Starting phenix.real_space_refine on Mon Nov 17 15:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6npj_0471/11_2025/6npj_0471.cif Found real_map, /net/cci-nas-00/data/ceres_data/6npj_0471/11_2025/6npj_0471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6npj_0471/11_2025/6npj_0471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6npj_0471/11_2025/6npj_0471.map" model { file = "/net/cci-nas-00/data/ceres_data/6npj_0471/11_2025/6npj_0471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6npj_0471/11_2025/6npj_0471.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.012 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 30 5.16 5 C 3936 2.51 5 N 1102 2.21 5 O 1118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6186 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3093 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 371} Chain breaks: 1 Chain: "B" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3093 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 371} Chain breaks: 1 Time building chain proxies: 1.49, per 1000 atoms: 0.24 Number of scatterers: 6186 At special positions: 0 Unit cell: (116.05, 88.62, 87.565, 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 30 16.00 O 1118 8.00 N 1102 7.00 C 3936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 234.7 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 43.4% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.753A pdb=" N HIS C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 699 " --> pdb=" O ALA C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 710 removed outlier: 4.018A pdb=" N LYS C 710 " --> pdb=" O ASP C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 733 removed outlier: 3.870A pdb=" N VAL C 733 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 761 removed outlier: 3.685A pdb=" N LEU C 760 " --> pdb=" O ASN C 756 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 756 through 761' Processing helix chain 'C' and resid 761 through 774 removed outlier: 3.612A pdb=" N ARG C 766 " --> pdb=" O SER C 762 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR C 767 " --> pdb=" O ASP C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 798 removed outlier: 3.898A pdb=" N TYR C 794 " --> pdb=" O GLN C 790 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET C 795 " --> pdb=" O GLY C 791 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 797 " --> pdb=" O GLN C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 824 Processing helix chain 'C' and resid 825 through 836 Processing helix chain 'C' and resid 929 through 937 removed outlier: 3.690A pdb=" N LEU C 934 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 935 " --> pdb=" O GLN C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 removed outlier: 4.052A pdb=" N LEU C 962 " --> pdb=" O GLY C 958 " (cutoff:3.500A) Proline residue: C 964 - end of helix Processing helix chain 'C' and resid 989 through 1003 removed outlier: 3.916A pdb=" N LEU C 999 " --> pdb=" O ALA C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1032 removed outlier: 3.763A pdb=" N GLU C1030 " --> pdb=" O THR C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1036 removed outlier: 3.704A pdb=" N LYS C1036 " --> pdb=" O GLU C1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1033 through 1036' Processing helix chain 'C' and resid 1041 through 1048 Processing helix chain 'C' and resid 1049 through 1051 No H-bonds generated for 'chain 'C' and resid 1049 through 1051' Processing helix chain 'C' and resid 1066 through 1084 removed outlier: 3.939A pdb=" N GLN C1073 " --> pdb=" O LYS C1069 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C1074 " --> pdb=" O GLY C1070 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C1078 " --> pdb=" O ILE C1074 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C1079 " --> pdb=" O ARG C1075 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS C1083 " --> pdb=" O LEU C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1114 removed outlier: 3.531A pdb=" N ALA C1109 " --> pdb=" O ALA C1105 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C1111 " --> pdb=" O TYR C1107 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C1112 " --> pdb=" O MET C1108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C1113 " --> pdb=" O ALA C1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.753A pdb=" N HIS B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 733 removed outlier: 3.870A pdb=" N VAL B 733 " --> pdb=" O ILE B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.685A pdb=" N LEU B 760 " --> pdb=" O ASN B 756 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 761 " --> pdb=" O PHE B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 761' Processing helix chain 'B' and resid 761 through 774 removed outlier: 3.612A pdb=" N ARG B 766 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR B 767 " --> pdb=" O ASP B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 798 removed outlier: 3.899A pdb=" N TYR B 794 " --> pdb=" O GLN B 790 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET B 795 " --> pdb=" O GLY B 791 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 824 Processing helix chain 'B' and resid 825 through 836 Processing helix chain 'B' and resid 929 through 937 removed outlier: 3.689A pdb=" N LEU B 934 " --> pdb=" O ASP B 930 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 969 removed outlier: 4.052A pdb=" N LEU B 962 " --> pdb=" O GLY B 958 " (cutoff:3.500A) Proline residue: B 964 - end of helix Processing helix chain 'B' and resid 989 through 1003 removed outlier: 3.915A pdb=" N LEU B 999 " --> pdb=" O ALA B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 3.764A pdb=" N GLU B1030 " --> pdb=" O THR B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1036 removed outlier: 3.703A pdb=" N LYS B1036 " --> pdb=" O GLU B1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1033 through 1036' Processing helix chain 'B' and resid 1041 through 1048 Processing helix chain 'B' and resid 1049 through 1051 No H-bonds generated for 'chain 'B' and resid 1049 through 1051' Processing helix chain 'B' and resid 1066 through 1084 removed outlier: 3.939A pdb=" N GLN B1073 " --> pdb=" O LYS B1069 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B1074 " --> pdb=" O GLY B1070 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B1078 " --> pdb=" O ILE B1074 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B1079 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B1083 " --> pdb=" O LEU B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1114 removed outlier: 3.532A pdb=" N ALA B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B1111 " --> pdb=" O TYR B1107 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B1112 " --> pdb=" O MET B1108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 778 through 785 removed outlier: 6.134A pdb=" N LEU C 717 " --> pdb=" O VAL C 810 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY C 812 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET C 719 " --> pdb=" O GLY C 812 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C1090 " --> pdb=" O LEU C1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C1124 " --> pdb=" O ILE C1090 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET C1092 " --> pdb=" O VAL C1124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C1089 " --> pdb=" O THR C 947 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 949 " --> pdb=" O LEU C1089 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C1093 " --> pdb=" O TRP C 951 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 977 " --> pdb=" O GLY C 946 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 778 through 785 removed outlier: 6.134A pdb=" N LEU C 717 " --> pdb=" O VAL C 810 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY C 812 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET C 719 " --> pdb=" O GLY C 812 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C1090 " --> pdb=" O LEU C1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C1124 " --> pdb=" O ILE C1090 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET C1092 " --> pdb=" O VAL C1124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C1089 " --> pdb=" O THR C 947 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 949 " --> pdb=" O LEU C1089 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C1093 " --> pdb=" O TRP C 951 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY C 983 " --> pdb=" O TRP C 952 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 980 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU C1013 " --> pdb=" O VAL C 980 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE C 982 " --> pdb=" O LEU C1013 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 778 through 785 removed outlier: 6.135A pdb=" N LEU B 717 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY B 812 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET B 719 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B1090 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B1124 " --> pdb=" O ILE B1090 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET B1092 " --> pdb=" O VAL B1124 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B1089 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 949 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B1093 " --> pdb=" O TRP B 951 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 977 " --> pdb=" O GLY B 946 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 778 through 785 removed outlier: 6.135A pdb=" N LEU B 717 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY B 812 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET B 719 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B1090 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B1124 " --> pdb=" O ILE B1090 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET B1092 " --> pdb=" O VAL B1124 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B1089 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 949 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B1093 " --> pdb=" O TRP B 951 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 983 " --> pdb=" O TRP B 952 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 980 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B1013 " --> pdb=" O VAL B 980 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B 982 " --> pdb=" O LEU B1013 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.46 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: 1881 1.34 - 1.45: 1057 1.45 - 1.57: 3320 1.57 - 1.69: 2 1.69 - 1.81: 50 Bond restraints: 6310 Sorted by residual: bond pdb=" N LEU C 933 " pdb=" CA LEU C 933 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.97e+00 bond pdb=" N ILE C 709 " pdb=" CA ILE C 709 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.83e+00 bond pdb=" CB THR C 792 " pdb=" CG2 THR C 792 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.52e+00 bond pdb=" CB THR B 792 " pdb=" CG2 THR B 792 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.40e+00 bond pdb=" N LYS C 710 " pdb=" CA LYS C 710 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.87e+00 ... (remaining 6305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 8326 3.61 - 7.21: 175 7.21 - 10.82: 16 10.82 - 14.43: 6 14.43 - 18.04: 1 Bond angle restraints: 8524 Sorted by residual: angle pdb=" CA GLN B 941 " pdb=" CB GLN B 941 " pdb=" CG GLN B 941 " ideal model delta sigma weight residual 114.10 127.34 -13.24 2.00e+00 2.50e-01 4.38e+01 angle pdb=" CA GLN C 941 " pdb=" CB GLN C 941 " pdb=" CG GLN C 941 " ideal model delta sigma weight residual 114.10 127.29 -13.19 2.00e+00 2.50e-01 4.35e+01 angle pdb=" N LEU C 933 " pdb=" CA LEU C 933 " pdb=" C LEU C 933 " ideal model delta sigma weight residual 111.14 117.95 -6.81 1.08e+00 8.57e-01 3.97e+01 angle pdb=" CA LEU B 933 " pdb=" CB LEU B 933 " pdb=" CG LEU B 933 " ideal model delta sigma weight residual 116.30 134.34 -18.04 3.50e+00 8.16e-02 2.66e+01 angle pdb=" CA LEU C 933 " pdb=" C LEU C 933 " pdb=" O LEU C 933 " ideal model delta sigma weight residual 120.70 115.84 4.86 1.03e+00 9.43e-01 2.22e+01 ... (remaining 8519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3291 17.54 - 35.08: 378 35.08 - 52.62: 96 52.62 - 70.16: 33 70.16 - 87.70: 12 Dihedral angle restraints: 3810 sinusoidal: 1580 harmonic: 2230 Sorted by residual: dihedral pdb=" CA GLN B 941 " pdb=" C GLN B 941 " pdb=" N LYS B 942 " pdb=" CA LYS B 942 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN C 941 " pdb=" C GLN C 941 " pdb=" N LYS C 942 " pdb=" CA LYS C 942 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ALA B 735 " pdb=" C ALA B 735 " pdb=" N PHE B 736 " pdb=" CA PHE B 736 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 730 0.074 - 0.148: 193 0.148 - 0.222: 22 0.222 - 0.296: 3 0.296 - 0.369: 2 Chirality restraints: 950 Sorted by residual: chirality pdb=" CG LEU C1050 " pdb=" CB LEU C1050 " pdb=" CD1 LEU C1050 " pdb=" CD2 LEU C1050 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CG LEU B1050 " pdb=" CB LEU B1050 " pdb=" CD1 LEU B1050 " pdb=" CD2 LEU B1050 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASP C 707 " pdb=" N ASP C 707 " pdb=" C ASP C 707 " pdb=" CB ASP C 707 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 947 not shown) Planarity restraints: 1086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 690 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU C 690 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU C 690 " 0.024 2.00e-02 2.50e+03 pdb=" N THR C 691 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 690 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU B 690 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU B 690 " 0.024 2.00e-02 2.50e+03 pdb=" N THR B 691 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C1119 " 0.060 5.00e-02 4.00e+02 9.17e-02 1.34e+01 pdb=" N PRO C1120 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO C1120 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C1120 " 0.051 5.00e-02 4.00e+02 ... (remaining 1083 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1328 2.78 - 3.31: 5451 3.31 - 3.84: 9638 3.84 - 4.37: 11199 4.37 - 4.90: 19271 Nonbonded interactions: 46887 Sorted by model distance: nonbonded pdb=" CB GLU B1030 " pdb=" OE2 GLU B1033 " model vdw 2.246 3.440 nonbonded pdb=" CB GLU C1030 " pdb=" OE2 GLU C1033 " model vdw 2.250 3.440 nonbonded pdb=" O VAL C 705 " pdb=" NH2 ARG B 769 " model vdw 2.301 3.120 nonbonded pdb=" OG SER B1052 " pdb=" O GLU B1054 " model vdw 2.314 3.040 nonbonded pdb=" OG SER C1052 " pdb=" O GLU C1054 " model vdw 2.314 3.040 ... (remaining 46882 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.008 0.096 6310 Z= 0.368 Angle : 1.244 18.035 8524 Z= 0.673 Chirality : 0.067 0.369 950 Planarity : 0.009 0.092 1086 Dihedral : 17.118 87.704 2366 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.25 % Allowed : 12.95 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -5.64 (0.22), residues: 760 helix: -3.93 (0.17), residues: 328 sheet: -2.35 (0.45), residues: 134 loop : -4.01 (0.24), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 753 TYR 0.018 0.003 TYR C 828 PHE 0.023 0.003 PHE C 736 TRP 0.013 0.002 TRP C 973 HIS 0.009 0.002 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00818 ( 6310) covalent geometry : angle 1.24355 ( 8524) hydrogen bonds : bond 0.23810 ( 201) hydrogen bonds : angle 8.88382 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 710 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5813 (mtpt) REVERT: C 1041 ASP cc_start: 0.5783 (m-30) cc_final: 0.4904 (m-30) REVERT: C 1074 ILE cc_start: 0.7971 (mt) cc_final: 0.7675 (mt) REVERT: B 729 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 1044 GLN cc_start: 0.7583 (pt0) cc_final: 0.6771 (tp40) outliers start: 42 outliers final: 10 residues processed: 194 average time/residue: 0.1265 time to fit residues: 29.5307 Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 1008 SER Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1008 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 774 ASN C 815 ASN C 833 HIS C1083 HIS B 731 HIS B 739 ASN B 774 ASN B 793 GLN B 833 HIS B1083 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.156289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129048 restraints weight = 9194.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131154 restraints weight = 6969.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132620 restraints weight = 5783.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133391 restraints weight = 5113.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134188 restraints weight = 4734.461| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6310 Z= 0.137 Angle : 0.660 12.348 8524 Z= 0.337 Chirality : 0.045 0.135 950 Planarity : 0.005 0.079 1086 Dihedral : 6.700 40.029 854 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.83 % Allowed : 17.86 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.65 (0.23), residues: 760 helix: -2.75 (0.21), residues: 330 sheet: -2.05 (0.44), residues: 144 loop : -3.90 (0.24), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 803 TYR 0.017 0.002 TYR B1135 PHE 0.016 0.002 PHE B 736 TRP 0.015 0.001 TRP C 770 HIS 0.005 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6310) covalent geometry : angle 0.65967 ( 8524) hydrogen bonds : bond 0.04472 ( 201) hydrogen bonds : angle 4.93526 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 954 PHE cc_start: 0.5782 (t80) cc_final: 0.5332 (t80) REVERT: C 1041 ASP cc_start: 0.5447 (m-30) cc_final: 0.4878 (m-30) REVERT: B 730 LEU cc_start: 0.8613 (mp) cc_final: 0.8260 (tt) REVERT: B 734 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7354 (t-90) REVERT: B 840 TYR cc_start: 0.8562 (m-80) cc_final: 0.8277 (m-80) REVERT: B 1042 MET cc_start: 0.6770 (tpp) cc_final: 0.6520 (ttt) REVERT: B 1075 ARG cc_start: 0.6730 (tpp-160) cc_final: 0.6123 (tpt170) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.0909 time to fit residues: 16.1971 Evaluate side-chains 106 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 986 ILE Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1116 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 724 ASN C 793 GLN C1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124561 restraints weight = 9149.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126512 restraints weight = 6894.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127914 restraints weight = 5738.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128705 restraints weight = 5087.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129034 restraints weight = 4703.759| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6310 Z= 0.155 Angle : 0.672 10.778 8524 Z= 0.335 Chirality : 0.046 0.258 950 Planarity : 0.005 0.067 1086 Dihedral : 6.183 36.352 845 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.91 % Allowed : 20.24 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.87 (0.26), residues: 760 helix: -1.82 (0.25), residues: 328 sheet: -1.78 (0.45), residues: 136 loop : -3.77 (0.26), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 803 TYR 0.014 0.002 TYR B1135 PHE 0.016 0.002 PHE B 736 TRP 0.014 0.001 TRP C 770 HIS 0.006 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6310) covalent geometry : angle 0.67198 ( 8524) hydrogen bonds : bond 0.04325 ( 201) hydrogen bonds : angle 4.50889 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 764 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7277 (tmm) REVERT: B 700 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 730 LEU cc_start: 0.8664 (mp) cc_final: 0.8261 (tt) REVERT: B 821 ASP cc_start: 0.7660 (t70) cc_final: 0.7455 (t70) REVERT: B 840 TYR cc_start: 0.8525 (m-80) cc_final: 0.8235 (m-80) REVERT: B 1075 ARG cc_start: 0.6807 (tpp-160) cc_final: 0.6268 (tpt170) outliers start: 33 outliers final: 21 residues processed: 133 average time/residue: 0.0921 time to fit residues: 15.6917 Evaluate side-chains 113 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 986 ILE Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1094 MET Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 731 HIS C 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129063 restraints weight = 9268.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131117 restraints weight = 6988.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132611 restraints weight = 5763.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133468 restraints weight = 5052.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134051 restraints weight = 4637.397| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6310 Z= 0.109 Angle : 0.591 8.870 8524 Z= 0.297 Chirality : 0.044 0.171 950 Planarity : 0.004 0.066 1086 Dihedral : 5.722 35.721 845 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.61 % Allowed : 21.43 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.27 (0.27), residues: 760 helix: -1.21 (0.27), residues: 316 sheet: -1.36 (0.49), residues: 124 loop : -3.52 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 988 TYR 0.014 0.001 TYR B1135 PHE 0.013 0.001 PHE C 736 TRP 0.012 0.001 TRP C 770 HIS 0.008 0.001 HIS C 734 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6310) covalent geometry : angle 0.59148 ( 8524) hydrogen bonds : bond 0.03638 ( 201) hydrogen bonds : angle 4.16388 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 700 LEU cc_start: 0.7790 (mm) cc_final: 0.7488 (mp) REVERT: C 764 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7156 (tmm) REVERT: B 730 LEU cc_start: 0.8583 (mp) cc_final: 0.8238 (tt) REVERT: B 821 ASP cc_start: 0.7251 (t70) cc_final: 0.6801 (m-30) outliers start: 31 outliers final: 20 residues processed: 130 average time/residue: 0.0978 time to fit residues: 16.1483 Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 0.0270 chunk 31 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 991 HIS B1061 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129663 restraints weight = 9276.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131651 restraints weight = 7065.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133075 restraints weight = 5868.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134081 restraints weight = 5180.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134540 restraints weight = 4738.562| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6310 Z= 0.107 Angle : 0.592 12.988 8524 Z= 0.291 Chirality : 0.044 0.131 950 Planarity : 0.004 0.063 1086 Dihedral : 5.432 34.614 845 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.06 % Allowed : 21.43 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.83 (0.28), residues: 760 helix: -0.71 (0.29), residues: 314 sheet: -1.12 (0.49), residues: 122 loop : -3.44 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 994 TYR 0.012 0.001 TYR B1135 PHE 0.030 0.002 PHE C 954 TRP 0.011 0.001 TRP C 770 HIS 0.006 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6310) covalent geometry : angle 0.59245 ( 8524) hydrogen bonds : bond 0.03454 ( 201) hydrogen bonds : angle 3.96534 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 700 LEU cc_start: 0.7695 (mm) cc_final: 0.7305 (mp) REVERT: C 764 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7044 (tmm) REVERT: B 700 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8485 (mm) REVERT: B 734 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7395 (t-90) REVERT: B 743 MET cc_start: 0.8646 (ttt) cc_final: 0.8243 (ttt) REVERT: B 1042 MET cc_start: 0.6696 (tpp) cc_final: 0.6366 (ttp) REVERT: B 1061 ASN cc_start: 0.6462 (t160) cc_final: 0.5613 (p0) outliers start: 34 outliers final: 21 residues processed: 135 average time/residue: 0.0938 time to fit residues: 16.1667 Evaluate side-chains 124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 991 HIS B1061 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128174 restraints weight = 9111.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130071 restraints weight = 6973.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131413 restraints weight = 5825.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132196 restraints weight = 5154.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133002 restraints weight = 4755.411| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6310 Z= 0.116 Angle : 0.608 11.800 8524 Z= 0.296 Chirality : 0.044 0.130 950 Planarity : 0.004 0.062 1086 Dihedral : 5.443 35.370 845 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.46 % Allowed : 22.32 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.51 (0.29), residues: 760 helix: -0.35 (0.30), residues: 302 sheet: -1.15 (0.47), residues: 130 loop : -3.23 (0.28), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 994 TYR 0.011 0.001 TYR B1135 PHE 0.013 0.001 PHE C 736 TRP 0.008 0.001 TRP C 770 HIS 0.006 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6310) covalent geometry : angle 0.60776 ( 8524) hydrogen bonds : bond 0.03398 ( 201) hydrogen bonds : angle 3.93004 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 764 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7115 (tmm) REVERT: C 933 LEU cc_start: 0.8581 (tp) cc_final: 0.8345 (mp) REVERT: B 700 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 734 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7503 (t-90) REVERT: B 743 MET cc_start: 0.8706 (ttt) cc_final: 0.8273 (ttt) REVERT: B 1042 MET cc_start: 0.6394 (tpp) cc_final: 0.6189 (ttp) outliers start: 30 outliers final: 20 residues processed: 122 average time/residue: 0.0916 time to fit residues: 14.6289 Evaluate side-chains 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/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-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0423 > 50: distance: 13 - 18: 24.622 distance: 18 - 19: 21.777 distance: 19 - 20: 13.894 distance: 19 - 22: 23.068 distance: 20 - 21: 15.874 distance: 20 - 29: 24.545 distance: 22 - 23: 9.476 distance: 23 - 24: 16.036 distance: 23 - 25: 18.304 distance: 24 - 26: 10.746 distance: 25 - 27: 15.885 distance: 26 - 28: 14.699 distance: 27 - 28: 21.856 distance: 29 - 30: 39.073 distance: 30 - 31: 6.545 distance: 30 - 33: 28.124 distance: 31 - 32: 17.087 distance: 31 - 40: 30.330 distance: 33 - 34: 14.499 distance: 34 - 35: 12.894 distance: 35 - 36: 14.718 distance: 36 - 37: 10.610 distance: 37 - 38: 4.756 distance: 40 - 41: 27.663 distance: 40 - 46: 3.063 distance: 41 - 42: 33.001 distance: 41 - 44: 13.656 distance: 42 - 43: 15.166 distance: 42 - 47: 9.730 distance: 44 - 45: 25.855 distance: 45 - 46: 49.607 distance: 47 - 48: 6.369 distance: 48 - 49: 9.772 distance: 48 - 51: 7.122 distance: 49 - 50: 17.730 distance: 49 - 56: 10.699 distance: 51 - 52: 8.062 distance: 52 - 53: 11.633 distance: 53 - 54: 7.062 distance: 53 - 55: 5.945 distance: 56 - 57: 13.866 distance: 57 - 60: 14.978 distance: 58 - 59: 16.295 distance: 58 - 62: 15.527 distance: 59 - 160: 20.780 distance: 60 - 61: 32.382 distance: 62 - 63: 31.733 distance: 63 - 64: 12.196 distance: 63 - 66: 19.714 distance: 64 - 65: 26.160 distance: 64 - 70: 18.557 distance: 66 - 67: 13.868 distance: 67 - 68: 19.975 distance: 67 - 69: 23.045 distance: 70 - 71: 9.212 distance: 70 - 163: 17.587 distance: 71 - 72: 8.212 distance: 71 - 74: 12.632 distance: 72 - 73: 23.456 distance: 72 - 77: 11.506 distance: 73 - 173: 19.928 distance: 74 - 75: 5.482 distance: 74 - 76: 13.473 distance: 77 - 78: 4.361 distance: 78 - 79: 6.700 distance: 78 - 81: 10.280 distance: 79 - 80: 13.254 distance: 79 - 85: 19.443 distance: 81 - 82: 13.273 distance: 82 - 83: 16.116 distance: 83 - 84: 6.834 distance: 86 - 87: 6.750 distance: 86 - 89: 13.661 distance: 87 - 88: 15.715 distance: 87 - 92: 13.832 distance: 89 - 90: 14.068 distance: 89 - 91: 16.614 distance: 92 - 93: 58.718 distance: 93 - 94: 20.213 distance: 94 - 95: 21.377 distance: 94 - 96: 14.547