Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 15:40:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/10_2023/7zmd_14795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/10_2023/7zmd_14795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/10_2023/7zmd_14795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/10_2023/7zmd_14795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/10_2023/7zmd_14795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/10_2023/7zmd_14795.pdb" } resolution = 2.93 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9290 atoms to isotropic. 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 S 40 5.16 5 C 5883 2.51 5 N 1575 2.21 5 O 1796 1.98 5 H 9106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 706": "OE1" <-> "OE2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 757": "OD1" <-> "OD2" Residue "A ASP 770": "OD1" <-> "OD2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1092": "OD1" <-> "OD2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B ASP 753": "OD1" <-> "OD2" Residue "B PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 757": "OD1" <-> "OD2" Residue "B ASP 770": "OD1" <-> "OD2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 989": "OE1" <-> "OE2" Residue "B TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1092": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 18400 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9205 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 25, 'TRANS': 570} Chain: "B" Number of atoms: 9195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9195 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 25, 'TRANS': 569} Time building chain proxies: 8.40, per 1000 atoms: 0.46 Number of scatterers: 18400 At special positions: 0 Unit cell: (106.858, 119.554, 79.35, 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 40 16.00 O 1796 8.00 N 1575 7.00 C 5883 6.00 H 9106 1.00 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 - 3.50 Amino acid : False - 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: 15.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 43.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 554 through 565 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 623 through 640 Processing helix chain 'A' and resid 643 through 648 removed outlier: 4.589A pdb=" N CYS A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 4.123A pdb=" N ALA A 674 " --> pdb=" O TYR A 670 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 695 through 710 Processing helix chain 'A' and resid 726 through 736 removed outlier: 4.309A pdb=" N TYR A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 733 " --> pdb=" O HIS A 729 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 801 through 817 Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.829A pdb=" N ILE A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 873 through 889 Processing helix chain 'A' and resid 905 through 909 Processing helix chain 'A' and resid 926 through 930 removed outlier: 3.653A pdb=" N GLY A 929 " --> pdb=" O GLU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1002 Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1018 Processing helix chain 'A' and resid 1032 through 1045 Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 4.025A pdb=" N ASP A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1084 removed outlier: 4.170A pdb=" N GLU A1075 " --> pdb=" O ASP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.609A pdb=" N LYS A1104 " --> pdb=" O ASP A1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 615 through 622 Processing helix chain 'B' and resid 623 through 640 Processing helix chain 'B' and resid 643 through 648 removed outlier: 4.588A pdb=" N CYS B 648 " --> pdb=" O PRO B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 4.122A pdb=" N ALA B 674 " --> pdb=" O TYR B 670 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 677 " --> pdb=" O ILE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 694 No H-bonds generated for 'chain 'B' and resid 692 through 694' Processing helix chain 'B' and resid 695 through 710 Processing helix chain 'B' and resid 726 through 736 removed outlier: 4.309A pdb=" N TYR B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 733 " --> pdb=" O HIS B 729 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 776 Processing helix chain 'B' and resid 801 through 817 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 835 through 850 removed outlier: 3.829A pdb=" N ILE B 839 " --> pdb=" O LEU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 870 through 872 No H-bonds generated for 'chain 'B' and resid 870 through 872' Processing helix chain 'B' and resid 873 through 889 Processing helix chain 'B' and resid 905 through 909 Processing helix chain 'B' and resid 983 through 1002 Processing helix chain 'B' and resid 1004 through 1006 No H-bonds generated for 'chain 'B' and resid 1004 through 1006' Processing helix chain 'B' and resid 1007 through 1018 Processing helix chain 'B' and resid 1032 through 1045 Processing helix chain 'B' and resid 1062 through 1071 removed outlier: 4.024A pdb=" N ASP B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1071 through 1084 removed outlier: 4.169A pdb=" N GLU B1075 " --> pdb=" O ASP B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1095 Processing helix chain 'B' and resid 1101 through 1106 removed outlier: 3.609A pdb=" N LYS B1104 " --> pdb=" O ASP B1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 823 through 827 removed outlier: 6.926A pdb=" N ILE A 937 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 825 " --> pdb=" O ILE A 937 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 949 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET A 788 " --> pdb=" O ASN A 949 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS A 951 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 786 " --> pdb=" O HIS A 951 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 953 " --> pdb=" O LYS A 784 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 781 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 765 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 545 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA A 763 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY A 547 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 761 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL A 688 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 655 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 690 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 657 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL B 688 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 655 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 690 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 657 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 761 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 547 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 763 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 545 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 765 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 781 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 953 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 786 " --> pdb=" O HIS B 951 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS B 951 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET B 788 " --> pdb=" O ASN B 949 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN B 949 " --> pdb=" O MET B 788 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 937 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 825 " --> pdb=" O ILE B 937 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 858 through 860 removed outlier: 6.209A pdb=" N CYS A 858 " --> pdb=" O VAL A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AA6, first strand: chain 'A' and resid 924 through 925 removed outlier: 3.567A pdb=" N VAL A 925 " --> pdb=" O ASN A 932 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 975 through 981 removed outlier: 3.505A pdb=" N ALA A1030 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A1056 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A1027 " --> pdb=" O TYR A1054 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 607 Processing sheet with id=AB1, first strand: chain 'B' and resid 858 through 860 removed outlier: 6.209A pdb=" N CYS B 858 " --> pdb=" O VAL B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AB3, first strand: chain 'B' and resid 924 through 925 removed outlier: 3.566A pdb=" N VAL B 925 " --> pdb=" O ASN B 932 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 975 through 981 removed outlier: 3.504A pdb=" N ALA B1030 " --> pdb=" O ALA B 975 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B1056 " --> pdb=" O ARG B1025 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B1027 " --> pdb=" O TYR B1054 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1128 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: 6.83 Time building geometry restraints manager: 15.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9094 1.03 - 1.23: 12 1.23 - 1.42: 3993 1.42 - 1.62: 5435 1.62 - 1.81: 66 Bond restraints: 18600 Sorted by residual: bond pdb=" CD ARG B1025 " pdb=" NE ARG B1025 " ideal model delta sigma weight residual 1.458 1.444 0.014 1.40e-02 5.10e+03 9.67e-01 bond pdb=" NH1 ARG A1025 " pdb="HH12 ARG A1025 " ideal model delta sigma weight residual 0.860 0.840 0.020 2.00e-02 2.50e+03 9.60e-01 bond pdb=" CD ARG A1025 " pdb=" NE ARG A1025 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.40e-02 5.10e+03 9.14e-01 bond pdb=" C TYR A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.336 1.346 -0.010 1.08e-02 8.57e+03 9.06e-01 bond pdb=" C TYR B 664 " pdb=" N PRO B 665 " ideal model delta sigma weight residual 1.336 1.346 -0.010 1.08e-02 8.57e+03 8.84e-01 ... (remaining 18595 not shown) Histogram of bond angle deviations from ideal: 71.69 - 84.76: 23 84.76 - 97.84: 0 97.84 - 110.91: 19949 110.91 - 123.99: 12375 123.99 - 137.06: 1267 Bond angle restraints: 33614 Sorted by residual: angle pdb=" N VAL A 536 " pdb=" CA VAL A 536 " pdb=" HA VAL A 536 " ideal model delta sigma weight residual 110.00 72.38 37.62 3.00e+00 1.11e-01 1.57e+02 angle pdb=" C VAL A 536 " pdb=" CA VAL A 536 " pdb=" HA VAL A 536 " ideal model delta sigma weight residual 109.00 71.69 37.31 3.00e+00 1.11e-01 1.55e+02 angle pdb=" OG1 THR A 699 " pdb=" CB THR A 699 " pdb=" HB THR A 699 " ideal model delta sigma weight residual 109.00 74.04 34.96 3.00e+00 1.11e-01 1.36e+02 angle pdb=" CG2 THR A 699 " pdb=" CB THR A 699 " pdb=" HB THR A 699 " ideal model delta sigma weight residual 108.00 73.69 34.31 3.00e+00 1.11e-01 1.31e+02 angle pdb=" OG1 THR A 669 " pdb=" CB THR A 669 " pdb=" HB THR A 669 " ideal model delta sigma weight residual 109.00 75.45 33.55 3.00e+00 1.11e-01 1.25e+02 ... (remaining 33609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 6826 15.90 - 31.80: 475 31.80 - 47.70: 79 47.70 - 63.60: 35 63.60 - 79.50: 16 Dihedral angle restraints: 7431 sinusoidal: 3414 harmonic: 4017 Sorted by residual: dihedral pdb=" CD ARG B1025 " pdb=" NE ARG B1025 " pdb=" CZ ARG B1025 " pdb=" NH1 ARG B1025 " ideal model delta sinusoidal sigma weight residual 0.00 51.82 -51.82 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CD ARG A1025 " pdb=" NE ARG A1025 " pdb=" CZ ARG A1025 " pdb=" NH1 ARG A1025 " ideal model delta sinusoidal sigma weight residual 0.00 51.80 -51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA LEU B 736 " pdb=" C LEU B 736 " pdb=" N THR B 737 " pdb=" CA THR B 737 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.342: 1405 0.342 - 0.684: 4 0.684 - 1.026: 0 1.026 - 1.368: 0 1.368 - 1.710: 2 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CG LEU A 826 " pdb=" CB LEU A 826 " pdb=" CD1 LEU A 826 " pdb=" CD2 LEU A 826 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.31e+01 chirality pdb=" CG LEU B 826 " pdb=" CB LEU B 826 " pdb=" CD1 LEU B 826 " pdb=" CD2 LEU B 826 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.27e+01 chirality pdb=" CB THR B 699 " pdb=" CA THR B 699 " pdb=" OG1 THR B 699 " pdb=" CG2 THR B 699 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.71e+00 ... (remaining 1408 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1025 " -0.820 9.50e-02 1.11e+02 2.74e-01 8.62e+01 pdb=" NE ARG A1025 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A1025 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1025 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A1025 " -0.012 2.00e-02 2.50e+03 pdb="HH11 ARG A1025 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A1025 " 0.023 2.00e-02 2.50e+03 pdb="HH21 ARG A1025 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A1025 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1025 " -0.835 9.50e-02 1.11e+02 2.79e-01 8.52e+01 pdb=" NE ARG B1025 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG B1025 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B1025 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B1025 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARG B1025 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B1025 " 0.013 2.00e-02 2.50e+03 pdb="HH21 ARG B1025 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG B1025 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 767 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO B 768 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 768 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 768 " 0.020 5.00e-02 4.00e+02 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 535 2.14 - 2.76: 34481 2.76 - 3.37: 51267 3.37 - 3.99: 67559 3.99 - 4.60: 107523 Nonbonded interactions: 261365 Sorted by model distance: nonbonded pdb="HH21 ARG B 986 " pdb=" OE2 GLU B 989 " model vdw 1.531 1.850 nonbonded pdb="HH21 ARG A 986 " pdb=" OE2 GLU A 989 " model vdw 1.531 1.850 nonbonded pdb=" HE3 LYS A1086 " pdb=" HZ2 LYS A1086 " model vdw 1.598 1.816 nonbonded pdb=" HE2 LYS A1086 " pdb=" HZ3 LYS A1086 " model vdw 1.599 1.816 nonbonded pdb=" HB THR A 669 " pdb="HG23 THR A 669 " model vdw 1.628 1.952 ... (remaining 261360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 536 through 1130) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.260 Extract box with map and model: 7.860 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 58.790 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.002 0.030 9494 Z= 0.135 Angle : 0.522 10.126 12870 Z= 0.261 Chirality : 0.081 1.710 1411 Planarity : 0.013 0.370 1681 Dihedral : 13.129 79.496 3486 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.93 (0.25), residues: 1187 helix: 1.91 (0.25), residues: 412 sheet: 0.95 (0.46), residues: 138 loop : -0.30 (0.25), residues: 637 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 2.8963 time to fit residues: 444.7232 Evaluate side-chains 96 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 GLN B 853 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9494 Z= 0.295 Angle : 0.643 24.025 12870 Z= 0.321 Chirality : 0.094 1.735 1411 Planarity : 0.004 0.036 1681 Dihedral : 4.213 21.957 1277 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.21 % Allowed : 9.59 % Favored : 89.20 % 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 (0.25), residues: 1187 helix: 1.55 (0.25), residues: 422 sheet: 0.42 (0.41), residues: 160 loop : -0.33 (0.26), residues: 605 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 117 average time/residue: 2.6441 time to fit residues: 332.0938 Evaluate side-chains 106 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.2031 time to fit residues: 2.6067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 GLN A 853 GLN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN B 751 GLN B 853 GLN B 856 GLN B1103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9494 Z= 0.312 Angle : 0.659 25.813 12870 Z= 0.324 Chirality : 0.095 1.771 1411 Planarity : 0.004 0.047 1681 Dihedral : 4.352 20.484 1277 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.82 % Allowed : 10.49 % Favored : 87.69 % 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: 0.35 (0.24), residues: 1187 helix: 1.40 (0.25), residues: 418 sheet: 0.16 (0.40), residues: 178 loop : -0.56 (0.26), residues: 591 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 119 average time/residue: 2.7320 time to fit residues: 348.4942 Evaluate side-chains 107 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.2097 time to fit residues: 2.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7957 > 50: distance: 118 - 185: 9.287 distance: 172 - 185: 7.924 distance: 185 - 196: 7.572 distance: 186 - 187: 4.497 distance: 186 - 189: 4.194 distance: 186 - 197: 8.242 distance: 187 - 188: 3.931 distance: 187 - 209: 3.901 distance: 189 - 190: 10.263 distance: 189 - 198: 11.599 distance: 189 - 199: 9.959 distance: 190 - 191: 4.896 distance: 190 - 201: 5.620 distance: 191 - 192: 5.020 distance: 191 - 203: 5.544 distance: 192 - 193: 3.074 distance: 192 - 204: 5.704 distance: 193 - 194: 3.770 distance: 193 - 195: 4.559 distance: 194 - 205: 3.781 distance: 194 - 206: 3.106 distance: 195 - 208: 3.567 distance: 209 - 210: 4.054 distance: 209 - 213: 6.450 distance: 210 - 211: 7.083 distance: 210 - 214: 5.152 distance: 210 - 215: 18.446 distance: 211 - 212: 3.215 distance: 211 - 216: 4.115 distance: 216 - 217: 7.631 distance: 216 - 225: 6.999 distance: 217 - 218: 6.788 distance: 217 - 220: 5.254 distance: 217 - 226: 14.541 distance: 218 - 219: 8.127 distance: 218 - 238: 7.011 distance: 219 - 292: 27.748 distance: 220 - 227: 8.737 distance: 220 - 228: 6.325 distance: 221 - 222: 6.073 distance: 221 - 229: 9.842 distance: 221 - 230: 4.081 distance: 222 - 223: 16.258 distance: 222 - 231: 17.415 distance: 222 - 232: 8.497 distance: 223 - 224: 9.157 distance: 223 - 233: 26.875 distance: 223 - 234: 23.248 distance: 224 - 235: 11.099 distance: 224 - 236: 6.926 distance: 238 - 239: 13.008 distance: 238 - 250: 27.326 distance: 239 - 240: 3.852 distance: 239 - 251: 13.032 distance: 240 - 241: 17.296 distance: 240 - 259: 11.116 distance: 241 - 311: 19.073 distance: 242 - 243: 7.832 distance: 242 - 252: 9.182 distance: 242 - 253: 18.926 distance: 243 - 244: 7.741 distance: 243 - 245: 4.281 distance: 244 - 246: 10.092 distance: 244 - 254: 11.018 distance: 245 - 247: 5.641 distance: 245 - 255: 9.928 distance: 246 - 248: 10.350 distance: 246 - 256: 9.859 distance: 247 - 248: 12.077 distance: 247 - 257: 6.850 distance: 248 - 249: 16.403 distance: 249 - 258: 38.441 distance: 259 - 260: 7.053 distance: 259 - 265: 21.240 distance: 260 - 261: 4.902 distance: 260 - 263: 10.109 distance: 260 - 266: 18.833 distance: 261 - 262: 4.652 distance: 261 - 270: 8.241 distance: 262 - 330: 18.936 distance: 263 - 264: 17.578 distance: 263 - 267: 12.583 distance: 263 - 268: 14.099 distance: 264 - 269: 24.421 distance: 270 - 271: 4.631 distance: 270 - 279: 18.115 distance: 271 - 272: 6.467 distance: 271 - 274: 8.177 distance: 271 - 280: 10.727 distance: 272 - 273: 16.839 distance: 272 - 292: 7.086 distance: 273 - 342: 8.739 distance: 274 - 275: 10.725 distance: 274 - 281: 13.874 distance: 274 - 282: 6.528 distance: 275 - 276: 4.733 distance: 275 - 283: 18.120 distance: 275 - 284: 12.123 distance: 276 - 277: 5.287 distance: 276 - 285: 9.753 distance: 276 - 286: 6.138 distance: 277 - 278: 9.059 distance: 277 - 288: 13.198 distance: 278 - 289: 4.469 distance: 278 - 291: 5.839 distance: 292 - 293: 18.021 distance: 292 - 300: 7.251 distance: 293 - 294: 8.694 distance: 293 - 296: 7.956 distance: 293 - 301: 14.783 distance: 294 - 295: 17.900 distance: 294 - 311: 11.582 distance: 295 - 361: 15.633 distance: 296 - 297: 7.080 distance: 296 - 302: 19.786 distance: 296 - 303: 10.637 distance: 297 - 298: 4.687 distance: 297 - 299: 10.995 distance: 297 - 304: 7.631 distance: 298 - 305: 7.729 distance: 298 - 306: 8.454 distance: 298 - 307: 14.030 distance: 299 - 308: 8.364 distance: 299 - 309: 5.960 distance: 299 - 310: 8.407 distance: 311 - 312: 11.458 distance: 311 - 319: 9.912 distance: 312 - 313: 9.329 distance: 312 - 315: 7.174 distance: 312 - 320: 24.798 distance: 313 - 314: 7.582 distance: 313 - 330: 14.562 distance: 314 - 376: 8.386 distance: 315 - 316: 11.066 distance: 315 - 321: 17.357 distance: 315 - 322: 16.834 distance: 316 - 318: 18.712 distance: 316 - 323: 14.047 distance: 317 - 324: 17.279 distance: 317 - 325: 29.778 distance: 317 - 326: 18.211 distance: 318 - 327: 6.569 distance: 318 - 328: 5.055 distance: 318 - 329: 12.581 distance: 330 - 331: 14.017 distance: 330 - 338: 23.534 distance: 331 - 332: 24.028 distance: 331 - 334: 10.090 distance: 331 - 339: 27.824 distance: 332 - 342: 20.920 distance: 334 - 335: 30.337 distance: 334 - 340: 21.866 distance: 334 - 341: 9.624 distance: 335 - 336: 21.275 distance: 335 - 337: 22.018 distance: 342 - 343: 20.746 distance: 342 - 350: 21.631 distance: 343 - 344: 15.911 distance: 343 - 346: 21.146 distance: 343 - 351: 25.152 distance: 344 - 345: 38.697 distance: 344 - 361: 12.915 distance: 346 - 352: 5.261 distance: 346 - 353: 16.462 distance: 347 - 348: 22.816 distance: 347 - 349: 8.484 distance: 347 - 354: 22.938 distance: 348 - 355: 8.695 distance: 348 - 356: 9.124 distance: 348 - 357: 12.900 distance: 349 - 358: 23.743 distance: 349 - 360: 10.249