Starting phenix.real_space_refine on Wed Sep 25 09:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/09_2024/8i4a_35167.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/09_2024/8i4a_35167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/09_2024/8i4a_35167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/09_2024/8i4a_35167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/09_2024/8i4a_35167.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/09_2024/8i4a_35167.cif" } resolution = 3.4 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= 0.001 sd= 0.045 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 43 5.16 5 C 6340 2.51 5 N 1645 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 9763 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9727 Classifications: {'peptide': 1218} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'H9F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.79, per 1000 atoms: 0.59 Number of scatterers: 9763 At special positions: 0 Unit cell: (77.04, 114.49, 146.59, 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 43 16.00 O 1735 8.00 N 1645 7.00 C 6340 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 66.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 52 through 75 Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.708A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 122 Proline residue: A 110 - end of helix removed outlier: 3.596A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 removed outlier: 3.519A pdb=" N ILE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 179 removed outlier: 4.012A pdb=" N HIS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.591A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.665A pdb=" N ASN A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.346A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.687A pdb=" N THR A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 4.108A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.590A pdb=" N SER A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 removed outlier: 4.652A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.547A pdb=" N ILE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 342 removed outlier: 3.788A pdb=" N PHE A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 390 removed outlier: 3.896A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.901A pdb=" N VAL A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 529 through 533 removed outlier: 4.129A pdb=" N GLY A 532 " --> pdb=" O GLY A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.975A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.790A pdb=" N TYR A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.657A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 removed outlier: 4.051A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 709 " --> pdb=" O PHE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.724A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 804 removed outlier: 3.524A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.758A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.764A pdb=" N ASP A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 4.191A pdb=" N LEU A 841 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 866 Processing helix chain 'A' and resid 872 through 884 Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.917A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 937 through 966 removed outlier: 3.969A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1017 removed outlier: 4.246A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 removed outlier: 3.918A pdb=" N SER A1086 " --> pdb=" O SER A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.663A pdb=" N PHE A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1278 through 1296 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 6.824A pdb=" N GLN A 429 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 416 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.643A pdb=" N ASP A 559 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 606 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1056 through 1065 removed outlier: 6.919A pdb=" N VAL A1057 " --> pdb=" O MET A1049 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET A1049 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 3.707A pdb=" N SER A1118 " --> pdb=" O ILE A1197 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1668 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: 3.06 Time building geometry restraints manager: 3.04 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: 2977 1.33 - 1.46: 1849 1.46 - 1.58: 5079 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 9975 Sorted by residual: bond pdb=" C5 H9F A1401 " pdb=" N8 H9F A1401 " ideal model delta sigma weight residual 1.348 1.451 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C2 H9F A1401 " pdb=" N7 H9F A1401 " ideal model delta sigma weight residual 1.360 1.451 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C3 H9F A1401 " pdb=" N5 H9F A1401 " ideal model delta sigma weight residual 1.365 1.452 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C6 H9F A1401 " pdb=" N6 H9F A1401 " ideal model delta sigma weight residual 1.364 1.450 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C4 H9F A1401 " pdb=" C5 H9F A1401 " ideal model delta sigma weight residual 1.456 1.386 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 9970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 13333 3.32 - 6.63: 165 6.63 - 9.95: 16 9.95 - 13.26: 0 13.26 - 16.58: 1 Bond angle restraints: 13515 Sorted by residual: angle pdb=" C LEU A 835 " pdb=" N LEU A 836 " pdb=" CA LEU A 836 " ideal model delta sigma weight residual 119.83 113.58 6.25 1.11e+00 8.12e-01 3.17e+01 angle pdb=" C LEU A 892 " pdb=" N GLU A 893 " pdb=" CA GLU A 893 " ideal model delta sigma weight residual 122.56 114.37 8.19 1.72e+00 3.38e-01 2.27e+01 angle pdb=" CA LEU A1214 " pdb=" CB LEU A1214 " pdb=" CG LEU A1214 " ideal model delta sigma weight residual 116.30 132.88 -16.58 3.50e+00 8.16e-02 2.24e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.42 108.41 5.01 1.17e+00 7.31e-01 1.84e+01 angle pdb=" C LYS A 305 " pdb=" N GLU A 306 " pdb=" CA GLU A 306 " ideal model delta sigma weight residual 121.92 114.56 7.36 1.73e+00 3.34e-01 1.81e+01 ... (remaining 13510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 5593 23.63 - 47.26: 341 47.26 - 70.89: 32 70.89 - 94.52: 8 94.52 - 118.15: 3 Dihedral angle restraints: 5977 sinusoidal: 2418 harmonic: 3559 Sorted by residual: dihedral pdb=" CA PHE A 352 " pdb=" C PHE A 352 " pdb=" N VAL A 353 " pdb=" CA VAL A 353 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA CYS A 253 " pdb=" C CYS A 253 " pdb=" N PHE A 254 " pdb=" CA PHE A 254 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA TRP A 291 " pdb=" C TRP A 291 " pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1165 0.060 - 0.120: 346 0.120 - 0.179: 47 0.179 - 0.239: 2 0.239 - 0.299: 1 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU A 582 " pdb=" CB LEU A 582 " pdb=" CD1 LEU A 582 " pdb=" CD2 LEU A 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 889 " pdb=" CA VAL A 889 " pdb=" CG1 VAL A 889 " pdb=" CG2 VAL A 889 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1558 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 869 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A 870 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 218 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 219 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1123 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A1124 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1124 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1124 " 0.029 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 241 2.67 - 3.23: 9944 3.23 - 3.79: 15184 3.79 - 4.34: 20372 4.34 - 4.90: 33410 Nonbonded interactions: 79151 Sorted by model distance: nonbonded pdb=" NH2 ARG A 272 " pdb=" O PHE A 825 " model vdw 2.115 3.120 nonbonded pdb=" OG SER A 794 " pdb=" OD1 ASP A 833 " model vdw 2.123 3.040 nonbonded pdb=" NE2 GLN A1183 " pdb=" O ALA A1203 " model vdw 2.137 3.120 nonbonded pdb=" O VAL A 410 " pdb=" OG1 THR A 434 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASP A 953 " pdb=" NE2 GLN A 994 " model vdw 2.227 3.120 ... (remaining 79146 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: 0.840 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.130 Find NCS groups from input model: 0.080 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.012 0.103 9975 Z= 0.750 Angle : 0.937 16.579 13515 Z= 0.503 Chirality : 0.055 0.299 1561 Planarity : 0.005 0.060 1676 Dihedral : 15.095 118.154 3671 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.46 (0.24), residues: 1212 helix: -0.84 (0.18), residues: 781 sheet: -1.03 (0.61), residues: 76 loop : -0.79 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.008 0.001 HIS A1060 PHE 0.036 0.003 PHE A 98 TYR 0.016 0.002 TYR A1016 ARG 0.010 0.001 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.116 Fit side-chains REVERT: A 611 MET cc_start: 0.4865 (tpt) cc_final: 0.3322 (tmm) REVERT: A 921 GLU cc_start: 0.8464 (pt0) cc_final: 0.8226 (pt0) REVERT: A 1049 MET cc_start: 0.8412 (mtp) cc_final: 0.7824 (mmm) REVERT: A 1069 GLU cc_start: 0.7498 (pt0) cc_final: 0.7177 (pt0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1863 time to fit residues: 28.6984 Evaluate side-chains 85 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 387 GLN A1134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9975 Z= 0.275 Angle : 0.624 8.398 13515 Z= 0.322 Chirality : 0.043 0.158 1561 Planarity : 0.004 0.054 1676 Dihedral : 8.082 87.537 1350 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.56 % Allowed : 6.69 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.42 (0.25), residues: 1212 helix: -0.00 (0.19), residues: 801 sheet: -0.83 (0.61), residues: 76 loop : -0.42 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 912 HIS 0.003 0.001 HIS A 152 PHE 0.024 0.002 PHE A 324 TYR 0.015 0.001 TYR A 157 ARG 0.004 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.8431 (tpt) cc_final: 0.7704 (mmt) REVERT: A 611 MET cc_start: 0.4705 (tpt) cc_final: 0.3319 (tmm) REVERT: A 893 GLU cc_start: 0.8425 (pp20) cc_final: 0.8124 (tm-30) REVERT: A 1059 LYS cc_start: 0.7999 (tptp) cc_final: 0.7741 (tptp) REVERT: A 1069 GLU cc_start: 0.7479 (pt0) cc_final: 0.7206 (pt0) outliers start: 6 outliers final: 4 residues processed: 112 average time/residue: 0.2011 time to fit residues: 32.9767 Evaluate side-chains 106 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 1130 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 109 optimal weight: 0.0050 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 551 GLN A 845 GLN A 909 GLN A 994 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9975 Z= 0.195 Angle : 0.531 6.078 13515 Z= 0.277 Chirality : 0.041 0.151 1561 Planarity : 0.004 0.049 1676 Dihedral : 7.368 89.290 1350 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 9.42 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.21 (0.25), residues: 1212 helix: 0.49 (0.19), residues: 801 sheet: -0.55 (0.61), residues: 76 loop : -0.23 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 912 HIS 0.003 0.001 HIS A 35 PHE 0.023 0.001 PHE A 324 TYR 0.013 0.001 TYR A 157 ARG 0.002 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 893 GLU cc_start: 0.8334 (pp20) cc_final: 0.8060 (tm-30) REVERT: A 1049 MET cc_start: 0.8246 (mtt) cc_final: 0.7798 (mmm) REVERT: A 1097 LYS cc_start: 0.7730 (mptt) cc_final: 0.7256 (mtmt) REVERT: A 1131 MET cc_start: 0.7987 (tpp) cc_final: 0.7665 (tpp) outliers start: 19 outliers final: 14 residues processed: 124 average time/residue: 0.2045 time to fit residues: 37.2351 Evaluate side-chains 118 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1016 TYR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 57.1024 > 50: distance: 35 - 59: 6.271 distance: 53 - 59: 4.127 distance: 59 - 60: 3.405 distance: 60 - 61: 8.871 distance: 61 - 62: 4.997 distance: 61 - 68: 6.655 distance: 63 - 64: 4.769 distance: 64 - 65: 5.261 distance: 65 - 67: 4.169 distance: 68 - 69: 7.897 distance: 69 - 70: 15.754 distance: 69 - 72: 14.569 distance: 70 - 71: 36.684 distance: 70 - 76: 25.607 distance: 72 - 73: 7.053 distance: 73 - 74: 18.332 distance: 73 - 75: 10.857 distance: 76 - 77: 34.133 distance: 77 - 78: 15.999 distance: 77 - 80: 10.680 distance: 78 - 79: 12.620 distance: 78 - 84: 10.647 distance: 80 - 81: 15.169 distance: 81 - 82: 17.766 distance: 81 - 83: 15.540 distance: 84 - 85: 12.805 distance: 84 - 90: 9.749 distance: 85 - 86: 16.056 distance: 85 - 88: 7.636 distance: 86 - 87: 16.149 distance: 86 - 91: 15.765 distance: 88 - 89: 10.384 distance: 89 - 90: 22.870 distance: 91 - 92: 17.850 distance: 92 - 93: 16.524 distance: 93 - 94: 28.220 distance: 93 - 95: 26.118 distance: 95 - 96: 18.187 distance: 96 - 97: 6.733 distance: 96 - 99: 15.166 distance: 97 - 98: 3.826 distance: 97 - 104: 19.995 distance: 99 - 100: 14.609 distance: 100 - 101: 8.074 distance: 101 - 102: 10.506 distance: 102 - 103: 6.546 distance: 104 - 105: 3.735 distance: 105 - 106: 7.617 distance: 105 - 108: 13.255 distance: 106 - 107: 21.838 distance: 106 - 112: 5.088 distance: 108 - 109: 17.476 distance: 109 - 110: 24.694 distance: 110 - 111: 7.118 distance: 112 - 113: 8.480 distance: 113 - 114: 4.065 distance: 113 - 116: 4.946 distance: 114 - 115: 4.762 distance: 114 - 120: 12.216 distance: 116 - 117: 3.294 distance: 117 - 118: 6.431 distance: 117 - 119: 9.447 distance: 120 - 121: 13.412 distance: 121 - 122: 15.255 distance: 121 - 124: 9.215 distance: 122 - 123: 12.821 distance: 122 - 127: 4.080 distance: 124 - 125: 14.133 distance: 124 - 126: 13.718 distance: 127 - 128: 7.888 distance: 128 - 129: 6.756 distance: 128 - 131: 13.833 distance: 129 - 130: 12.586 distance: 129 - 136: 11.747 distance: 131 - 132: 7.183 distance: 132 - 133: 7.651 distance: 133 - 134: 11.295 distance: 133 - 135: 8.213