 GLU cc_start: 0.7837 (tp30) cc_final: 0.7177 (tp30) REVERT: A 346 GLU cc_start: 0.7942 (tp30) cc_final: 0.7723 (tp30) REVERT: A 355 MET cc_start: 0.8347 (ttp) cc_final: 0.7975 (ttp) REVERT: A 366 MET cc_start: 0.8558 (mmm) cc_final: 0.8315 (mmm) REVERT: A 383 MET cc_start: 0.7821 (mmt) cc_final: 0.7436 (mmt) REVERT: A 386 PHE cc_start: 0.8086 (t80) cc_final: 0.7851 (t80) REVERT: A 411 SER cc_start: 0.8108 (t) cc_final: 0.7639 (p) REVERT: A 419 TRP cc_start: 0.8179 (p-90) cc_final: 0.7721 (p-90) REVERT: A 443 GLU cc_start: 0.7847 (tt0) cc_final: 0.7323 (tp30) REVERT: A 444 ASN cc_start: 0.8361 (t0) cc_final: 0.7910 (t0) REVERT: A 445 LEU cc_start: 0.8908 (mt) cc_final: 0.8656 (mt) REVERT: A 485 ASP cc_start: 0.7710 (p0) cc_final: 0.7500 (m-30) REVERT: A 500 ARG cc_start: 0.7052 (ptt180) cc_final: 0.5493 (mmm-85) REVERT: A 503 GLU cc_start: 0.8055 (tt0) cc_final: 0.7824 (tt0) REVERT: A 577 ASP cc_start: 0.8029 (m-30) cc_final: 0.7799 (m-30) REVERT: A 579 MET cc_start: 0.8142 (mtt) cc_final: 0.7899 (ttt) REVERT: A 585 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7223 (mtm180) REVERT: A 586 MET cc_start: 0.8399 (ttm) cc_final: 0.8182 (ttm) REVERT: A 587 LEU cc_start: 0.8799 (mt) cc_final: 0.8490 (mt) REVERT: A 591 LYS cc_start: 0.8337 (mttt) cc_final: 0.8130 (mtpp) REVERT: A 592 ILE cc_start: 0.8611 (mt) cc_final: 0.8387 (mm) REVERT: A 641 TYR cc_start: 0.7939 (m-80) cc_final: 0.7118 (m-80) REVERT: A 647 LYS cc_start: 0.8240 (mptt) cc_final: 0.7876 (mptt) REVERT: A 670 LEU cc_start: 0.2538 (OUTLIER) cc_final: 0.0786 (mp) REVERT: A 697 MET cc_start: 0.6953 (tpt) cc_final: 0.5977 (tpt) REVERT: A 729 GLU cc_start: 0.7770 (tp30) cc_final: 0.6757 (tp30) REVERT: A 733 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7549 (mmt180) REVERT: A 743 TYR cc_start: 0.7574 (t80) cc_final: 0.7218 (t80) REVERT: A 758 TYR cc_start: 0.5965 (m-80) cc_final: 0.5629 (m-80) REVERT: A 769 PHE cc_start: 0.7921 (t80) cc_final: 0.7511 (t80) REVERT: A 782 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6407 (tp30) REVERT: A 808 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7806 (tp) REVERT: A 810 MET cc_start: 0.5769 (ptt) cc_final: 0.5322 (ptt) REVERT: A 821 LEU cc_start: 0.8383 (mt) cc_final: 0.8010 (mt) REVERT: A 828 LYS cc_start: 0.8207 (mttt) cc_final: 0.7596 (mttt) REVERT: A 837 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: A 857 MET cc_start: 0.7058 (mtt) cc_final: 0.6496 (mtt) REVERT: A 865 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7769 (ptp-170) REVERT: A 872 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7904 (tp30) REVERT: A 967 MET cc_start: 0.7848 (mtp) cc_final: 0.7260 (mtp) REVERT: A 968 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7521 (mmmm) REVERT: A 971 ASP cc_start: 0.8152 (m-30) cc_final: 0.7789 (m-30) REVERT: A 1045 MET cc_start: 0.8652 (mmm) cc_final: 0.8264 (mmt) REVERT: A 1056 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8663 (t) REVERT: A 1063 VAL cc_start: 0.8121 (t) cc_final: 0.7905 (p) REVERT: A 1089 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7368 (mtm180) REVERT: A 1104 MET cc_start: 0.8070 (mmm) cc_final: 0.7332 (tpp) REVERT: A 1110 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7594 (mm-40) REVERT: A 1116 LYS cc_start: 0.8656 (tttp) cc_final: 0.8365 (tptp) REVERT: A 1134 PHE cc_start: 0.8219 (m-80) cc_final: 0.7670 (m-80) REVERT: A 1139 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6308 (m-30) REVERT: A 1178 TYR cc_start: 0.6470 (t80) cc_final: 0.6074 (t80) outliers start: 35 outliers final: 10 residues processed: 300 average time/residue: 0.2131 time to fit residues: 84.6222 Evaluate side-chains 280 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111685 restraints weight = 12802.741| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.05 r_work: 0.3247 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8218 Z= 0.245 Angle : 0.572 7.750 11144 Z= 0.300 Chirality : 0.041 0.248 1341 Planarity : 0.004 0.038 1371 Dihedral : 5.392 53.995 1104 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.56 % Allowed : 20.50 % Favored : 74.94 % 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: 0.82 (0.27), residues: 1008 helix: 1.21 (0.19), residues: 746 sheet: 0.34 (0.91), residues: 31 loop : -1.55 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1112 HIS 0.003 0.001 HIS A 458 PHE 0.026 0.002 PHE A 766 TYR 0.009 0.001 TYR A1035 ARG 0.008 0.001 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8756 (t80) REVERT: A 199 MET cc_start: 0.8296 (mmm) cc_final: 0.8069 (tpp) REVERT: A 200 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8097 (ttm) REVERT: A 217 LEU cc_start: 0.8003 (mt) cc_final: 0.7781 (mt) REVERT: A 233 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 236 LEU cc_start: 0.8214 (mt) cc_final: 0.7959 (mp) REVERT: A 250 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7477 (mmmt) REVERT: A 263 GLN cc_start: 0.8206 (mt0) cc_final: 0.7840 (mt0) REVERT: A 264 ASN cc_start: 0.8024 (m-40) cc_final: 0.7446 (m110) REVERT: A 267 TYR cc_start: 0.8350 (t80) cc_final: 0.7914 (t80) REVERT: A 335 ASN cc_start: 0.7913 (t0) cc_final: 0.7568 (t0) REVERT: A 337 GLU cc_start: 0.7836 (tp30) cc_final: 0.7074 (tp30) REVERT: A 346 GLU cc_start: 0.7787 (tp30) cc_final: 0.7530 (tp30) REVERT: A 383 MET cc_start: 0.7619 (mmt) cc_final: 0.6843 (mmt) REVERT: A 387 TYR cc_start: 0.8183 (m-10) cc_final: 0.7344 (m-10) REVERT: A 411 SER cc_start: 0.8174 (t) cc_final: 0.7704 (p) REVERT: A 419 TRP cc_start: 0.8077 (p-90) cc_final: 0.7710 (p-90) REVERT: A 427 TRP cc_start: 0.8558 (t-100) cc_final: 0.8326 (t-100) REVERT: A 443 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7127 (tp30) REVERT: A 444 ASN cc_start: 0.8283 (t0) cc_final: 0.7833 (t0) REVERT: A 445 LEU cc_start: 0.8837 (mt) cc_final: 0.8614 (mt) REVERT: A 500 ARG cc_start: 0.6987 (ptt180) cc_final: 0.5429 (mmm-85) REVERT: A 577 ASP cc_start: 0.8173 (m-30) cc_final: 0.7894 (m-30) REVERT: A 579 MET cc_start: 0.8100 (mtt) cc_final: 0.7861 (ttt) REVERT: A 585 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7242 (mtm180) REVERT: A 587 LEU cc_start: 0.8785 (mt) cc_final: 0.8482 (mt) REVERT: A 591 LYS cc_start: 0.8499 (mttt) cc_final: 0.8205 (mtpp) REVERT: A 592 ILE cc_start: 0.8666 (mt) cc_final: 0.8459 (mm) REVERT: A 598 PHE cc_start: 0.8995 (t80) cc_final: 0.8726 (t80) REVERT: A 628 VAL cc_start: 0.8589 (t) cc_final: 0.8297 (m) REVERT: A 632 LYS cc_start: 0.8574 (mttt) cc_final: 0.8341 (mttt) REVERT: A 697 MET cc_start: 0.7114 (tpt) cc_final: 0.6734 (tpt) REVERT: A 743 TYR cc_start: 0.7577 (t80) cc_final: 0.7223 (t80) REVERT: A 758 TYR cc_start: 0.6084 (m-80) cc_final: 0.5710 (m-80) REVERT: A 808 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7579 (tp) REVERT: A 810 MET cc_start: 0.5712 (ptt) cc_final: 0.5246 (ptt) REVERT: A 828 LYS cc_start: 0.8327 (mttt) cc_final: 0.8082 (mttt) REVERT: A 837 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: A 857 MET cc_start: 0.7221 (mtt) cc_final: 0.6682 (mtt) REVERT: A 868 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7861 (mmtt) REVERT: A 872 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7877 (tp30) REVERT: A 916 LEU cc_start: 0.8385 (mt) cc_final: 0.8126 (mp) REVERT: A 938 MET cc_start: 0.8423 (mmm) cc_final: 0.8207 (mmm) REVERT: A 967 MET cc_start: 0.7963 (mtp) cc_final: 0.7313 (mtp) REVERT: A 968 LYS cc_start: 0.7816 (mmmm) cc_final: 0.7466 (mmmm) REVERT: A 971 ASP cc_start: 0.8184 (m-30) cc_final: 0.7809 (m-30) REVERT: A 1033 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 1045 MET cc_start: 0.8644 (mmm) cc_final: 0.8318 (mmt) REVERT: A 1063 VAL cc_start: 0.8164 (t) cc_final: 0.7912 (p) REVERT: A 1104 MET cc_start: 0.7980 (mmm) cc_final: 0.7554 (tpp) REVERT: A 1116 LYS cc_start: 0.8703 (tttp) cc_final: 0.8337 (tttm) REVERT: A 1134 PHE cc_start: 0.8242 (m-80) cc_final: 0.7593 (m-80) REVERT: A 1135 GLN cc_start: 0.7905 (pt0) cc_final: 0.7552 (pt0) REVERT: A 1139 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6366 (m-30) REVERT: A 1178 TYR cc_start: 0.6502 (t80) cc_final: 0.6092 (t80) outliers start: 40 outliers final: 24 residues processed: 281 average time/residue: 0.2061 time to fit residues: 77.1321 Evaluate side-chains 273 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 597 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 = 0.3647 r_free = 0.3647 target = 0.130126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111579 restraints weight = 12696.975| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.06 r_work: 0.3255 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8218 Z= 0.251 Angle : 0.578 10.080 11144 Z= 0.303 Chirality : 0.041 0.208 1341 Planarity : 0.004 0.034 1371 Dihedral : 5.240 54.092 1101 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.33 % Allowed : 21.18 % Favored : 74.49 % 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: 1.03 (0.27), residues: 1008 helix: 1.39 (0.19), residues: 746 sheet: 0.21 (0.87), residues: 31 loop : -1.52 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1112 HIS 0.003 0.001 HIS A 458 PHE 0.026 0.002 PHE A 766 TYR 0.009 0.001 TYR A 672 ARG 0.006 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8696 (t80) REVERT: A 199 MET cc_start: 0.8256 (mmm) cc_final: 0.8048 (tpp) REVERT: A 217 LEU cc_start: 0.7981 (mt) cc_final: 0.7771 (mt) REVERT: A 233 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7267 (tm-30) REVERT: A 236 LEU cc_start: 0.8134 (mt) cc_final: 0.7892 (mp) REVERT: A 250 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7532 (mmmt) REVERT: A 263 GLN cc_start: 0.8181 (mt0) cc_final: 0.7786 (mt0) REVERT: A 264 ASN cc_start: 0.8025 (m-40) cc_final: 0.7413 (m-40) REVERT: A 267 TYR cc_start: 0.8327 (t80) cc_final: 0.7894 (t80) REVERT: A 335 ASN cc_start: 0.7906 (t0) cc_final: 0.7605 (t0) REVERT: A 383 MET cc_start: 0.7606 (mmt) cc_final: 0.6844 (mmt) REVERT: A 387 TYR cc_start: 0.8149 (m-10) cc_final: 0.7324 (m-10) REVERT: A 411 SER cc_start: 0.8171 (t) cc_final: 0.7713 (p) REVERT: A 427 TRP cc_start: 0.8513 (t-100) cc_final: 0.8302 (t-100) REVERT: A 443 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7134 (tp30) REVERT: A 444 ASN cc_start: 0.8290 (t0) cc_final: 0.7838 (t0) REVERT: A 445 LEU cc_start: 0.8850 (mt) cc_final: 0.8636 (mt) REVERT: A 500 ARG cc_start: 0.6965 (ptt180) cc_final: 0.5454 (mmm-85) REVERT: A 579 MET cc_start: 0.8087 (mtt) cc_final: 0.7859 (ttt) REVERT: A 587 LEU cc_start: 0.8752 (mt) cc_final: 0.8449 (mt) REVERT: A 588 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8166 (mmtt) REVERT: A 591 LYS cc_start: 0.8569 (mttt) cc_final: 0.8248 (mtpp) REVERT: A 592 ILE cc_start: 0.8662 (mt) cc_final: 0.8460 (mm) REVERT: A 598 PHE cc_start: 0.8995 (t80) cc_final: 0.8743 (t80) REVERT: A 628 VAL cc_start: 0.8579 (t) cc_final: 0.8294 (m) REVERT: A 632 LYS cc_start: 0.8591 (mttt) cc_final: 0.8328 (mttt) REVERT: A 697 MET cc_start: 0.7152 (tpt) cc_final: 0.6814 (tpt) REVERT: A 743 TYR cc_start: 0.7568 (t80) cc_final: 0.7233 (t80) REVERT: A 769 PHE cc_start: 0.7965 (t80) cc_final: 0.7548 (t80) REVERT: A 808 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7494 (tp) REVERT: A 810 MET cc_start: 0.5748 (ptt) cc_final: 0.5255 (ptt) REVERT: A 828 LYS cc_start: 0.8205 (mttt) cc_final: 0.7892 (mttt) REVERT: A 837 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: A 848 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7615 (mt-10) REVERT: A 872 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7879 (tp30) REVERT: A 916 LEU cc_start: 0.8373 (mt) cc_final: 0.8110 (mp) REVERT: A 967 MET cc_start: 0.7955 (mtp) cc_final: 0.7382 (mtp) REVERT: A 968 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7442 (mmmm) REVERT: A 971 ASP cc_start: 0.8170 (m-30) cc_final: 0.7837 (m-30) REVERT: A 1033 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 1045 MET cc_start: 0.8613 (mmm) cc_final: 0.8282 (mmt) REVERT: A 1063 VAL cc_start: 0.8172 (t) cc_final: 0.7919 (p) REVERT: A 1089 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8076 (mtm110) REVERT: A 1104 MET cc_start: 0.7991 (mmm) cc_final: 0.7508 (tpp) REVERT: A 1116 LYS cc_start: 0.8652 (tttp) cc_final: 0.8327 (tttm) REVERT: A 1134 PHE cc_start: 0.8214 (m-80) cc_final: 0.7610 (m-80) REVERT: A 1135 GLN cc_start: 0.7938 (pt0) cc_final: 0.7574 (pt0) REVERT: A 1139 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6278 (m-30) REVERT: A 1178 TYR cc_start: 0.6530 (t80) cc_final: 0.6154 (t80) outliers start: 38 outliers final: 28 residues processed: 273 average time/residue: 0.2136 time to fit residues: 77.8686 Evaluate side-chains 273 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 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 = 0.3652 r_free = 0.3652 target = 0.130392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111957 restraints weight = 12612.040| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.01 r_work: 0.3266 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8218 Z= 0.241 Angle : 0.571 11.412 11144 Z= 0.299 Chirality : 0.041 0.178 1341 Planarity : 0.004 0.037 1371 Dihedral : 5.248 54.189 1101 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.90 % Allowed : 21.18 % Favored : 73.92 % 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: 1.09 (0.27), residues: 1008 helix: 1.45 (0.19), residues: 746 sheet: 0.20 (0.84), residues: 31 loop : -1.59 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1112 HIS 0.008 0.001 HIS A 132 PHE 0.026 0.002 PHE A 766 TYR 0.008 0.001 TYR A 358 ARG 0.007 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8091 (ttm) cc_final: 0.7735 (ttm) REVERT: A 152 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8705 (t80) REVERT: A 199 MET cc_start: 0.8211 (mmm) cc_final: 0.7522 (mpp) REVERT: A 217 LEU cc_start: 0.7914 (mt) cc_final: 0.7702 (mt) REVERT: A 233 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 236 LEU cc_start: 0.8132 (mt) cc_final: 0.7896 (mp) REVERT: A 250 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7540 (mmmt) REVERT: A 263 GLN cc_start: 0.8171 (mt0) cc_final: 0.7777 (mt0) REVERT: A 264 ASN cc_start: 0.8021 (m-40) cc_final: 0.7360 (m-40) REVERT: A 267 TYR cc_start: 0.8312 (t80) cc_final: 0.7889 (t80) REVERT: A 335 ASN cc_start: 0.7882 (t0) cc_final: 0.7568 (t0) REVERT: A 383 MET cc_start: 0.7550 (mmt) cc_final: 0.6806 (mmt) REVERT: A 387 TYR cc_start: 0.8138 (m-10) cc_final: 0.7327 (m-10) REVERT: A 411 SER cc_start: 0.8174 (t) cc_final: 0.7713 (p) REVERT: A 419 TRP cc_start: 0.8023 (p-90) cc_final: 0.7760 (p-90) REVERT: A 444 ASN cc_start: 0.8286 (t0) cc_final: 0.7856 (t0) REVERT: A 449 ASP cc_start: 0.8315 (t0) cc_final: 0.7945 (t0) REVERT: A 500 ARG cc_start: 0.6961 (ptt180) cc_final: 0.5432 (mmm-85) REVERT: A 579 MET cc_start: 0.8062 (mtt) cc_final: 0.7824 (ttt) REVERT: A 587 LEU cc_start: 0.8741 (mt) cc_final: 0.8464 (mt) REVERT: A 591 LYS cc_start: 0.8570 (mttt) cc_final: 0.8240 (mtpp) REVERT: A 592 ILE cc_start: 0.8671 (mt) cc_final: 0.8452 (mm) REVERT: A 597 GLN cc_start: 0.8819 (mt0) cc_final: 0.8605 (mt0) REVERT: A 598 PHE cc_start: 0.8995 (t80) cc_final: 0.8748 (t80) REVERT: A 628 VAL cc_start: 0.8549 (t) cc_final: 0.8300 (m) REVERT: A 632 LYS cc_start: 0.8570 (mttt) cc_final: 0.8301 (mttt) REVERT: A 671 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6301 (ptp) REVERT: A 697 MET cc_start: 0.7128 (tpt) cc_final: 0.6817 (tpt) REVERT: A 729 GLU cc_start: 0.7775 (tp30) cc_final: 0.7450 (tp30) REVERT: A 743 TYR cc_start: 0.7560 (t80) cc_final: 0.7206 (t80) REVERT: A 769 PHE cc_start: 0.7946 (t80) cc_final: 0.7538 (t80) REVERT: A 808 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7436 (tp) REVERT: A 810 MET cc_start: 0.5784 (ptt) cc_final: 0.5267 (ptt) REVERT: A 828 LYS cc_start: 0.8199 (mttt) cc_final: 0.7877 (mttt) REVERT: A 837 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: A 848 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7651 (mt-10) REVERT: A 868 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7850 (mmtt) REVERT: A 872 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7790 (tp30) REVERT: A 911 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: A 916 LEU cc_start: 0.8356 (mt) cc_final: 0.8110 (mp) REVERT: A 967 MET cc_start: 0.7956 (mtp) cc_final: 0.7372 (mtp) REVERT: A 968 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7396 (mmmm) REVERT: A 971 ASP cc_start: 0.8139 (m-30) cc_final: 0.7786 (m-30) REVERT: A 1045 MET cc_start: 0.8547 (mmm) cc_final: 0.8240 (mmt) REVERT: A 1051 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8544 (ttpp) REVERT: A 1063 VAL cc_start: 0.8171 (t) cc_final: 0.7921 (p) REVERT: A 1104 MET cc_start: 0.7943 (mmm) cc_final: 0.7495 (tpp) REVERT: A 1116 LYS cc_start: 0.8643 (tttp) cc_final: 0.8310 (tttm) REVERT: A 1134 PHE cc_start: 0.8203 (m-80) cc_final: 0.7579 (m-80) REVERT: A 1135 GLN cc_start: 0.7920 (pt0) cc_final: 0.7557 (pt0) REVERT: A 1178 TYR cc_start: 0.6523 (t80) cc_final: 0.6153 (t80) outliers start: 43 outliers final: 30 residues processed: 274 average time/residue: 0.2110 time to fit residues: 77.4587 Evaluate side-chains 270 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 0.0370 chunk 0 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 165 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112651 restraints weight = 12594.204| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.00 r_work: 0.3277 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8218 Z= 0.219 Angle : 0.560 11.582 11144 Z= 0.293 Chirality : 0.040 0.177 1341 Planarity : 0.003 0.032 1371 Dihedral : 5.220 54.275 1101 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.44 % Allowed : 21.30 % Favored : 74.26 % 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: 1.16 (0.27), residues: 1008 helix: 1.50 (0.19), residues: 746 sheet: 0.17 (0.83), residues: 31 loop : -1.54 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1112 HIS 0.002 0.001 HIS A 458 PHE 0.026 0.002 PHE A 766 TYR 0.010 0.001 TYR A1088 ARG 0.005 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8222 (mmm) cc_final: 0.7448 (tpp) REVERT: A 217 LEU cc_start: 0.7925 (mt) cc_final: 0.7706 (mt) REVERT: A 233 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7145 (tm-30) REVERT: A 236 LEU cc_start: 0.8141 (mt) cc_final: 0.7909 (mp) REVERT: A 250 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7516 (mmmt) REVERT: A 263 GLN cc_start: 0.8162 (mt0) cc_final: 0.7740 (mt0) REVERT: A 264 ASN cc_start: 0.8018 (m-40) cc_final: 0.7345 (m-40) REVERT: A 267 TYR cc_start: 0.8307 (t80) cc_final: 0.7872 (t80) REVERT: A 289 PHE cc_start: 0.8120 (t80) cc_final: 0.7889 (t80) REVERT: A 335 ASN cc_start: 0.7881 (t0) cc_final: 0.7588 (t0) REVERT: A 383 MET cc_start: 0.7545 (mmt) cc_final: 0.6814 (mmt) REVERT: A 387 TYR cc_start: 0.8070 (m-10) cc_final: 0.7265 (m-10) REVERT: A 391 LEU cc_start: 0.8286 (tp) cc_final: 0.8061 (tt) REVERT: A 411 SER cc_start: 0.8089 (t) cc_final: 0.7686 (p) REVERT: A 419 TRP cc_start: 0.8021 (p-90) cc_final: 0.7817 (p-90) REVERT: A 449 ASP cc_start: 0.8341 (t0) cc_final: 0.7960 (t0) REVERT: A 500 ARG cc_start: 0.6909 (ptt180) cc_final: 0.5402 (mmm-85) REVERT: A 579 MET cc_start: 0.8008 (mtt) cc_final: 0.7774 (ttt) REVERT: A 585 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7484 (mtt-85) REVERT: A 587 LEU cc_start: 0.8759 (mt) cc_final: 0.8499 (mt) REVERT: A 591 LYS cc_start: 0.8555 (mttt) cc_final: 0.8243 (mtpp) REVERT: A 598 PHE cc_start: 0.8949 (t80) cc_final: 0.8693 (t80) REVERT: A 628 VAL cc_start: 0.8517 (t) cc_final: 0.8228 (m) REVERT: A 632 LYS cc_start: 0.8544 (mttt) cc_final: 0.8281 (mttt) REVERT: A 647 LYS cc_start: 0.8158 (mptt) cc_final: 0.7875 (mptt) REVERT: A 697 MET cc_start: 0.7106 (tpt) cc_final: 0.6753 (tpt) REVERT: A 743 TYR cc_start: 0.7445 (t80) cc_final: 0.7149 (t80) REVERT: A 769 PHE cc_start: 0.7911 (t80) cc_final: 0.7491 (t80) REVERT: A 808 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7388 (tp) REVERT: A 810 MET cc_start: 0.5773 (ptt) cc_final: 0.5324 (ptt) REVERT: A 828 LYS cc_start: 0.8173 (mttt) cc_final: 0.7896 (mttt) REVERT: A 837 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: A 848 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7703 (mt-10) REVERT: A 868 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7863 (mmtt) REVERT: A 872 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7768 (tp30) REVERT: A 911 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 916 LEU cc_start: 0.8348 (mt) cc_final: 0.8096 (mp) REVERT: A 943 ASN cc_start: 0.7988 (m-40) cc_final: 0.7595 (p0) REVERT: A 968 LYS cc_start: 0.7725 (mmmm) cc_final: 0.7437 (mmmm) REVERT: A 1033 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 1045 MET cc_start: 0.8507 (mmm) cc_final: 0.8218 (mmt) REVERT: A 1051 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8545 (ttpp) REVERT: A 1063 VAL cc_start: 0.8180 (t) cc_final: 0.7919 (p) REVERT: A 1104 MET cc_start: 0.7987 (mmm) cc_final: 0.7559 (tpp) REVERT: A 1116 LYS cc_start: 0.8600 (tttp) cc_final: 0.8272 (tttm) REVERT: A 1134 PHE cc_start: 0.8179 (m-80) cc_final: 0.7580 (m-80) REVERT: A 1135 GLN cc_start: 0.7888 (pt0) cc_final: 0.7513 (pt0) REVERT: A 1178 TYR cc_start: 0.6500 (t80) cc_final: 0.6186 (t80) outliers start: 39 outliers final: 31 residues processed: 257 average time/residue: 0.2078 time to fit residues: 71.5954 Evaluate side-chains 264 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.9039 > 50: distance: 46 - 63: 3.136 distance: 49 - 70: 4.579 distance: 55 - 77: 6.209 distance: 61 - 85: 24.346 distance: 66 - 94: 11.868 distance: 70 - 71: 3.694 distance: 71 - 72: 5.374 distance: 72 - 73: 9.482 distance: 72 - 77: 8.108 distance: 73 - 101: 7.885 distance: 74 - 75: 4.260 distance: 74 - 76: 5.698 distance: 77 - 78: 5.331 distance: 78 - 79: 8.740 distance: 78 - 81: 5.924 distance: 79 - 80: 7.718 distance: 79 - 85: 20.498 distance: 80 - 109: 9.318 distance: 81 - 82: 6.836 distance: 81 - 83: 5.680 distance: 85 - 86: 32.049 distance: 86 - 87: 7.987 distance: 86 - 89: 18.972 distance: 87 - 88: 12.099 distance: 87 - 94: 15.178 distance: 88 - 117: 6.082 distance: 89 - 90: 11.888 distance: 90 - 91: 21.518 distance: 91 - 92: 12.286 distance: 91 - 93: 3.213 distance: 94 - 95: 6.857 distance: 95 - 98: 3.948 distance: 96 - 101: 3.612 distance: 97 - 128: 3.971 distance: 98 - 99: 6.845 distance: 98 - 100: 5.492 distance: 101 - 102: 4.032 distance: 102 - 103: 4.235 distance: 103 - 104: 6.843 distance: 103 - 109: 7.602 distance: 104 - 136: 6.865 distance: 105 - 106: 3.057 distance: 106 - 107: 4.027 distance: 106 - 108: 4.295 distance: 109 - 110: 6.254 distance: 110 - 111: 7.366 distance: 110 - 113: 4.246 distance: 111 - 112: 12.738 distance: 111 - 117: 11.353 distance: 113 - 114: 5.681 distance: 114 - 115: 4.182 distance: 114 - 116: 10.130 distance: 117 - 118: 4.013 distance: 118 - 119: 5.037 distance: 118 - 121: 3.618 distance: 119 - 120: 8.899 distance: 119 - 128: 3.878 distance: 123 - 124: 5.082 distance: 124 - 125: 4.275 distance: 125 - 126: 7.072 distance: 125 - 127: 5.260 distance: 129 - 130: 6.812 distance: 129 - 132: 8.580 distance: 130 - 131: 6.256 distance: 130 - 136: 4.522 distance: 132 - 133: 3.536 distance: 132 - 134: 8.781 distance: 133 - 135: 11.711 distance: 136 - 137: 3.658 distance: 137 - 138: 6.746 distance: 137 - 140: 4.006 distance: 138 - 139: 8.232 distance: 138 - 144: 4.556 distance: 140 - 141: 13.385 distance: 141 - 142: 18.819 distance: 141 - 143: 16.096 distance: 145 - 146: 4.197 distance: 146 - 147: 6.126 distance: 146 - 148: 6.029