Starting phenix.real_space_refine on Thu May 1 04:15:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wb0_32391/05_2025/7wb0_32391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb0_32391/05_2025/7wb0_32391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/05_2025/7wb0_32391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb0_32391/05_2025/7wb0_32391.map" model { file = "/net/cci-nas-00/data/ceres_data/7wb0_32391/05_2025/7wb0_32391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb0_32391/05_2025/7wb0_32391.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 175 5.49 5 S 24 5.16 5 C 5765 2.51 5 N 1804 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10096 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 674 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 55, 'rna3p_pyr': 47} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain breaks: 1 Chain: "A" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6429 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 35, 'TRANS': 761} Chain breaks: 4 Time building chain proxies: 6.99, per 1000 atoms: 0.69 Number of scatterers: 10096 At special positions: 0 Unit cell: (104.34, 141, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 175 15.00 O 2328 8.00 N 1804 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 912 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 898.0 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 40.8% alpha, 18.4% beta 55 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.618A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.533A pdb=" N HIS A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 221 through 272 removed outlier: 3.662A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 647 through 650 removed outlier: 3.590A pdb=" N ILE A 650 " --> pdb=" O SER A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 697 through 717 removed outlier: 3.645A pdb=" N LYS A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 removed outlier: 3.539A pdb=" N ARG A 774 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 removed outlier: 3.998A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 821 through 829 removed outlier: 3.681A pdb=" N VAL A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 881 through 885 removed outlier: 3.596A pdb=" N SER A 884 " --> pdb=" O ASP A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 898 Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.569A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 removed outlier: 3.649A pdb=" N LYS A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 973 removed outlier: 3.708A pdb=" N VAL A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.928A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.671A pdb=" N LYS A 544 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 571 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 12.726A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694 removed outlier: 3.663A pdb=" N ALA A 666 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A 654 " --> pdb=" O MET A 752 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 754 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 656 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ALA A 756 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ILE A 658 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AA8, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.551A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.583A pdb=" N TYR A 853 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 862 " --> pdb=" O TYR A 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911 298 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2062 1.33 - 1.45: 3183 1.45 - 1.57: 5025 1.57 - 1.69: 346 1.69 - 1.81: 36 Bond restraints: 10652 Sorted by residual: bond pdb=" CA ASP A 522 " pdb=" CB ASP A 522 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.27e-02 6.20e+03 1.88e+00 bond pdb=" C ALA A 320 " pdb=" N LYS A 321 " ideal model delta sigma weight residual 1.331 1.357 -0.026 2.07e-02 2.33e+03 1.63e+00 bond pdb=" C LYS A 210 " pdb=" O LYS A 210 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.45e+00 bond pdb=" CG GLN A 702 " pdb=" CD GLN A 702 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CA ASN A 528 " pdb=" C ASN A 528 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.08e-02 8.57e+03 1.35e+00 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14949 2.09 - 4.18: 207 4.18 - 6.27: 16 6.27 - 8.35: 2 8.35 - 10.44: 1 Bond angle restraints: 15175 Sorted by residual: angle pdb=" C LYS A 899 " pdb=" N ARG A 900 " pdb=" CA ARG A 900 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LYS A 701 " pdb=" N GLN A 702 " pdb=" CA GLN A 702 " ideal model delta sigma weight residual 120.72 115.48 5.24 1.67e+00 3.59e-01 9.83e+00 angle pdb=" C LEU A 529 " pdb=" N TYR A 530 " pdb=" CA TYR A 530 " ideal model delta sigma weight residual 121.87 126.97 -5.10 1.64e+00 3.72e-01 9.67e+00 angle pdb=" C PHE A 901 " pdb=" N SER A 902 " pdb=" CA SER A 902 " ideal model delta sigma weight residual 122.56 117.92 4.64 1.50e+00 4.44e-01 9.58e+00 angle pdb=" N GLN A 702 " pdb=" CA GLN A 702 " pdb=" CB GLN A 702 " ideal model delta sigma weight residual 110.39 115.51 -5.12 1.66e+00 3.63e-01 9.53e+00 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 5699 29.54 - 59.07: 599 59.07 - 88.61: 128 88.61 - 118.14: 2 118.14 - 147.68: 1 Dihedral angle restraints: 6429 sinusoidal: 4103 harmonic: 2326 Sorted by residual: dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual 232.00 84.32 147.68 1 1.70e+01 3.46e-03 6.13e+01 dihedral pdb=" CA HIS A 903 " pdb=" C HIS A 903 " pdb=" N ARG A 904 " pdb=" CA ARG A 904 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 333 " pdb=" C PRO A 333 " pdb=" N LEU A 334 " pdb=" CA LEU A 334 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1355 0.033 - 0.067: 313 0.067 - 0.100: 72 0.100 - 0.133: 36 0.133 - 0.166: 2 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CB THR A 953 " pdb=" CA THR A 953 " pdb=" OG1 THR A 953 " pdb=" CG2 THR A 953 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CB ILE A 114 " pdb=" CA ILE A 114 " pdb=" CG1 ILE A 114 " pdb=" CG2 ILE A 114 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA VAL A 667 " pdb=" N VAL A 667 " pdb=" C VAL A 667 " pdb=" CB VAL A 667 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1775 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 889 " 0.164 9.50e-02 1.11e+02 7.37e-02 3.41e+00 pdb=" NE ARG A 889 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 889 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 889 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 889 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 20 " 0.020 2.00e-02 2.50e+03 1.04e-02 2.44e+00 pdb=" N1 U D 20 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U D 20 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U D 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U D 20 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U D 20 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 20 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U D 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U D 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 39 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.021 5.00e-02 4.00e+02 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 394 2.69 - 3.24: 8735 3.24 - 3.79: 16669 3.79 - 4.35: 20645 4.35 - 4.90: 31638 Nonbonded interactions: 78081 Sorted by model distance: nonbonded pdb=" OD1 ASP A 733 " pdb=" ND2 ASN A 737 " model vdw 2.136 3.120 nonbonded pdb=" OG1 THR A 38 " pdb=" OD1 ASP A 40 " model vdw 2.198 3.040 nonbonded pdb=" O6 DG B 22 " pdb=" NZ LYS A 227 " model vdw 2.246 3.120 nonbonded pdb=" O2 U D 45 " pdb=" N4 C D 46 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN A 737 " pdb=" NH2 ARG A 740 " model vdw 2.257 3.120 ... (remaining 78076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.150 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10653 Z= 0.133 Angle : 0.579 10.444 15177 Z= 0.323 Chirality : 0.034 0.166 1778 Planarity : 0.004 0.074 1303 Dihedral : 21.369 147.677 4922 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 0.54 (0.31), residues: 787 helix: 2.01 (0.30), residues: 297 sheet: 0.14 (0.46), residues: 134 loop : -1.01 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 304 HIS 0.001 0.001 HIS A 920 PHE 0.006 0.001 PHE A 917 TYR 0.016 0.001 TYR A 698 ARG 0.005 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.14720 ( 434) hydrogen bonds : angle 5.92054 ( 1115) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.54146 ( 2) covalent geometry : bond 0.00259 (10652) covalent geometry : angle 0.57858 (15175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.849 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2324 time to fit residues: 21.7306 Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 804 GLN A 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.173370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.122363 restraints weight = 21924.425| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.21 r_work: 0.3603 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10653 Z= 0.126 Angle : 0.540 6.769 15177 Z= 0.289 Chirality : 0.034 0.152 1778 Planarity : 0.004 0.046 1303 Dihedral : 23.296 148.477 3268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 0.57 % Allowed : 6.29 % Favored : 93.14 % 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: 0.81 (0.31), residues: 787 helix: 2.22 (0.30), residues: 304 sheet: 0.37 (0.48), residues: 123 loop : -0.91 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 304 HIS 0.002 0.001 HIS A 173 PHE 0.008 0.001 PHE A 588 TYR 0.017 0.001 TYR A 244 ARG 0.003 0.000 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 434) hydrogen bonds : angle 4.39216 ( 1115) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.70420 ( 2) covalent geometry : bond 0.00264 (10652) covalent geometry : angle 0.53960 (15175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.838 Fit side-chains REVERT: A 141 LYS cc_start: 0.6795 (ttmt) cc_final: 0.6190 (ttpt) REVERT: A 618 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 627 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7660 (mtt-85) REVERT: A 709 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7077 (tttm) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.2887 time to fit residues: 21.8193 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 924 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.167637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.117436 restraints weight = 21961.307| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.07 r_work: 0.3487 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10653 Z= 0.248 Angle : 0.667 8.438 15177 Z= 0.355 Chirality : 0.040 0.180 1778 Planarity : 0.005 0.061 1303 Dihedral : 23.423 132.864 3268 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer: Outliers : 1.00 % Allowed : 9.57 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.30), residues: 787 helix: 1.80 (0.30), residues: 297 sheet: -0.30 (0.45), residues: 133 loop : -1.27 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 86 HIS 0.005 0.002 HIS A 920 PHE 0.014 0.002 PHE A 588 TYR 0.029 0.002 TYR A 244 ARG 0.013 0.001 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.06826 ( 434) hydrogen bonds : angle 4.54694 ( 1115) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.69758 ( 2) covalent geometry : bond 0.00554 (10652) covalent geometry : angle 0.66720 (15175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6918 (ttmt) cc_final: 0.6510 (ttpp) REVERT: A 247 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7616 (tp) REVERT: A 627 ARG cc_start: 0.8239 (mtt90) cc_final: 0.7748 (mtt-85) REVERT: A 660 ARG cc_start: 0.6534 (mtm180) cc_final: 0.4748 (ttm110) REVERT: A 709 LYS cc_start: 0.7639 (ttmt) cc_final: 0.7278 (tttt) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.3222 time to fit residues: 25.9775 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 962 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.0670 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.172408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.123054 restraints weight = 22100.518| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.84 r_work: 0.3579 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10653 Z= 0.111 Angle : 0.520 7.640 15177 Z= 0.282 Chirality : 0.034 0.132 1778 Planarity : 0.004 0.049 1303 Dihedral : 23.203 138.258 3268 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 0.86 % Allowed : 10.71 % Favored : 88.43 % 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: 0.57 (0.31), residues: 787 helix: 2.31 (0.30), residues: 298 sheet: -0.33 (0.45), residues: 136 loop : -1.05 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 304 HIS 0.003 0.001 HIS A 251 PHE 0.009 0.001 PHE A 509 TYR 0.015 0.001 TYR A 244 ARG 0.008 0.000 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 434) hydrogen bonds : angle 4.00193 ( 1115) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.23673 ( 2) covalent geometry : bond 0.00225 (10652) covalent geometry : angle 0.51995 (15175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.876 Fit side-chains REVERT: A 141 LYS cc_start: 0.6911 (ttmt) cc_final: 0.6494 (ttpp) REVERT: A 153 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8051 (t) REVERT: A 234 MET cc_start: 0.8433 (mmp) cc_final: 0.8034 (mmp) REVERT: A 618 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 627 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7609 (mtt-85) REVERT: A 660 ARG cc_start: 0.6474 (mtm180) cc_final: 0.4634 (ttm110) REVERT: A 702 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6786 (tp-100) REVERT: A 709 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7481 (tttm) REVERT: A 723 TYR cc_start: 0.5204 (m-80) cc_final: 0.4330 (m-80) outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 0.3314 time to fit residues: 27.5048 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 0.0970 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 54 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.173829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.122934 restraints weight = 22270.522| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.22 r_work: 0.3623 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10653 Z= 0.106 Angle : 0.494 6.976 15177 Z= 0.268 Chirality : 0.032 0.129 1778 Planarity : 0.004 0.048 1303 Dihedral : 23.096 144.905 3268 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.29 % Allowed : 11.57 % Favored : 87.14 % 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: 0.84 (0.31), residues: 787 helix: 2.39 (0.30), residues: 305 sheet: 0.05 (0.46), residues: 132 loop : -0.93 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 304 HIS 0.004 0.001 HIS A 251 PHE 0.006 0.001 PHE A 509 TYR 0.011 0.001 TYR A 244 ARG 0.008 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 434) hydrogen bonds : angle 3.79236 ( 1115) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.17285 ( 2) covalent geometry : bond 0.00218 (10652) covalent geometry : angle 0.49367 (15175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6795 (ttmt) cc_final: 0.6367 (ttpp) REVERT: A 153 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8251 (t) REVERT: A 234 MET cc_start: 0.8341 (mmp) cc_final: 0.7907 (mmp) REVERT: A 618 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 627 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7626 (mtt-85) REVERT: A 660 ARG cc_start: 0.6278 (mtm180) cc_final: 0.4821 (ttm110) REVERT: A 702 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6689 (tp-100) REVERT: A 709 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7516 (tttm) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.3693 time to fit residues: 27.4790 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 813 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.0170 chunk 46 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 57 optimal weight: 0.2980 chunk 81 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.172273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.118686 restraints weight = 22118.742| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.07 r_work: 0.3603 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10653 Z= 0.121 Angle : 0.508 7.001 15177 Z= 0.275 Chirality : 0.033 0.131 1778 Planarity : 0.004 0.047 1303 Dihedral : 23.076 144.625 3268 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.71 % Allowed : 12.29 % Favored : 86.00 % 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: 0.77 (0.31), residues: 787 helix: 2.36 (0.30), residues: 305 sheet: -0.24 (0.45), residues: 139 loop : -0.88 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 304 HIS 0.003 0.001 HIS A 251 PHE 0.017 0.001 PHE A 815 TYR 0.017 0.001 TYR A 622 ARG 0.006 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 434) hydrogen bonds : angle 3.82151 ( 1115) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.24940 ( 2) covalent geometry : bond 0.00258 (10652) covalent geometry : angle 0.50794 (15175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.920 Fit side-chains REVERT: A 141 LYS cc_start: 0.6780 (ttmt) cc_final: 0.6341 (ttpp) REVERT: A 153 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8300 (t) REVERT: A 234 MET cc_start: 0.8409 (mmp) cc_final: 0.7810 (mmp) REVERT: A 618 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 627 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7524 (mtt-85) REVERT: A 660 ARG cc_start: 0.6452 (mtm180) cc_final: 0.4724 (ttm110) REVERT: A 702 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6599 (tp-100) REVERT: A 709 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7611 (tttm) REVERT: A 776 TYR cc_start: 0.5394 (OUTLIER) cc_final: 0.3437 (m-80) outliers start: 12 outliers final: 4 residues processed: 60 average time/residue: 0.3711 time to fit residues: 29.9329 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 776 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 74 optimal weight: 0.0670 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.169950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.121453 restraints weight = 21928.489| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.87 r_work: 0.3540 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10653 Z= 0.162 Angle : 0.551 7.719 15177 Z= 0.297 Chirality : 0.035 0.141 1778 Planarity : 0.004 0.047 1303 Dihedral : 23.127 139.091 3268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 1.43 % Allowed : 13.86 % Favored : 84.71 % 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: 0.56 (0.31), residues: 787 helix: 2.29 (0.30), residues: 299 sheet: -0.42 (0.45), residues: 137 loop : -1.01 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 304 HIS 0.004 0.001 HIS A 251 PHE 0.016 0.001 PHE A 588 TYR 0.019 0.001 TYR A 244 ARG 0.004 0.000 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 434) hydrogen bonds : angle 3.96846 ( 1115) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.37451 ( 2) covalent geometry : bond 0.00355 (10652) covalent geometry : angle 0.55083 (15175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6893 (ttmt) cc_final: 0.6455 (ttpp) REVERT: A 153 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8377 (t) REVERT: A 234 MET cc_start: 0.8543 (mmp) cc_final: 0.8139 (mmp) REVERT: A 306 ASN cc_start: 0.6887 (t0) cc_final: 0.6393 (t0) REVERT: A 618 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 627 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7334 (mtt-85) REVERT: A 660 ARG cc_start: 0.6418 (mtm180) cc_final: 0.4838 (ttm110) REVERT: A 702 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6502 (tp-100) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.3806 time to fit residues: 31.4751 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 776 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 0.0010 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 overall best weight: 1.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.171711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.125737 restraints weight = 21742.336| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.09 r_work: 0.3566 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10653 Z= 0.115 Angle : 0.516 7.856 15177 Z= 0.278 Chirality : 0.033 0.130 1778 Planarity : 0.004 0.045 1303 Dihedral : 23.073 141.659 3268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 1.43 % Allowed : 14.71 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.31), residues: 787 helix: 2.41 (0.30), residues: 299 sheet: -0.60 (0.43), residues: 149 loop : -0.91 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 304 HIS 0.003 0.001 HIS A 251 PHE 0.009 0.001 PHE A 588 TYR 0.013 0.001 TYR A 244 ARG 0.004 0.000 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 434) hydrogen bonds : angle 3.81784 ( 1115) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.24712 ( 2) covalent geometry : bond 0.00242 (10652) covalent geometry : angle 0.51583 (15175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8059 (mtm) REVERT: A 141 LYS cc_start: 0.6876 (ttmt) cc_final: 0.6431 (ttpp) REVERT: A 153 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8436 (t) REVERT: A 234 MET cc_start: 0.8460 (mmp) cc_final: 0.8117 (mmp) REVERT: A 618 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 627 ARG cc_start: 0.7692 (mtt90) cc_final: 0.7346 (mtt-85) REVERT: A 660 ARG cc_start: 0.6503 (mtm180) cc_final: 0.4888 (ttm110) REVERT: A 705 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7406 (mm) REVERT: A 754 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8333 (mp) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.3135 time to fit residues: 22.3839 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 779 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.0722 > 50: distance: 0 - 3: 3.046 distance: 31 - 87: 20.818 distance: 35 - 38: 12.872 distance: 38 - 39: 11.383 distance: 38 - 74: 15.803 distance: 39 - 40: 9.709 distance: 39 - 42: 18.444 distance: 40 - 41: 20.568 distance: 40 - 44: 7.961 distance: 41 - 71: 11.425 distance: 42 - 43: 18.277 distance: 44 - 45: 17.013 distance: 45 - 46: 12.278 distance: 45 - 48: 16.704 distance: 46 - 47: 16.198 distance: 46 - 50: 34.429 distance: 48 - 49: 30.956 distance: 50 - 51: 30.371 distance: 51 - 52: 19.528 distance: 51 - 54: 27.122 distance: 52 - 53: 33.791 distance: 52 - 59: 9.844 distance: 54 - 55: 10.311 distance: 55 - 56: 8.452 distance: 56 - 57: 8.946 distance: 56 - 58: 6.963 distance: 59 - 60: 3.864 distance: 60 - 61: 26.512 distance: 60 - 63: 18.939 distance: 61 - 62: 19.370 distance: 61 - 65: 40.209 distance: 63 - 64: 24.436 distance: 65 - 66: 7.750 distance: 66 - 67: 37.033 distance: 66 - 69: 31.376 distance: 67 - 68: 22.237 distance: 67 - 71: 12.872 distance: 69 - 70: 10.794 distance: 71 - 72: 19.489 distance: 72 - 73: 10.754 distance: 72 - 75: 12.956 distance: 73 - 74: 12.197 distance: 73 - 80: 18.990 distance: 75 - 76: 14.413 distance: 76 - 77: 15.030 distance: 77 - 78: 24.558 distance: 77 - 79: 20.868 distance: 80 - 81: 22.235 distance: 80 - 86: 20.444 distance: 81 - 82: 24.834 distance: 81 - 84: 12.295 distance: 82 - 83: 31.924 distance: 82 - 87: 22.971 distance: 84 - 85: 19.846 distance: 85 - 86: 19.079 distance: 87 - 88: 20.108 distance: 88 - 89: 23.262 distance: 88 - 91: 18.524 distance: 89 - 90: 32.993 distance: 89 - 95: 25.540 distance: 91 - 92: 12.138 distance: 92 - 93: 21.197 distance: 95 - 96: 11.608 distance: 95 - 138: 15.291 distance: 96 - 97: 9.369 distance: 96 - 99: 12.332 distance: 97 - 98: 21.832 distance: 97 - 107: 11.556 distance: 98 - 135: 15.674 distance: 100 - 101: 14.104 distance: 100 - 102: 6.047 distance: 101 - 103: 4.111 distance: 102 - 104: 7.451 distance: 103 - 105: 5.264 distance: 105 - 106: 6.330 distance: 107 - 108: 7.917 distance: 108 - 109: 9.093 distance: 108 - 111: 15.157 distance: 109 - 110: 18.691 distance: 111 - 112: 20.911 distance: 111 - 113: 22.466