Starting phenix.real_space_refine on Sun Aug 4 03:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/08_2024/7qks_14050.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/08_2024/7qks_14050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/08_2024/7qks_14050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/08_2024/7qks_14050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/08_2024/7qks_14050.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qks_14050/08_2024/7qks_14050.cif" } resolution = 3.1 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= 0.005 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 47 5.16 5 C 6011 2.51 5 N 1541 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1263": "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: 9339 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1199, 9300 Classifications: {'peptide': 1199} Link IDs: {'PTRANS': 27, 'TRANS': 1171} Chain breaks: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.01, per 1000 atoms: 0.64 Number of scatterers: 9339 At special positions: 0 Unit cell: (132.246, 105.462, 102.114, 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 47 16.00 O 1740 8.00 N 1541 7.00 C 6011 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: 3.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 72.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 58 through 59 No H-bonds generated for 'chain 'A' and resid 58 through 59' Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 80 removed outlier: 3.588A pdb=" N ALA A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 4.000A pdb=" N LEU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 159 removed outlier: 3.592A pdb=" N HIS A 158 " --> pdb=" O TRP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.555A pdb=" N ILE A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 212 removed outlier: 3.676A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 261 removed outlier: 3.756A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.682A pdb=" N PHE A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 326 removed outlier: 3.648A pdb=" N LYS A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 345 Processing helix chain 'A' and resid 345 through 372 removed outlier: 3.628A pdb=" N ALA A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 442 removed outlier: 4.406A pdb=" N ILE A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 528 through 532 removed outlier: 4.169A pdb=" N ASP A 531 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 removed outlier: 4.406A pdb=" N SER A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 588 removed outlier: 4.226A pdb=" N GLY A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.053A pdb=" N GLN A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 630 through 645 Processing helix chain 'A' and resid 698 through 706 removed outlier: 3.730A pdb=" N LEU A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 741 Proline residue: A 715 - end of helix removed outlier: 4.065A pdb=" N PHE A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix removed outlier: 4.132A pdb=" N LEU A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 802 removed outlier: 3.664A pdb=" N PHE A 762 " --> pdb=" O LYS A 758 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 removed outlier: 3.840A pdb=" N PHE A 808 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 809 " --> pdb=" O MET A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 804 through 809' Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 829 Proline residue: A 826 - end of helix Processing helix chain 'A' and resid 830 through 833 Processing helix chain 'A' and resid 834 through 858 Processing helix chain 'A' and resid 858 through 894 removed outlier: 4.125A pdb=" N VAL A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 866 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 869 " --> pdb=" O CYS A 865 " (cutoff:3.500A) Proline residue: A 870 - end of helix removed outlier: 3.861A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 907 removed outlier: 4.028A pdb=" N ALA A 907 " --> pdb=" O GLU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 914 removed outlier: 3.546A pdb=" N VAL A 911 " --> pdb=" O ALA A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 971 removed outlier: 3.615A pdb=" N LYS A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 938 " --> pdb=" O ARG A 934 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 944 " --> pdb=" O SER A 940 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 945 " --> pdb=" O ARG A 941 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN A 953 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 974 through 993 Processing helix chain 'A' and resid 994 through 997 Processing helix chain 'A' and resid 998 through 1018 removed outlier: 3.649A pdb=" N MET A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1091 removed outlier: 3.876A pdb=" N GLY A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1111 No H-bonds generated for 'chain 'A' and resid 1109 through 1111' Processing helix chain 'A' and resid 1112 through 1119 Processing helix chain 'A' and resid 1133 through 1139 Processing helix chain 'A' and resid 1140 through 1142 No H-bonds generated for 'chain 'A' and resid 1140 through 1142' Processing helix chain 'A' and resid 1153 through 1162 Processing helix chain 'A' and resid 1164 through 1171 Processing helix chain 'A' and resid 1187 through 1202 removed outlier: 4.542A pdb=" N ARG A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1232 removed outlier: 3.764A pdb=" N MET A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1274 Processing helix chain 'A' and resid 1275 through 1288 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 418 removed outlier: 6.821A pdb=" N VAL A 410 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG A 401 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER A 412 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 399 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE A 414 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE A 395 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 453 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN A 397 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A 451 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.260A pdb=" N ALA A 472 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP A 565 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 474 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A 562 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE A 595 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 564 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 424 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A 423 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL A 609 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA A 425 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A 611 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 427 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 618 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER A 612 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A 616 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1067 removed outlier: 6.989A pdb=" N VAL A1059 " --> pdb=" O ARG A1050 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ARG A1050 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A1061 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A1048 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A1063 " --> pdb=" O ASP A1046 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A1047 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A1098 " --> pdb=" O VAL A1047 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 6.466A pdb=" N ALA A1121 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP A1210 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1123 " --> pdb=" O ASP A1210 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A1263 " --> pdb=" O VAL A1255 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP A1257 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE A1261 " --> pdb=" O ASP A1257 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1815 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: 3.49 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2087 1.33 - 1.45: 1923 1.45 - 1.57: 5412 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 9500 Sorted by residual: bond pdb=" N VAL A1076 " pdb=" CA VAL A1076 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.11e-02 8.12e+03 9.76e+00 bond pdb=" C ARG A 405 " pdb=" N PRO A 406 " ideal model delta sigma weight residual 1.334 1.359 -0.026 8.40e-03 1.42e+04 9.45e+00 bond pdb=" N ILE A 346 " pdb=" CA ILE A 346 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.44e+00 bond pdb=" N ILE A 722 " pdb=" CA ILE A 722 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.19e-02 7.06e+03 9.44e+00 bond pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 8.99e+00 ... (remaining 9495 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.55: 171 106.55 - 113.46: 5309 113.46 - 120.38: 3824 120.38 - 127.30: 3500 127.30 - 134.21: 53 Bond angle restraints: 12857 Sorted by residual: angle pdb=" N LYS A 354 " pdb=" CA LYS A 354 " pdb=" C LYS A 354 " ideal model delta sigma weight residual 111.07 106.92 4.15 1.07e+00 8.73e-01 1.50e+01 angle pdb=" N GLY A1174 " pdb=" CA GLY A1174 " pdb=" C GLY A1174 " ideal model delta sigma weight residual 113.18 104.15 9.03 2.37e+00 1.78e-01 1.45e+01 angle pdb=" CA GLY A 170 " pdb=" C GLY A 170 " pdb=" O GLY A 170 " ideal model delta sigma weight residual 120.45 116.61 3.84 1.02e+00 9.61e-01 1.41e+01 angle pdb=" N ASP A 179 " pdb=" CA ASP A 179 " pdb=" C ASP A 179 " ideal model delta sigma weight residual 113.72 109.00 4.72 1.30e+00 5.92e-01 1.32e+01 angle pdb=" N ILE A 523 " pdb=" CA ILE A 523 " pdb=" C ILE A 523 " ideal model delta sigma weight residual 111.45 108.09 3.36 9.30e-01 1.16e+00 1.31e+01 ... (remaining 12852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.27: 5434 24.27 - 48.55: 294 48.55 - 72.82: 31 72.82 - 97.09: 6 97.09 - 121.37: 4 Dihedral angle restraints: 5769 sinusoidal: 2307 harmonic: 3462 Sorted by residual: dihedral pdb=" C21 9Z9 A1301 " pdb=" C22 9Z9 A1301 " pdb=" C23 9Z9 A1301 " pdb=" C24 9Z9 A1301 " ideal model delta sinusoidal sigma weight residual 77.99 -43.38 121.37 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C PHE A 987 " pdb=" N PHE A 987 " pdb=" CA PHE A 987 " pdb=" CB PHE A 987 " ideal model delta harmonic sigma weight residual -122.60 -132.39 9.79 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C18 9Z9 A1301 " pdb=" C17 9Z9 A1301 " pdb=" O20 9Z9 A1301 " pdb=" C21 9Z9 A1301 " ideal model delta sinusoidal sigma weight residual 163.81 -92.29 -103.90 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 5766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1254 0.059 - 0.118: 212 0.118 - 0.177: 31 0.177 - 0.236: 15 0.236 - 0.295: 2 Chirality restraints: 1514 Sorted by residual: chirality pdb=" CA PHE A 987 " pdb=" N PHE A 987 " pdb=" C PHE A 987 " pdb=" CB PHE A 987 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU A1075 " pdb=" N LEU A1075 " pdb=" C LEU A1075 " pdb=" CB LEU A1075 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN A 706 " pdb=" N ASN A 706 " pdb=" C ASN A 706 " pdb=" CB ASN A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1511 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1092 " -0.256 9.50e-02 1.11e+02 1.15e-01 8.06e+00 pdb=" NE ARG A1092 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A1092 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1092 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1092 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 344 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C LEU A 344 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 344 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 345 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 372 " -0.232 9.50e-02 1.11e+02 1.04e-01 6.67e+00 pdb=" NE ARG A 372 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 372 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 372 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 372 " -0.009 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 972 2.75 - 3.29: 9394 3.29 - 3.82: 15174 3.82 - 4.36: 18529 4.36 - 4.90: 32404 Nonbonded interactions: 76473 Sorted by model distance: nonbonded pdb=" OE2 GLU A 142 " pdb=" NH2 ARG A 889 " model vdw 2.210 3.120 nonbonded pdb=" O GLY A 862 " pdb=" OG1 THR A 866 " model vdw 2.221 3.040 nonbonded pdb=" O ILE A1090 " pdb=" OH TYR A1116 " model vdw 2.228 3.040 nonbonded pdb=" O VAL A 939 " pdb=" OG1 THR A 943 " model vdw 2.317 3.040 nonbonded pdb=" O LYS A 909 " pdb=" OG SER A 913 " model vdw 2.346 3.040 ... (remaining 76468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.430 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.005 0.039 9500 Z= 0.322 Angle : 0.738 9.091 12857 Z= 0.506 Chirality : 0.050 0.295 1514 Planarity : 0.007 0.115 1608 Dihedral : 14.589 121.366 3549 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % 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: 0.65 (0.24), residues: 1193 helix: 1.06 (0.18), residues: 779 sheet: -1.59 (0.78), residues: 48 loop : -0.50 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 955 HIS 0.004 0.001 HIS A 103 PHE 0.021 0.001 PHE A 119 TYR 0.025 0.001 TYR A 248 ARG 0.006 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.7896 (m-30) cc_final: 0.7452 (m-30) REVERT: A 1248 GLN cc_start: 0.8532 (tt0) cc_final: 0.8294 (tp40) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.2498 time to fit residues: 40.3575 Evaluate side-chains 95 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 637 GLN A1242 HIS A1248 GLN A1267 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9500 Z= 0.236 Angle : 0.506 9.585 12857 Z= 0.263 Chirality : 0.039 0.127 1514 Planarity : 0.004 0.054 1608 Dihedral : 6.334 108.946 1395 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.99 % Allowed : 7.42 % Favored : 91.59 % 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: 1.24 (0.25), residues: 1193 helix: 1.51 (0.18), residues: 787 sheet: -1.52 (0.79), residues: 48 loop : -0.25 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.007 0.001 HIS A 103 PHE 0.018 0.002 PHE A1167 TYR 0.024 0.001 TYR A 248 ARG 0.007 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.060 Fit side-chains REVERT: A 165 ASP cc_start: 0.7973 (m-30) cc_final: 0.7626 (m-30) REVERT: A 756 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 1017 ASP cc_start: 0.7772 (t0) cc_final: 0.7515 (t0) REVERT: A 1046 ASP cc_start: 0.7842 (t70) cc_final: 0.7319 (t0) REVERT: A 1050 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6870 (mtp85) REVERT: A 1168 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 1248 GLN cc_start: 0.8603 (tt0) cc_final: 0.8263 (tp40) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.2445 time to fit residues: 37.4329 Evaluate side-chains 104 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9500 Z= 0.192 Angle : 0.467 8.948 12857 Z= 0.242 Chirality : 0.038 0.128 1514 Planarity : 0.004 0.047 1608 Dihedral : 5.909 100.612 1391 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.48 % Allowed : 9.30 % Favored : 89.22 % 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: 1.55 (0.25), residues: 1193 helix: 1.78 (0.19), residues: 785 sheet: -1.47 (0.80), residues: 48 loop : -0.20 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 213 HIS 0.005 0.001 HIS A 103 PHE 0.021 0.001 PHE A1167 TYR 0.024 0.001 TYR A 248 ARG 0.003 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.014 Fit side-chains REVERT: A 165 ASP cc_start: 0.7956 (m-30) cc_final: 0.7658 (m-30) REVERT: A 756 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 1046 ASP cc_start: 0.7788 (t70) cc_final: 0.7158 (t0) REVERT: A 1168 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7862 (mp) REVERT: A 1248 GLN cc_start: 0.8611 (tt0) cc_final: 0.8265 (tp40) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 0.2430 time to fit residues: 37.1942 Evaluate side-chains 105 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 0.0070 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 ASN A1242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9500 Z= 0.259 Angle : 0.493 9.815 12857 Z= 0.254 Chirality : 0.039 0.126 1514 Planarity : 0.004 0.047 1608 Dihedral : 5.800 94.709 1391 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 10.78 % Favored : 87.24 % 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: 1.47 (0.25), residues: 1193 helix: 1.69 (0.19), residues: 792 sheet: -1.56 (0.77), residues: 48 loop : -0.19 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 213 HIS 0.006 0.001 HIS A 103 PHE 0.018 0.002 PHE A 979 TYR 0.027 0.001 TYR A 248 ARG 0.004 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.132 Fit side-chains REVERT: A 165 ASP cc_start: 0.7989 (m-30) cc_final: 0.7686 (m-30) REVERT: A 189 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: A 756 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 1046 ASP cc_start: 0.7704 (t70) cc_final: 0.7071 (t0) REVERT: A 1168 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 1248 GLN cc_start: 0.8633 (tt0) cc_final: 0.8267 (tp40) outliers start: 20 outliers final: 15 residues processed: 108 average time/residue: 0.2427 time to fit residues: 36.9549 Evaluate side-chains 108 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A1242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9500 Z= 0.220 Angle : 0.485 9.560 12857 Z= 0.246 Chirality : 0.038 0.148 1514 Planarity : 0.003 0.045 1608 Dihedral : 5.648 89.961 1391 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.98 % Allowed : 11.57 % Favored : 86.45 % 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: 1.59 (0.25), residues: 1193 helix: 1.80 (0.19), residues: 792 sheet: -1.57 (0.77), residues: 48 loop : -0.17 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.006 0.001 HIS A 103 PHE 0.016 0.001 PHE A 979 TYR 0.025 0.001 TYR A 248 ARG 0.006 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.222 Fit side-chains REVERT: A 165 ASP cc_start: 0.7983 (m-30) cc_final: 0.7690 (m-30) REVERT: A 366 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8533 (mp) REVERT: A 756 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 1046 ASP cc_start: 0.7673 (t70) cc_final: 0.7011 (t0) REVERT: A 1168 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7784 (mp) REVERT: A 1248 GLN cc_start: 0.8622 (tt0) cc_final: 0.8266 (tp40) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 0.2445 time to fit residues: 37.6885 Evaluate side-chains 107 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A1242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9500 Z= 0.196 Angle : 0.471 9.289 12857 Z= 0.239 Chirality : 0.038 0.128 1514 Planarity : 0.003 0.044 1608 Dihedral : 5.409 82.291 1391 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.18 % Allowed : 12.56 % Favored : 85.26 % 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: 1.70 (0.25), residues: 1193 helix: 1.90 (0.19), residues: 792 sheet: -1.19 (0.70), residues: 58 loop : -0.19 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.005 0.001 HIS A 103 PHE 0.015 0.001 PHE A 979 TYR 0.024 0.001 TYR A 248 ARG 0.005 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.063 Fit side-chains REVERT: A 165 ASP cc_start: 0.7984 (m-30) cc_final: 0.7693 (m-30) REVERT: A 189 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: A 366 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 756 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8582 (mp) REVERT: A 1046 ASP cc_start: 0.7683 (t70) cc_final: 0.6993 (t0) REVERT: A 1168 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 1248 GLN cc_start: 0.8624 (tt0) cc_final: 0.8265 (tp40) outliers start: 22 outliers final: 15 residues processed: 116 average time/residue: 0.2089 time to fit residues: 34.2534 Evaluate side-chains 113 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9500 Z= 0.176 Angle : 0.467 9.115 12857 Z= 0.236 Chirality : 0.038 0.129 1514 Planarity : 0.003 0.044 1608 Dihedral : 5.178 74.144 1391 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.27 % Allowed : 13.35 % Favored : 84.37 % 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: 1.82 (0.25), residues: 1193 helix: 2.00 (0.19), residues: 791 sheet: -1.18 (0.70), residues: 58 loop : -0.16 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.005 0.001 HIS A 103 PHE 0.014 0.001 PHE A 979 TYR 0.023 0.001 TYR A 248 ARG 0.004 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.081 Fit side-chains REVERT: A 165 ASP cc_start: 0.7978 (m-30) cc_final: 0.7691 (m-30) REVERT: A 189 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: A 277 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8522 (mtmm) REVERT: A 366 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 756 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 1046 ASP cc_start: 0.7698 (t70) cc_final: 0.7293 (t0) REVERT: A 1050 ARG cc_start: 0.7269 (mtp85) cc_final: 0.7009 (mtp85) REVERT: A 1168 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 1248 GLN cc_start: 0.8621 (tt0) cc_final: 0.8267 (tp40) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.2232 time to fit residues: 37.1376 Evaluate side-chains 118 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1163 ASN A1242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9500 Z= 0.141 Angle : 0.449 8.173 12857 Z= 0.227 Chirality : 0.037 0.131 1514 Planarity : 0.003 0.043 1608 Dihedral : 4.355 52.757 1391 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.98 % Allowed : 13.55 % Favored : 84.47 % 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: 2.00 (0.25), residues: 1193 helix: 2.17 (0.19), residues: 787 sheet: -1.03 (0.70), residues: 58 loop : -0.15 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 PHE 0.011 0.001 PHE A 979 TYR 0.020 0.001 TYR A 248 ARG 0.005 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.073 Fit side-chains REVERT: A 165 ASP cc_start: 0.7929 (m-30) cc_final: 0.7644 (m-30) REVERT: A 189 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: A 366 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 756 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8568 (mp) REVERT: A 1046 ASP cc_start: 0.7688 (t70) cc_final: 0.7410 (t0) REVERT: A 1050 ARG cc_start: 0.7214 (mtp85) cc_final: 0.7000 (mtp85) REVERT: A 1168 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7746 (mp) REVERT: A 1248 GLN cc_start: 0.8598 (tt0) cc_final: 0.8257 (tp40) outliers start: 20 outliers final: 12 residues processed: 119 average time/residue: 0.2282 time to fit residues: 38.2402 Evaluate side-chains 114 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 72.665 > 50: distance: 12 - 34: 36.951 distance: 30 - 34: 34.026 distance: 35 - 36: 40.279 distance: 35 - 38: 39.996 distance: 36 - 37: 41.165 distance: 38 - 39: 39.875 distance: 39 - 40: 67.159 distance: 39 - 41: 41.100 distance: 40 - 42: 40.770 distance: 41 - 43: 38.917 distance: 42 - 44: 39.061 distance: 43 - 44: 41.146 distance: 44 - 45: 39.779 distance: 46 - 47: 40.939 distance: 47 - 48: 40.464 distance: 48 - 50: 68.755 distance: 50 - 51: 57.494 distance: 51 - 52: 39.847 distance: 51 - 54: 56.123 distance: 52 - 53: 56.516 distance: 55 - 57: 40.133 distance: 58 - 59: 40.824 distance: 59 - 62: 39.744 distance: 60 - 61: 40.639 distance: 62 - 63: 39.780 distance: 62 - 64: 39.405 distance: 65 - 66: 38.962 distance: 66 - 67: 40.152 distance: 67 - 68: 40.769 distance: 67 - 69: 56.033 distance: 75 - 76: 39.021 distance: 76 - 77: 38.561 distance: 76 - 79: 40.083 distance: 77 - 78: 40.022 distance: 77 - 84: 41.038 distance: 82 - 83: 39.992 distance: 85 - 86: 38.873 distance: 85 - 88: 55.724 distance: 88 - 89: 39.939 distance: 89 - 90: 42.577 distance: 89 - 91: 56.374 distance: 90 - 92: 8.877 distance: 91 - 93: 40.104 distance: 92 - 94: 40.482 distance: 93 - 94: 40.069 distance: 97 - 98: 28.122 distance: 97 - 100: 41.057 distance: 98 - 99: 29.807 distance: 98 - 105: 11.469 distance: 101 - 102: 56.612 distance: 102 - 103: 41.165 distance: 102 - 104: 39.516 distance: 107 - 113: 34.146 distance: 109 - 110: 38.886 distance: 110 - 111: 40.987 distance: 110 - 112: 55.949