Starting phenix.real_space_refine on Thu Jul 2 08:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6a69_6987/07_2026/6a69_6987.cif" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 39 5.16 5 C 5045 2.51 5 N 1324 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7851 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6839 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 36, 'TRANS': 847} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 5, 'TYR:plan': 2, 'GLU:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 998 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1014 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.98, per 1000 atoms: 0.25 Number of scatterers: 7851 At special positions: 0 Unit cell: (134.193, 103.645, 128.738, 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 39 16.00 O 1443 8.00 N 1324 7.00 C 5045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 200 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 301 " - " ASN B 168 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 545.9 milliseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 43.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 153 through 190 removed outlier: 3.994A pdb=" N ALA A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 362 through 397 removed outlier: 3.815A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.969A pdb=" N VAL A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.945A pdb=" N MET A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.733A pdb=" N CYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 removed outlier: 4.086A pdb=" N VAL A 563 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 625 through 632 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.842A pdb=" N LYS A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.973A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.857A pdb=" N LEU A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 834 through 877 removed outlier: 3.726A pdb=" N ILE A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 896 through 903 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.672A pdb=" N LEU A 912 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 913 " --> pdb=" O SER A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 925 through 949 Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.667A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1026 removed outlier: 4.004A pdb=" N LEU A1014 " --> pdb=" O CYS A1010 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A1025 " --> pdb=" O ILE A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1058 removed outlier: 3.913A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 245 removed outlier: 3.533A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.982A pdb=" N ILE A 472 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 707 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER A 474 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU A 765 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N MET A 706 " --> pdb=" O LEU A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.866A pdb=" N GLU A 683 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.650A pdb=" N MET A 585 " --> pdb=" O LYS A 601 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 613 through 616 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.471A pdb=" N LYS B 144 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 143 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.202A pdb=" N GLU B 131 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 211 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 200 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 197 " --> pdb=" O LYS B 158 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1038 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: 0.93 Time building geometry restraints manager: 0.79 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: 2391 1.34 - 1.46: 1487 1.46 - 1.58: 4055 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 7994 Sorted by residual: bond pdb=" C TRP A 759 " pdb=" N PRO A 760 " ideal model delta sigma weight residual 1.331 1.364 -0.032 7.90e-03 1.60e+04 1.64e+01 bond pdb=" C ALA B 222 " pdb=" N PRO B 223 " ideal model delta sigma weight residual 1.333 1.363 -0.030 7.80e-03 1.64e+04 1.46e+01 bond pdb=" CG GLN A1020 " pdb=" CD GLN A1020 " ideal model delta sigma weight residual 1.516 1.452 0.064 2.50e-02 1.60e+03 6.61e+00 bond pdb=" CB TRP A 759 " pdb=" CG TRP A 759 " ideal model delta sigma weight residual 1.498 1.423 0.075 3.10e-02 1.04e+03 5.81e+00 bond pdb=" CB VAL A 792 " pdb=" CG2 VAL A 792 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.40e+00 ... (remaining 7989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 10327 2.96 - 5.91: 425 5.91 - 8.87: 86 8.87 - 11.82: 22 11.82 - 14.78: 6 Bond angle restraints: 10866 Sorted by residual: angle pdb=" C HIS A 965 " pdb=" N ALA A 966 " pdb=" CA ALA A 966 " ideal model delta sigma weight residual 121.70 134.77 -13.07 1.80e+00 3.09e-01 5.28e+01 angle pdb=" N HIS A 965 " pdb=" CA HIS A 965 " pdb=" C HIS A 965 " ideal model delta sigma weight residual 111.07 118.76 -7.69 1.07e+00 8.73e-01 5.17e+01 angle pdb=" C SER A 642 " pdb=" N GLU A 643 " pdb=" CA GLU A 643 " ideal model delta sigma weight residual 121.70 134.07 -12.37 1.80e+00 3.09e-01 4.72e+01 angle pdb=" N GLY A 228 " pdb=" CA GLY A 228 " pdb=" C GLY A 228 " ideal model delta sigma weight residual 111.42 121.78 -10.36 1.51e+00 4.39e-01 4.71e+01 angle pdb=" N PRO A 67 " pdb=" CA PRO A 67 " pdb=" CB PRO A 67 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.48e+01 ... (remaining 10861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 4372 15.21 - 30.42: 323 30.42 - 45.64: 72 45.64 - 60.85: 11 60.85 - 76.06: 4 Dihedral angle restraints: 4782 sinusoidal: 1801 harmonic: 2981 Sorted by residual: dihedral pdb=" CA VAL A 680 " pdb=" C VAL A 680 " pdb=" N GLY A 681 " pdb=" CA GLY A 681 " ideal model delta harmonic sigma weight residual 180.00 126.37 53.63 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ASN A 565 " pdb=" C ASN A 565 " pdb=" N GLU A 566 " pdb=" CA GLU A 566 " ideal model delta harmonic sigma weight residual 0.00 44.37 -44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA PHE A 953 " pdb=" C PHE A 953 " pdb=" N PHE A 954 " pdb=" CA PHE A 954 " ideal model delta harmonic sigma weight residual -180.00 -137.23 -42.77 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 4779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1015 0.080 - 0.160: 260 0.160 - 0.240: 28 0.240 - 0.320: 4 0.320 - 0.400: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CB ILE A1061 " pdb=" CA ILE A1061 " pdb=" CG1 ILE A1061 " pdb=" CG2 ILE A1061 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA HIS A 965 " pdb=" N HIS A 965 " pdb=" C HIS A 965 " pdb=" CB HIS A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL A 680 " pdb=" CA VAL A 680 " pdb=" CG1 VAL A 680 " pdb=" CG2 VAL A 680 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1305 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 94 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO A 95 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 638 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 639 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 225 " 0.015 2.00e-02 2.50e+03 1.81e-02 8.22e+00 pdb=" CG TRP B 225 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 225 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 225 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 225 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 225 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2026 2.80 - 3.32: 7367 3.32 - 3.85: 12435 3.85 - 4.37: 13360 4.37 - 4.90: 22735 Nonbonded interactions: 57923 Sorted by model distance: nonbonded pdb=" O VAL A 515 " pdb=" OG SER A 519 " model vdw 2.275 3.040 nonbonded pdb=" O TYR A 513 " pdb=" OG1 THR A 516 " model vdw 2.308 3.040 nonbonded pdb=" O LEU A 947 " pdb=" NH1 ARG A 960 " model vdw 2.344 3.120 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 125 " model vdw 2.345 3.040 nonbonded pdb=" OE2 GLU B 135 " pdb=" NE2 GLN B 190 " model vdw 2.350 3.120 ... (remaining 57918 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.500 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.011 0.105 7996 Z= 0.483 Angle : 1.480 14.780 10871 Z= 0.816 Chirality : 0.069 0.400 1308 Planarity : 0.009 0.077 1372 Dihedral : 11.862 76.061 2851 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.53 % Favored : 86.37 % Rotamer: Outliers : 1.81 % Allowed : 4.58 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.43 % Twisted Proline : 0.00 % Twisted General : 0.91 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.21), residues: 1021 helix: -2.43 (0.19), residues: 449 sheet: -2.74 (0.46), residues: 103 loop : -3.93 (0.22), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 272 TYR 0.032 0.003 TYR A 445 PHE 0.036 0.004 PHE A 953 TRP 0.047 0.004 TRP B 225 HIS 0.009 0.003 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.01075 / 0.48 ( 7994) covalent geometry : angle 1.48034 / 0.82 (10866) SS BOND : bond 0.00490 / 0.31 ( 1) SS BOND : angle 1.29656 / 0.62 ( 2) hydrogen bonds : bond 0.17936 / 13.03 ( 358) hydrogen bonds : angle 7.61429 / 5.36 ( 1038) link_NAG-ASN : bond 0.00008 / 0.01 ( 1) link_NAG-ASN : angle 1.63205 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8689 (mt-10) REVERT: A 217 GLN cc_start: 0.8337 (tt0) cc_final: 0.7901 (tp40) REVERT: A 235 ASP cc_start: 0.8010 (m-30) cc_final: 0.7797 (t0) REVERT: A 466 MET cc_start: 0.8832 (tmm) cc_final: 0.8292 (tmm) REVERT: A 752 GLN cc_start: 0.8888 (tt0) cc_final: 0.8684 (tm-30) REVERT: A 794 VAL cc_start: 0.9608 (t) cc_final: 0.9408 (p) REVERT: A 814 MET cc_start: 0.8765 (mmp) cc_final: 0.8410 (mmp) REVERT: A 859 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8992 (tm-30) REVERT: A 887 MET cc_start: 0.8963 (tpp) cc_final: 0.8446 (tpp) REVERT: A 911 LEU cc_start: 0.9705 (mt) cc_final: 0.9472 (mp) REVERT: A 1017 PHE cc_start: 0.8919 (t80) cc_final: 0.8648 (t80) REVERT: B 218 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7903 (mtp-110) outliers start: 15 outliers final: 6 residues processed: 240 average time/residue: 0.0771 time to fit residues: 25.6547 Evaluate side-chains 145 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN A 540 HIS A 711 ASN A 886 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 HIS A1056 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106305 restraints weight = 19361.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105872 restraints weight = 11143.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106121 restraints weight = 8548.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106713 restraints weight = 7088.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107048 restraints weight = 6503.804| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7996 Z= 0.155 Angle : 0.817 12.918 10871 Z= 0.423 Chirality : 0.047 0.195 1308 Planarity : 0.006 0.074 1372 Dihedral : 7.084 41.152 1090 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.53 % Favored : 91.27 % Rotamer: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.24), residues: 1021 helix: -0.63 (0.23), residues: 461 sheet: -2.72 (0.42), residues: 114 loop : -3.67 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 558 TYR 0.012 0.001 TYR B 244 PHE 0.025 0.001 PHE A 953 TRP 0.013 0.001 TRP B 225 HIS 0.007 0.001 HIS A 971 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 7994) covalent geometry : angle 0.81704 / 0.42 (10866) SS BOND : bond 0.00233 / 0.15 ( 1) SS BOND : angle 0.11090 / 0.05 ( 2) hydrogen bonds : bond 0.05608 / 4.04 ( 358) hydrogen bonds : angle 5.67215 / 4.00 ( 1038) link_NAG-ASN : bond 0.00100 / 0.06 ( 1) link_NAG-ASN : angle 1.56940 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8152 (mp0) REVERT: A 217 GLN cc_start: 0.8208 (tt0) cc_final: 0.7959 (tp40) REVERT: A 268 GLU cc_start: 0.8224 (pp20) cc_final: 0.7958 (pp20) REVERT: A 411 ILE cc_start: 0.9258 (tp) cc_final: 0.9045 (mm) REVERT: A 421 ILE cc_start: 0.9577 (tp) cc_final: 0.9368 (tp) REVERT: A 466 MET cc_start: 0.8631 (tmm) cc_final: 0.7950 (tmm) REVERT: A 797 ASP cc_start: 0.8295 (p0) cc_final: 0.8085 (p0) REVERT: A 814 MET cc_start: 0.8675 (mmp) cc_final: 0.8263 (mmp) REVERT: A 887 MET cc_start: 0.8869 (tpp) cc_final: 0.8367 (tpp) REVERT: A 982 MET cc_start: 0.9292 (ttm) cc_final: 0.9090 (ttm) REVERT: A 1006 ASN cc_start: 0.8470 (m-40) cc_final: 0.7767 (m-40) REVERT: A 1049 MET cc_start: 0.7718 (mmt) cc_final: 0.7397 (tpp) REVERT: B 157 LYS cc_start: 0.6249 (tptp) cc_final: 0.5608 (mmmt) REVERT: B 199 GLU cc_start: 0.5416 (pt0) cc_final: 0.5187 (pt0) outliers start: 2 outliers final: 2 residues processed: 215 average time/residue: 0.0676 time to fit residues: 21.0344 Evaluate side-chains 139 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 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 = 0.3796 r_free = 0.3796 target = 0.142092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107649 restraints weight = 19381.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107925 restraints weight = 10868.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108215 restraints weight = 9593.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110189 restraints weight = 7185.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110199 restraints weight = 5458.254| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7996 Z= 0.141 Angle : 0.778 12.665 10871 Z= 0.401 Chirality : 0.046 0.192 1308 Planarity : 0.006 0.087 1372 Dihedral : 6.500 40.051 1090 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.61 % Favored : 90.20 % Rotamer: Outliers : 0.12 % Allowed : 2.41 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.25), residues: 1021 helix: 0.19 (0.24), residues: 455 sheet: -2.58 (0.44), residues: 113 loop : -3.45 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 767 TYR 0.010 0.001 TYR A 445 PHE 0.019 0.001 PHE A 953 TRP 0.007 0.001 TRP B 225 HIS 0.006 0.001 HIS A 971 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 7994) covalent geometry : angle 0.77738 / 0.40 (10866) SS BOND : bond 0.00184 / 0.11 ( 1) SS BOND : angle 0.37541 / 0.18 ( 2) hydrogen bonds : bond 0.04788 / 3.44 ( 358) hydrogen bonds : angle 5.14835 / 3.63 ( 1038) link_NAG-ASN : bond 0.00234 / 0.15 ( 1) link_NAG-ASN : angle 1.34015 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8082 (mp0) REVERT: A 466 MET cc_start: 0.8686 (tmm) cc_final: 0.8058 (tmm) REVERT: A 887 MET cc_start: 0.8939 (tpp) cc_final: 0.8396 (tpp) REVERT: A 928 MET cc_start: 0.8239 (tpp) cc_final: 0.7884 (tpp) REVERT: A 964 LEU cc_start: 0.8473 (tt) cc_final: 0.8263 (tt) REVERT: A 982 MET cc_start: 0.9270 (ttm) cc_final: 0.9050 (ttm) REVERT: A 1006 ASN cc_start: 0.8446 (m-40) cc_final: 0.7970 (m-40) REVERT: A 1049 MET cc_start: 0.7943 (mmt) cc_final: 0.7423 (mtt) REVERT: B 157 LYS cc_start: 0.6326 (tptp) cc_final: 0.5829 (mmmt) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.0554 time to fit residues: 15.3346 Evaluate side-chains 131 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 ASN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 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 = 0.3779 r_free = 0.3779 target = 0.140841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105742 restraints weight = 20099.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105895 restraints weight = 11344.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106114 restraints weight = 10289.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107668 restraints weight = 7835.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107655 restraints weight = 6308.496| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 7996 Z= 0.160 Angle : 0.746 12.334 10871 Z= 0.388 Chirality : 0.046 0.191 1308 Planarity : 0.006 0.082 1372 Dihedral : 6.183 41.021 1090 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.80 % Favored : 90.00 % Rotamer: Outliers : 0.24 % Allowed : 2.53 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.25), residues: 1021 helix: 0.45 (0.25), residues: 458 sheet: -2.44 (0.44), residues: 113 loop : -3.44 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 716 TYR 0.012 0.001 TYR A 445 PHE 0.016 0.001 PHE A 954 TRP 0.007 0.001 TRP A 759 HIS 0.004 0.001 HIS A 971 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 7994) covalent geometry : angle 0.74557 / 0.39 (10866) SS BOND : bond 0.00141 / 0.09 ( 1) SS BOND : angle 0.43114 / 0.18 ( 2) hydrogen bonds : bond 0.04623 / 3.29 ( 358) hydrogen bonds : angle 4.96667 / 3.51 ( 1038) link_NAG-ASN : bond 0.00206 / 0.13 ( 1) link_NAG-ASN : angle 0.98324 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8086 (mp0) REVERT: A 217 GLN cc_start: 0.7579 (tp40) cc_final: 0.7225 (mm110) REVERT: A 466 MET cc_start: 0.8745 (tmm) cc_final: 0.8116 (tmm) REVERT: A 757 LYS cc_start: 0.8402 (mmpt) cc_final: 0.8146 (mmtp) REVERT: A 905 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 982 MET cc_start: 0.9285 (ttm) cc_final: 0.8951 (ttm) REVERT: A 1049 MET cc_start: 0.7831 (mmt) cc_final: 0.7341 (mtt) REVERT: B 157 LYS cc_start: 0.6426 (tptp) cc_final: 0.5936 (mmmt) REVERT: B 162 MET cc_start: 0.7021 (pmm) cc_final: 0.6820 (pmm) outliers start: 2 outliers final: 1 residues processed: 177 average time/residue: 0.0470 time to fit residues: 12.6830 Evaluate side-chains 136 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 93 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 HIS ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 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 = 0.3788 r_free = 0.3788 target = 0.141082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104611 restraints weight = 36237.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104929 restraints weight = 16547.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106587 restraints weight = 11679.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107161 restraints weight = 8046.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108171 restraints weight = 6912.693| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7996 Z= 0.154 Angle : 0.732 12.102 10871 Z= 0.382 Chirality : 0.045 0.179 1308 Planarity : 0.006 0.091 1372 Dihedral : 6.084 40.930 1090 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.31 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.25), residues: 1021 helix: 0.58 (0.25), residues: 457 sheet: -2.21 (0.45), residues: 115 loop : -3.41 (0.24), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.017 0.001 TYR A 560 PHE 0.016 0.001 PHE A 954 TRP 0.007 0.001 TRP A 404 HIS 0.007 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7994) covalent geometry : angle 0.73201 / 0.38 (10866) SS BOND : bond 0.00100 / 0.06 ( 1) SS BOND : angle 0.48347 / 0.22 ( 2) hydrogen bonds : bond 0.04502 / 3.23 ( 358) hydrogen bonds : angle 4.78387 / 3.40 ( 1038) link_NAG-ASN : bond 0.00184 / 0.11 ( 1) link_NAG-ASN : angle 0.90455 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8076 (mp0) REVERT: A 466 MET cc_start: 0.8730 (tmm) cc_final: 0.8384 (tmm) REVERT: A 485 MET cc_start: 0.7954 (pmm) cc_final: 0.7718 (pmm) REVERT: A 711 ASN cc_start: 0.7696 (p0) cc_final: 0.7437 (p0) REVERT: A 757 LYS cc_start: 0.8399 (mmpt) cc_final: 0.8050 (mmtp) REVERT: A 887 MET cc_start: 0.9224 (tpp) cc_final: 0.8404 (tpp) REVERT: A 905 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 928 MET cc_start: 0.8318 (tpp) cc_final: 0.7840 (tpp) REVERT: A 1049 MET cc_start: 0.7888 (mmt) cc_final: 0.7411 (mtt) REVERT: B 157 LYS cc_start: 0.6450 (tptp) cc_final: 0.5976 (mmmt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0521 time to fit residues: 14.6083 Evaluate side-chains 133 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 60 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 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 = 0.3805 r_free = 0.3805 target = 0.142594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107585 restraints weight = 19817.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107643 restraints weight = 11442.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108074 restraints weight = 10414.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108798 restraints weight = 7726.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109165 restraints weight = 6796.024| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7996 Z= 0.134 Angle : 0.704 12.182 10871 Z= 0.370 Chirality : 0.044 0.182 1308 Planarity : 0.006 0.093 1372 Dihedral : 5.947 40.868 1090 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.14 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.26), residues: 1021 helix: 0.78 (0.25), residues: 455 sheet: -1.97 (0.46), residues: 114 loop : -3.23 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.007 0.001 TYR A 445 PHE 0.030 0.001 PHE A 953 TRP 0.005 0.001 TRP A 404 HIS 0.006 0.001 HIS A 971 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7994) covalent geometry : angle 0.70407 / 0.37 (10866) SS BOND : bond 0.00045 / 0.03 ( 1) SS BOND : angle 0.49556 / 0.21 ( 2) hydrogen bonds : bond 0.04093 / 2.92 ( 358) hydrogen bonds : angle 4.68842 / 3.33 ( 1038) link_NAG-ASN : bond 0.00297 / 0.19 ( 1) link_NAG-ASN : angle 0.73023 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8035 (mp0) REVERT: A 268 GLU cc_start: 0.7811 (pp20) cc_final: 0.7586 (pp20) REVERT: A 451 MET cc_start: 0.8264 (tpp) cc_final: 0.8054 (tmm) REVERT: A 466 MET cc_start: 0.8800 (tmm) cc_final: 0.8482 (tmm) REVERT: A 482 MET cc_start: 0.7609 (mmp) cc_final: 0.7095 (mmp) REVERT: A 711 ASN cc_start: 0.7509 (p0) cc_final: 0.7259 (p0) REVERT: A 757 LYS cc_start: 0.8324 (mmpt) cc_final: 0.7875 (mptt) REVERT: A 887 MET cc_start: 0.9138 (tpp) cc_final: 0.8460 (tpp) REVERT: A 1049 MET cc_start: 0.7832 (mmt) cc_final: 0.7570 (mmt) REVERT: B 157 LYS cc_start: 0.6591 (tptp) cc_final: 0.5935 (mmmt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0589 time to fit residues: 16.0629 Evaluate side-chains 130 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6929 > 50: distance: 27 - 57: 6.324 distance: 32 - 39: 12.783 distance: 33 - 62: 8.307 distance: 39 - 40: 9.616 distance: 40 - 41: 4.720 distance: 40 - 43: 3.386 distance: 41 - 42: 4.843 distance: 41 - 48: 4.857 distance: 42 - 70: 11.365 distance: 43 - 44: 3.467 distance: 44 - 45: 3.621 distance: 45 - 46: 11.213 distance: 45 - 47: 14.086 distance: 48 - 49: 4.983 distance: 49 - 50: 3.416 distance: 49 - 52: 8.341 distance: 50 - 51: 10.440 distance: 50 - 57: 6.402 distance: 51 - 78: 10.391 distance: 53 - 54: 7.753 distance: 54 - 55: 4.880 distance: 54 - 56: 17.559 distance: 57 - 58: 10.727 distance: 58 - 59: 4.457 distance: 58 - 61: 4.668 distance: 59 - 60: 9.892 distance: 59 - 62: 4.682 distance: 62 - 63: 3.910 distance: 63 - 64: 4.297 distance: 63 - 66: 6.131 distance: 64 - 65: 19.249 distance: 64 - 70: 4.488 distance: 66 - 67: 8.268 distance: 66 - 68: 13.845 distance: 67 - 69: 18.511 distance: 70 - 71: 7.576 distance: 71 - 72: 3.916 distance: 72 - 78: 4.682 distance: 74 - 75: 3.733 distance: 75 - 76: 8.351 distance: 75 - 77: 14.147 distance: 78 - 79: 6.664 distance: 79 - 82: 12.122 distance: 80 - 81: 4.993 distance: 80 - 87: 14.962 distance: 82 - 83: 5.204 distance: 85 - 86: 7.350 distance: 87 - 88: 18.744 distance: 88 - 89: 15.803 distance: 88 - 91: 4.266 distance: 89 - 90: 16.962 distance: 89 - 95: 31.205 distance: 91 - 92: 47.095 distance: 91 - 93: 22.097 distance: 92 - 94: 3.668 distance: 95 - 96: 23.347 distance: 96 - 97: 20.507 distance: 96 - 99: 8.424 distance: 97 - 98: 8.648 distance: 97 - 109: 8.569 distance: 99 - 100: 3.330 distance: 100 - 101: 9.529 distance: 100 - 102: 5.291 distance: 101 - 103: 7.539 distance: 102 - 105: 5.649 distance: 103 - 104: 6.131 distance: 104 - 106: 9.111 distance: 105 - 107: 8.937 distance: 106 - 108: 6.454 distance: 107 - 108: 5.953 distance: 109 - 110: 6.848 distance: 109 - 115: 6.046 distance: 110 - 111: 11.708 distance: 110 - 113: 12.359 distance: 111 - 112: 15.272 distance: 111 - 116: 13.177 distance: 113 - 114: 4.115 distance: 114 - 115: 10.570 distance: 116 - 117: 37.181 distance: 117 - 118: 18.757 distance: 117 - 120: 3.821 distance: 118 - 119: 7.683 distance: 118 - 121: 8.931