Starting phenix.real_space_refine on Mon Aug 5 04:08:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/08_2024/8j89_36064.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/08_2024/8j89_36064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/08_2024/8j89_36064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/08_2024/8j89_36064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/08_2024/8j89_36064.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j89_36064/08_2024/8j89_36064.cif" } resolution = 2.31 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= 0.011 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 50 5.16 5 C 7855 2.51 5 N 2097 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "B ASP 633": "OD1" <-> "OD2" Residue "B ASP 701": "OD1" <-> "OD2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B GLU 835": "OE1" <-> "OE2" Residue "B TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 997": "OD1" <-> "OD2" Residue "B GLU 1050": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6105 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 30, 'TRANS': 720} Chain breaks: 1 Chain: "B" Number of atoms: 6117 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 6105 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 30, 'TRANS': 720} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 751, 6105 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 30, 'TRANS': 720} Chain breaks: 1 bond proxies already assigned to first conformer: 6237 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR B1029 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B1029 " occ=0.50 Time building chain proxies: 10.78, per 1000 atoms: 0.88 Number of scatterers: 12222 At special positions: 0 Unit cell: (115.37, 103.75, 111.22, 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 50 16.00 O 2220 8.00 N 2097 7.00 C 7855 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 - 3.50 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: 4.94 Conformation dependent library (CDL) restraints added in 3.3 seconds 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 51.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.923A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.709A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.566A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 659 through 664 removed outlier: 3.707A pdb=" N GLU A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 removed outlier: 3.523A pdb=" N VAL A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.524A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.676A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.505A pdb=" N MET A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 847' Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 891 removed outlier: 3.839A pdb=" N LYS A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.718A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1071 removed outlier: 3.735A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix Processing helix chain 'A' and resid 1075 through 1079 Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1118 removed outlier: 4.541A pdb=" N LEU A1118 " --> pdb=" O ASN A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.927A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.757A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.607A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.596A pdb=" N HIS B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.517A pdb=" N GLU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 removed outlier: 3.518A pdb=" N VAL B 682 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 705 Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 765 Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.669A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.545A pdb=" N MET B 846 " --> pdb=" O PRO B 842 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 842 through 847' Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 882 through 891 removed outlier: 3.860A pdb=" N LYS B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 982 through 991 removed outlier: 3.684A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 988 " --> pdb=" O ASN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1071 removed outlier: 3.721A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix Processing helix chain 'B' and resid 1075 through 1079 Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1118 removed outlier: 4.554A pdb=" N LEU B1118 " --> pdb=" O ASN B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1134 through 1160 Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.279A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.514A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 926 removed outlier: 5.876A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.454A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 465 through 469 removed outlier: 6.170A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB2, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.487A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB4, first strand: chain 'B' and resid 922 through 926 removed outlier: 5.867A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 962 " --> pdb=" O LYS B 977 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1014 through 1016 566 hydrogen bonds defined for protein. 1590 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: 3.94 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3943 1.35 - 1.46: 2969 1.46 - 1.58: 5526 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 12516 Sorted by residual: bond pdb=" CB ILE A 801 " pdb=" CG2 ILE A 801 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB ILE B 801 " pdb=" CG2 ILE B 801 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CA THR A 895 " pdb=" CB THR A 895 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.61e-02 3.86e+03 6.12e-01 bond pdb=" CG LEU B 843 " pdb=" CD2 LEU B 843 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.84e-01 bond pdb=" CA THR B 895 " pdb=" CB THR B 895 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.61e-02 3.86e+03 5.71e-01 ... (remaining 12511 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.89: 341 106.89 - 113.66: 6836 113.66 - 120.42: 4752 120.42 - 127.19: 4842 127.19 - 133.95: 140 Bond angle restraints: 16911 Sorted by residual: angle pdb=" C GLU B1106 " pdb=" CA GLU B1106 " pdb=" CB GLU B1106 " ideal model delta sigma weight residual 116.54 110.48 6.06 1.15e+00 7.56e-01 2.78e+01 angle pdb=" N ILE A 845 " pdb=" CA ILE A 845 " pdb=" C ILE A 845 " ideal model delta sigma weight residual 112.96 109.42 3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" N ILE B 845 " pdb=" CA ILE B 845 " pdb=" C ILE B 845 " ideal model delta sigma weight residual 112.96 109.42 3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" CA GLU B1106 " pdb=" C GLU B1106 " pdb=" N PHE B1107 " ideal model delta sigma weight residual 119.52 117.00 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" C SER B 657 " pdb=" N GLU B 658 " pdb=" CA GLU B 658 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.73e+00 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 6968 15.88 - 31.77: 441 31.77 - 47.65: 86 47.65 - 63.53: 13 63.53 - 79.41: 5 Dihedral angle restraints: 7513 sinusoidal: 3102 harmonic: 4411 Sorted by residual: dihedral pdb=" CA GLU B1073 " pdb=" C GLU B1073 " pdb=" N LEU B1074 " pdb=" CA LEU B1074 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO B 938 " pdb=" C PRO B 938 " pdb=" N LEU B 939 " pdb=" CA LEU B 939 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PRO A 938 " pdb=" C PRO A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 7510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1036 0.026 - 0.053: 467 0.053 - 0.079: 204 0.079 - 0.105: 82 0.105 - 0.132: 38 Chirality restraints: 1827 Sorted by residual: chirality pdb=" CA THR B 895 " pdb=" N THR B 895 " pdb=" C THR B 895 " pdb=" CB THR B 895 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA THR A 895 " pdb=" N THR A 895 " pdb=" C THR A 895 " pdb=" CB THR A 895 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL A 669 " pdb=" N VAL A 669 " pdb=" C VAL A 669 " pdb=" CB VAL A 669 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1824 not shown) Planarity restraints: 2157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 938 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 938 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 858 " 0.014 2.00e-02 2.50e+03 8.40e-03 1.41e+00 pdb=" CG TYR B 858 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 858 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 858 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 858 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 858 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 858 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 858 " 0.001 2.00e-02 2.50e+03 ... (remaining 2154 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1623 2.75 - 3.29: 11801 3.29 - 3.83: 20557 3.83 - 4.36: 26228 4.36 - 4.90: 43818 Nonbonded interactions: 104027 Sorted by model distance: nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 923 " pdb=" OD2 ASP B 997 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.225 3.040 nonbonded pdb=" O ARG A 447 " pdb=" OG1 THR A 451 " model vdw 2.261 3.040 nonbonded pdb=" O PRO A1095 " pdb=" OH TYR A1124 " model vdw 2.274 3.040 ... (remaining 104022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 414 through 1028 or resid 1030 through 1192)) selection = (chain 'B' and (resid 414 through 1028 or resid 1030 through 1192)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.430 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12516 Z= 0.180 Angle : 0.458 6.059 16911 Z= 0.253 Chirality : 0.040 0.132 1827 Planarity : 0.003 0.046 2157 Dihedral : 10.981 79.413 4687 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % 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: 0.51 (0.22), residues: 1497 helix: 1.05 (0.20), residues: 659 sheet: -0.49 (0.40), residues: 182 loop : -0.01 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.003 0.001 HIS B1192 PHE 0.008 0.001 PHE A 990 TYR 0.018 0.001 TYR B 858 ARG 0.002 0.000 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.476 Fit side-chains REVERT: A 756 MET cc_start: 0.8055 (tpp) cc_final: 0.7755 (tpt) REVERT: A 970 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 970 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 1111 GLU cc_start: 0.8266 (pm20) cc_final: 0.8039 (pm20) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 1.7227 time to fit residues: 153.0350 Evaluate side-chains 60 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 HIS A1092 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12516 Z= 0.222 Angle : 0.513 6.429 16911 Z= 0.276 Chirality : 0.042 0.149 1827 Planarity : 0.004 0.047 2157 Dihedral : 4.238 25.444 1671 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.61 % Allowed : 3.94 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1497 helix: 1.43 (0.20), residues: 689 sheet: -0.40 (0.39), residues: 192 loop : -0.06 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 599 HIS 0.018 0.001 HIS A1078 PHE 0.011 0.001 PHE B 990 TYR 0.019 0.001 TYR B 858 ARG 0.008 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.331 Fit side-chains REVERT: A 970 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7853 (mt-10) REVERT: B 756 MET cc_start: 0.7918 (tpp) cc_final: 0.7601 (tpp) REVERT: B 970 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7801 (mt-10) outliers start: 8 outliers final: 2 residues processed: 68 average time/residue: 1.6900 time to fit residues: 123.9060 Evaluate side-chains 60 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 121 optimal weight: 0.0870 chunk 135 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12516 Z= 0.177 Angle : 0.470 5.980 16911 Z= 0.252 Chirality : 0.041 0.141 1827 Planarity : 0.004 0.048 2157 Dihedral : 4.103 25.498 1671 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.53 % Allowed : 5.69 % Favored : 93.78 % 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: 0.89 (0.22), residues: 1497 helix: 1.62 (0.20), residues: 687 sheet: -0.43 (0.39), residues: 192 loop : -0.15 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B1078 PHE 0.012 0.001 PHE A 990 TYR 0.019 0.001 TYR B 858 ARG 0.007 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 1.579 Fit side-chains REVERT: A 929 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7775 (ptm-80) REVERT: A 931 ILE cc_start: 0.8723 (mm) cc_final: 0.8438 (mm) REVERT: A 970 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 983 LEU cc_start: 0.9072 (tm) cc_final: 0.8753 (tp) REVERT: B 970 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7808 (mt-10) outliers start: 7 outliers final: 2 residues processed: 72 average time/residue: 1.5134 time to fit residues: 118.2756 Evaluate side-chains 64 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 HIS B1078 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12516 Z= 0.210 Angle : 0.478 5.650 16911 Z= 0.256 Chirality : 0.042 0.138 1827 Planarity : 0.004 0.048 2157 Dihedral : 4.158 25.845 1671 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.68 % Allowed : 6.29 % Favored : 93.03 % 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: 0.91 (0.22), residues: 1497 helix: 1.68 (0.20), residues: 685 sheet: -0.42 (0.40), residues: 192 loop : -0.19 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.021 0.001 HIS B1078 PHE 0.013 0.001 PHE A 990 TYR 0.020 0.001 TYR B 858 ARG 0.007 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.418 Fit side-chains REVERT: A 970 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7844 (mt-10) REVERT: B 970 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 983 LEU cc_start: 0.9033 (tm) cc_final: 0.8726 (tp) outliers start: 9 outliers final: 2 residues processed: 67 average time/residue: 1.4921 time to fit residues: 108.6504 Evaluate side-chains 61 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain B residue 960 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 HIS B1092 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12516 Z= 0.257 Angle : 0.491 5.774 16911 Z= 0.263 Chirality : 0.042 0.138 1827 Planarity : 0.004 0.048 2157 Dihedral : 4.273 26.529 1671 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.68 % Allowed : 7.05 % Favored : 92.27 % 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: 0.86 (0.22), residues: 1497 helix: 1.65 (0.20), residues: 689 sheet: -0.50 (0.39), residues: 192 loop : -0.23 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 820 HIS 0.013 0.001 HIS B1078 PHE 0.013 0.001 PHE A 990 TYR 0.021 0.001 TYR B 858 ARG 0.008 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.477 Fit side-chains REVERT: A 926 SER cc_start: 0.8995 (m) cc_final: 0.8585 (p) REVERT: A 929 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7675 (ptm-80) REVERT: A 970 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 929 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7912 (ptm-80) REVERT: B 970 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 983 LEU cc_start: 0.9053 (tm) cc_final: 0.8751 (tp) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 1.4658 time to fit residues: 107.0594 Evaluate side-chains 66 residues out of total 1317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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: 52.0107 > 50: distance: 79 - 84: 19.594 distance: 84 - 85: 17.317 distance: 85 - 86: 9.923 distance: 85 - 88: 16.380 distance: 86 - 87: 8.480 distance: 86 - 93: 31.507 distance: 88 - 89: 20.801 distance: 89 - 90: 13.752 distance: 90 - 91: 16.467 distance: 91 - 92: 13.434 distance: 93 - 94: 12.834 distance: 94 - 95: 9.467 distance: 94 - 97: 17.907 distance: 95 - 96: 32.924 distance: 95 - 103: 14.886 distance: 97 - 98: 7.877 distance: 98 - 99: 11.581 distance: 98 - 100: 9.155 distance: 99 - 101: 8.599 distance: 100 - 102: 12.162 distance: 103 - 104: 13.626 distance: 104 - 105: 14.646 distance: 104 - 107: 19.223 distance: 105 - 106: 13.443 distance: 105 - 112: 8.524 distance: 107 - 108: 10.731 distance: 108 - 109: 18.865 distance: 109 - 110: 13.501 distance: 110 - 111: 23.299 distance: 112 - 113: 6.918 distance: 113 - 114: 8.422 distance: 114 - 115: 5.329 distance: 114 - 120: 20.239 distance: 116 - 117: 6.305 distance: 116 - 118: 6.780 distance: 117 - 119: 18.084 distance: 121 - 122: 8.845 distance: 121 - 124: 14.291 distance: 122 - 123: 11.465 distance: 122 - 127: 24.746 distance: 124 - 125: 7.480 distance: 124 - 126: 11.581 distance: 127 - 128: 15.493 distance: 128 - 129: 16.103 distance: 128 - 131: 12.858 distance: 129 - 130: 20.011 distance: 129 - 135: 32.007 distance: 131 - 132: 23.826 distance: 131 - 133: 34.143 distance: 132 - 134: 31.676 distance: 135 - 136: 15.637 distance: 136 - 137: 32.649 distance: 136 - 139: 28.571 distance: 137 - 138: 21.357 distance: 137 - 143: 32.612 distance: 139 - 140: 26.225 distance: 140 - 141: 24.566 distance: 140 - 142: 31.674 distance: 143 - 144: 12.516 distance: 143 - 149: 8.407 distance: 144 - 145: 17.671 distance: 144 - 147: 27.541 distance: 145 - 146: 20.397 distance: 145 - 150: 19.714 distance: 147 - 148: 6.797 distance: 148 - 149: 27.013 distance: 150 - 151: 27.320 distance: 151 - 152: 9.635 distance: 151 - 154: 21.142 distance: 152 - 153: 20.783 distance: 152 - 158: 7.028 distance: 154 - 155: 24.746 distance: 155 - 156: 22.117 distance: 155 - 157: 29.519 distance: 158 - 159: 9.707 distance: 159 - 160: 13.773 distance: 159 - 162: 21.808 distance: 160 - 169: 13.380 distance: 162 - 163: 4.713 distance: 163 - 164: 9.336 distance: 164 - 165: 5.757 distance: 166 - 167: 3.153