Starting phenix.real_space_refine on Wed Sep 25 04:28:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9aso_43821/09_2024/9aso_43821.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9aso_43821/09_2024/9aso_43821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9aso_43821/09_2024/9aso_43821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9aso_43821/09_2024/9aso_43821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9aso_43821/09_2024/9aso_43821.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9aso_43821/09_2024/9aso_43821.cif" } resolution = 2.9 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= 0.010 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 71 5.49 5 S 52 5.16 5 C 5709 2.51 5 N 1652 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7497 Classifications: {'peptide': 916} Link IDs: {'PTRANS': 52, 'TRANS': 863} Chain breaks: 1 Chain: "B" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 220 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 203 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1500 Classifications: {'RNA': 71} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 38} Link IDs: {'rna2p': 4, 'rna3p': 66} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 961 SG CYS A 561 51.073 71.653 120.870 1.00172.12 S ATOM 1919 SG CYS A 676 53.071 68.480 120.056 1.00178.36 S ATOM 769 SG CYS A 536 62.414 49.991 102.297 1.00181.72 S ATOM 784 SG CYS A 538 63.025 49.510 98.508 1.00190.39 S Time building chain proxies: 7.38, per 1000 atoms: 0.78 Number of scatterers: 9426 At special positions: 0 Unit cell: (82.176, 98.44, 158.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 52 16.00 P 71 15.00 O 1938 8.00 N 1652 7.00 C 5709 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: 2.70 Conformation dependent library (CDL) restraints added in 928.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 680 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A1026 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A 549 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 536 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 538 " Number of angles added : 4 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 56.1% alpha, 11.6% beta 17 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.538A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.629A pdb=" N ALA A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 removed outlier: 3.559A pdb=" N GLU A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.698A pdb=" N THR A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.527A pdb=" N ILE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.574A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 726 through 738 removed outlier: 3.524A pdb=" N GLU A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.644A pdb=" N ASN A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 830 removed outlier: 3.786A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.734A pdb=" N LEU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N HIS A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 879 " --> pdb=" O CYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 removed outlier: 3.616A pdb=" N LEU A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.594A pdb=" N VAL A 932 " --> pdb=" O ASP A 929 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS A 933 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.752A pdb=" N ILE A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 988 removed outlier: 3.670A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 Processing helix chain 'A' and resid 1005 through 1017 removed outlier: 3.768A pdb=" N LEU A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1021 Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 4.024A pdb=" N LEU A1030 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A1031 " --> pdb=" O PRO A1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1031' Processing helix chain 'A' and resid 1032 through 1055 Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.573A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 Processing helix chain 'A' and resid 1084 through 1090 removed outlier: 3.919A pdb=" N GLU A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 removed outlier: 4.220A pdb=" N GLU A1099 " --> pdb=" O GLN A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1115 removed outlier: 3.672A pdb=" N THR A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A1109 " --> pdb=" O GLN A1105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A1110 " --> pdb=" O LYS A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 removed outlier: 4.057A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1166 removed outlier: 3.714A pdb=" N GLU A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE A1148 " --> pdb=" O GLN A1144 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 Processing helix chain 'A' and resid 1183 through 1195 removed outlier: 3.571A pdb=" N ALA A1188 " --> pdb=" O ASN A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 4.232A pdb=" N LYS A1207 " --> pdb=" O ASN A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1232 Processing helix chain 'A' and resid 1234 through 1245 Processing helix chain 'A' and resid 1248 through 1256 Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 3.584A pdb=" N THR A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1332 Processing helix chain 'A' and resid 1334 through 1348 removed outlier: 3.573A pdb=" N ALA A1338 " --> pdb=" O PHE A1334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1358 Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.808A pdb=" N LEU B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 749 Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.484A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.484A pdb=" N ARG A 414 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 711 through 712 removed outlier: 3.815A pdb=" N LYS A 711 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 850 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 741 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 756 through 758 removed outlier: 3.558A pdb=" N GLN A 756 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1283 through 1290 removed outlier: 6.901A pdb=" N THR A1299 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR A1289 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A1297 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A1310 " --> pdb=" O VAL A1302 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 2.85 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: 2811 1.34 - 1.46: 1975 1.46 - 1.58: 4774 1.58 - 1.70: 140 1.70 - 1.82: 84 Bond restraints: 9784 Sorted by residual: bond pdb=" O5' C E 24 " pdb=" C5' C E 24 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.72e+00 bond pdb=" O5' C E 22 " pdb=" C5' C E 22 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.62e+00 bond pdb=" O5' A E 19 " pdb=" C5' A E 19 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.58e+00 bond pdb=" O5' U E 20 " pdb=" C5' U E 20 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.54e+00 bond pdb=" O5' C E 25 " pdb=" C5' C E 25 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.34e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 13400 2.37 - 4.73: 123 4.73 - 7.10: 23 7.10 - 9.47: 6 9.47 - 11.83: 6 Bond angle restraints: 13558 Sorted by residual: angle pdb=" C3' C E 22 " pdb=" O3' C E 22 " pdb=" P U E 23 " ideal model delta sigma weight residual 120.20 108.37 11.83 1.50e+00 4.44e-01 6.22e+01 angle pdb=" C3' G E 21 " pdb=" O3' G E 21 " pdb=" P C E 22 " ideal model delta sigma weight residual 120.20 108.49 11.71 1.50e+00 4.44e-01 6.10e+01 angle pdb=" C3' C E 24 " pdb=" O3' C E 24 " pdb=" P C E 25 " ideal model delta sigma weight residual 120.20 109.27 10.93 1.50e+00 4.44e-01 5.31e+01 angle pdb=" C3' U E 20 " pdb=" O3' U E 20 " pdb=" P G E 21 " ideal model delta sigma weight residual 120.20 109.49 10.71 1.50e+00 4.44e-01 5.10e+01 angle pdb=" C3' A E 19 " pdb=" O3' A E 19 " pdb=" P U E 20 " ideal model delta sigma weight residual 120.20 109.50 10.70 1.50e+00 4.44e-01 5.09e+01 ... (remaining 13553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.42: 5548 25.42 - 50.84: 368 50.84 - 76.25: 139 76.25 - 101.67: 1 101.67 - 127.09: 1 Dihedral angle restraints: 6057 sinusoidal: 3220 harmonic: 2837 Sorted by residual: dihedral pdb=" O4' C E 22 " pdb=" C1' C E 22 " pdb=" N1 C E 22 " pdb=" C2 C E 22 " ideal model delta sinusoidal sigma weight residual -160.00 -32.91 -127.09 1 1.50e+01 4.44e-03 6.84e+01 dihedral pdb=" O4' A E 90 " pdb=" C1' A E 90 " pdb=" N9 A E 90 " pdb=" C4 A E 90 " ideal model delta sinusoidal sigma weight residual -90.00 -22.97 -67.03 1 2.00e+01 2.50e-03 1.46e+01 dihedral pdb=" CA MET A 935 " pdb=" C MET A 935 " pdb=" N HIS A 936 " pdb=" CA HIS A 936 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1438 0.081 - 0.161: 79 0.161 - 0.242: 5 0.242 - 0.322: 0 0.322 - 0.403: 7 Chirality restraints: 1529 Sorted by residual: chirality pdb=" P A E 19 " pdb=" OP1 A E 19 " pdb=" OP2 A E 19 " pdb=" O5' A E 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.81 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" P U E 20 " pdb=" OP1 U E 20 " pdb=" OP2 U E 20 " pdb=" O5' U E 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" P U E 23 " pdb=" OP1 U E 23 " pdb=" OP2 U E 23 " pdb=" O5' U E 23 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 1526 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 745 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" CD GLU C 745 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU C 745 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 745 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 744 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" CD GLU C 744 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU C 744 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 744 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 737 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" CD GLU B 737 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 737 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 737 " -0.012 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2334 2.80 - 3.33: 8160 3.33 - 3.85: 15244 3.85 - 4.38: 17752 4.38 - 4.90: 29543 Nonbonded interactions: 73033 Sorted by model distance: nonbonded pdb=" N ASP A 955 " pdb=" OD1 ASP A 955 " model vdw 2.281 3.120 nonbonded pdb=" OP1 U E 31 " pdb=" O HOH E 201 " model vdw 2.319 3.040 nonbonded pdb=" OE2 GLU A1147 " pdb="CA CA A1403 " model vdw 2.356 2.510 nonbonded pdb=" NH2 ARG A1213 " pdb=" OP2 U E 89 " model vdw 2.380 3.120 nonbonded pdb=" NH1 ARG A1095 " pdb=" O PHE A1118 " model vdw 2.395 3.120 ... (remaining 73028 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 'B' and resid 726 through 749) selection = chain 'C' } 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: 7.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.390 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 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 0.039 9784 Z= 0.180 Angle : 0.602 11.832 13558 Z= 0.324 Chirality : 0.045 0.403 1529 Planarity : 0.003 0.031 1497 Dihedral : 17.619 127.090 4215 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.04 % Allowed : 14.06 % Favored : 84.91 % 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: 1.28 (0.27), residues: 958 helix: 2.01 (0.24), residues: 480 sheet: 0.63 (0.50), residues: 92 loop : -0.57 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1357 HIS 0.004 0.001 HIS A 873 PHE 0.011 0.001 PHE A 970 TYR 0.006 0.001 TYR A1229 ARG 0.007 0.000 ARG C 746 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 63 average time/residue: 1.7054 time to fit residues: 113.8232 Evaluate side-chains 64 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1274 THR Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain C residue 731 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 42 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.0020 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1340 GLN C 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9784 Z= 0.130 Angle : 0.486 6.621 13558 Z= 0.247 Chirality : 0.035 0.143 1529 Planarity : 0.003 0.032 1497 Dihedral : 17.855 109.784 2191 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.27 % Allowed : 13.02 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 958 helix: 2.13 (0.24), residues: 495 sheet: 0.62 (0.48), residues: 102 loop : -0.47 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1357 HIS 0.005 0.001 HIS C 730 PHE 0.011 0.001 PHE A1148 TYR 0.006 0.001 TYR A 705 ARG 0.005 0.000 ARG C 746 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 835 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7534 (mtm-85) REVERT: C 734 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8573 (mtmt) outliers start: 11 outliers final: 3 residues processed: 63 average time/residue: 1.5909 time to fit residues: 106.2836 Evaluate side-chains 57 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1048 ILE Chi-restraints excluded: chain A residue 1283 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN A1340 GLN C 730 HIS C 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9784 Z= 0.354 Angle : 0.569 6.762 13558 Z= 0.294 Chirality : 0.040 0.181 1529 Planarity : 0.004 0.036 1497 Dihedral : 17.845 103.375 2178 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.04 % Allowed : 13.94 % Favored : 85.02 % 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: 1.28 (0.27), residues: 958 helix: 1.97 (0.24), residues: 494 sheet: 0.33 (0.48), residues: 103 loop : -0.55 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1357 HIS 0.006 0.001 HIS A 873 PHE 0.011 0.001 PHE A1148 TYR 0.013 0.001 TYR A1332 ARG 0.006 0.000 ARG C 746 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 835 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7566 (mtm-85) REVERT: A 877 MET cc_start: 0.8006 (mpp) cc_final: 0.7706 (mmt) REVERT: C 737 GLU cc_start: 0.8442 (pm20) cc_final: 0.8233 (pm20) outliers start: 9 outliers final: 1 residues processed: 60 average time/residue: 1.6529 time to fit residues: 105.1678 Evaluate side-chains 54 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 1048 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN A 936 HIS A1340 GLN C 730 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9784 Z= 0.142 Angle : 0.473 5.994 13558 Z= 0.243 Chirality : 0.035 0.173 1529 Planarity : 0.003 0.035 1497 Dihedral : 17.809 94.955 2176 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.15 % Allowed : 14.29 % Favored : 84.56 % 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: 1.40 (0.28), residues: 958 helix: 2.07 (0.24), residues: 494 sheet: 0.39 (0.49), residues: 103 loop : -0.50 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1357 HIS 0.006 0.001 HIS C 730 PHE 0.011 0.001 PHE A1148 TYR 0.007 0.001 TYR A 705 ARG 0.009 0.000 ARG C 746 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 835 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7576 (mtm-85) outliers start: 10 outliers final: 2 residues processed: 61 average time/residue: 1.7191 time to fit residues: 111.3022 Evaluate side-chains 55 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 933 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1340 GLN C 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9784 Z= 0.159 Angle : 0.479 5.891 13558 Z= 0.244 Chirality : 0.035 0.166 1529 Planarity : 0.003 0.034 1497 Dihedral : 17.553 88.347 2174 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.38 % Allowed : 14.17 % Favored : 84.45 % 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: 1.48 (0.28), residues: 958 helix: 2.17 (0.24), residues: 494 sheet: 0.42 (0.48), residues: 103 loop : -0.51 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1357 HIS 0.005 0.001 HIS C 730 PHE 0.010 0.001 PHE A1148 TYR 0.007 0.001 TYR A1332 ARG 0.006 0.000 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 835 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7597 (mtm-85) REVERT: C 734 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8501 (mtmt) outliers start: 12 outliers final: 3 residues processed: 62 average time/residue: 1.6992 time to fit residues: 111.7196 Evaluate side-chains 56 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1048 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 71.9883 > 50: distance: 38 - 42: 27.462 distance: 42 - 43: 14.415 distance: 43 - 44: 38.200 distance: 43 - 46: 19.014 distance: 44 - 45: 22.571 distance: 44 - 50: 35.200 distance: 46 - 47: 17.905 distance: 47 - 48: 49.045 distance: 47 - 49: 19.980 distance: 50 - 51: 34.634 distance: 51 - 52: 13.228 distance: 51 - 54: 33.475 distance: 52 - 53: 20.961 distance: 52 - 64: 19.456 distance: 54 - 55: 33.213 distance: 55 - 56: 25.986 distance: 55 - 57: 17.204 distance: 56 - 58: 13.438 distance: 57 - 59: 13.011 distance: 57 - 60: 5.947 distance: 59 - 61: 12.612 distance: 60 - 62: 14.898 distance: 61 - 63: 14.423 distance: 62 - 63: 12.244 distance: 64 - 65: 39.313 distance: 65 - 66: 56.774 distance: 65 - 68: 17.133 distance: 66 - 67: 13.754 distance: 66 - 76: 8.822 distance: 68 - 69: 20.578 distance: 69 - 70: 14.083 distance: 69 - 71: 12.202 distance: 70 - 72: 21.090 distance: 71 - 73: 42.307 distance: 72 - 74: 13.468 distance: 73 - 74: 9.853 distance: 76 - 77: 31.250 distance: 77 - 78: 57.166 distance: 77 - 80: 28.213 distance: 78 - 79: 46.326 distance: 78 - 84: 23.842 distance: 80 - 81: 29.735 distance: 81 - 82: 47.279 distance: 84 - 85: 26.217 distance: 85 - 86: 43.244 distance: 85 - 88: 25.531 distance: 86 - 87: 39.815 distance: 86 - 92: 63.330 distance: 88 - 89: 39.239 distance: 89 - 90: 56.704 distance: 89 - 91: 39.074 distance: 92 - 93: 40.067 distance: 92 - 98: 12.859 distance: 93 - 94: 57.577 distance: 93 - 96: 56.742 distance: 94 - 99: 56.409 distance: 96 - 97: 45.637 distance: 97 - 98: 21.958 distance: 99 - 100: 10.865 distance: 100 - 101: 37.916 distance: 101 - 102: 41.761 distance: 101 - 103: 26.474 distance: 103 - 104: 17.800 distance: 104 - 105: 9.037 distance: 104 - 107: 49.718 distance: 105 - 106: 15.156 distance: 105 - 112: 44.433 distance: 107 - 108: 23.660 distance: 108 - 109: 31.472 distance: 109 - 110: 8.349 distance: 109 - 111: 59.895 distance: 113 - 114: 56.575 distance: 114 - 115: 32.643 distance: 116 - 117: 38.828 distance: 117 - 118: 40.766 distance: 118 - 119: 33.905 distance: 121 - 124: 33.426 distance: 122 - 128: 34.197 distance: 124 - 125: 40.514 distance: 125 - 126: 40.187 distance: 125 - 127: 52.984