Starting phenix.real_space_refine on Fri Mar 15 08:42:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe7_12861/03_2024/7oe7_12861.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe7_12861/03_2024/7oe7_12861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe7_12861/03_2024/7oe7_12861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe7_12861/03_2024/7oe7_12861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe7_12861/03_2024/7oe7_12861.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe7_12861/03_2024/7oe7_12861.pdb" } resolution = 3.73 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= 0.002 sd= 0.018 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 Mg 1 5.21 5 S 63 5.16 5 C 7088 2.51 5 N 1881 2.21 5 O 2082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 253": "OE1" <-> "OE2" Residue "L GLU 312": "OE1" <-> "OE2" Residue "L GLU 490": "OE1" <-> "OE2" Residue "L GLU 538": "OE1" <-> "OE2" Residue "L GLU 1132": "OE1" <-> "OE2" Residue "L GLU 1166": "OE1" <-> "OE2" Residue "L GLU 1653": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 1 Chain: "L" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1384, 11116 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'peptide': 1382, 'undetermined': 2} Link IDs: {'PTRANS': 42, 'TRANS': 1339, None: 2} Not linked: pdbres="HIS L1823 " pdbres=" ZN L2301 " Not linked: pdbres=" ZN L2301 " pdbres=" MG L2302 " Chain breaks: 11 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 998 SG CYS L 321 41.658 105.490 68.143 1.00100.99 S ATOM 1360 SG CYS L 366 39.678 105.920 71.466 1.00108.15 S Time building chain proxies: 6.88, per 1000 atoms: 0.62 Number of scatterers: 11116 At special positions: 0 Unit cell: (97.44, 133.11, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 63 16.00 Mg 1 11.99 O 2082 8.00 N 1881 7.00 C 7088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L1690 " - pdb=" SG CYS L1790 " distance=2.03 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: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 316 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " Number of angles added : 2 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 54.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.713A pdb=" N VAL L 205 " --> pdb=" O SER L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 222 removed outlier: 4.263A pdb=" N GLU L 216 " --> pdb=" O SER L 212 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE L 217 " --> pdb=" O HIS L 213 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L 218 " --> pdb=" O TYR L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 252 removed outlier: 3.505A pdb=" N GLN L 237 " --> pdb=" O GLU L 233 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS L 251 " --> pdb=" O ASN L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 removed outlier: 3.577A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 302 Processing helix chain 'L' and resid 312 through 317 removed outlier: 3.811A pdb=" N THR L 317 " --> pdb=" O GLU L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 336 removed outlier: 3.542A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 361 removed outlier: 3.850A pdb=" N LEU L 352 " --> pdb=" O ILE L 348 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE L 353 " --> pdb=" O PHE L 349 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU L 354 " --> pdb=" O ASP L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 404 Processing helix chain 'L' and resid 414 through 436 removed outlier: 4.099A pdb=" N ILE L 418 " --> pdb=" O ASN L 414 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL L 435 " --> pdb=" O ALA L 431 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY L 436 " --> pdb=" O LEU L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 443 removed outlier: 3.526A pdb=" N TYR L 442 " --> pdb=" O VAL L 439 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS L 443 " --> pdb=" O GLU L 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 439 through 443' Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.576A pdb=" N VAL L 448 " --> pdb=" O ASN L 445 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 449 " --> pdb=" O MET L 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 445 through 449' Processing helix chain 'L' and resid 453 through 458 removed outlier: 3.627A pdb=" N LEU L 458 " --> pdb=" O TYR L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 507 removed outlier: 3.864A pdb=" N GLU L 495 " --> pdb=" O SER L 491 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG L 496 " --> pdb=" O THR L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 599 Processing helix chain 'L' and resid 604 through 608 removed outlier: 3.950A pdb=" N GLU L 608 " --> pdb=" O SER L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 628 removed outlier: 3.596A pdb=" N ASN L 615 " --> pdb=" O LEU L 611 " (cutoff:3.500A) Processing helix chain 'L' and resid 633 through 639 removed outlier: 3.628A pdb=" N LEU L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN L 639 " --> pdb=" O LYS L 635 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 648 removed outlier: 3.513A pdb=" N PHE L 643 " --> pdb=" O ASN L 639 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL L 648 " --> pdb=" O ILE L 644 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 660 Processing helix chain 'L' and resid 668 through 684 Processing helix chain 'L' and resid 693 through 703 Processing helix chain 'L' and resid 704 through 709 removed outlier: 3.542A pdb=" N HIS L 707 " --> pdb=" O TYR L 704 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE L 709 " --> pdb=" O CYS L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 717 through 729 removed outlier: 4.087A pdb=" N LYS L 722 " --> pdb=" O THR L 718 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS L 723 " --> pdb=" O ASP L 719 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE L 724 " --> pdb=" O GLN L 720 " (cutoff:3.500A) Processing helix chain 'L' and resid 729 through 734 removed outlier: 3.939A pdb=" N GLU L 733 " --> pdb=" O GLU L 729 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE L 734 " --> pdb=" O PRO L 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 729 through 734' Processing helix chain 'L' and resid 746 through 760 Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 800 through 804 removed outlier: 3.656A pdb=" N LYS L 803 " --> pdb=" O SER L 800 " (cutoff:3.500A) Processing helix chain 'L' and resid 818 through 823 Processing helix chain 'L' and resid 843 through 862 removed outlier: 4.485A pdb=" N ARG L 860 " --> pdb=" O GLU L 856 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS L 861 " --> pdb=" O VAL L 857 " (cutoff:3.500A) Processing helix chain 'L' and resid 870 through 881 removed outlier: 3.663A pdb=" N ALA L 878 " --> pdb=" O LYS L 874 " (cutoff:3.500A) Processing helix chain 'L' and resid 907 through 925 removed outlier: 3.965A pdb=" N LYS L 915 " --> pdb=" O PHE L 911 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU L 916 " --> pdb=" O ASP L 912 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR L 917 " --> pdb=" O GLN L 913 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL L 918 " --> pdb=" O LEU L 914 " (cutoff:3.500A) Processing helix chain 'L' and resid 1059 through 1068 Processing helix chain 'L' and resid 1075 through 1084 Processing helix chain 'L' and resid 1093 through 1098 removed outlier: 3.714A pdb=" N CYS L1097 " --> pdb=" O LEU L1093 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 3.664A pdb=" N ARG L1145 " --> pdb=" O LYS L1141 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU L1146 " --> pdb=" O MET L1142 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1166 through 1182 removed outlier: 3.646A pdb=" N GLU L1170 " --> pdb=" O GLU L1166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU L1182 " --> pdb=" O LEU L1178 " (cutoff:3.500A) Processing helix chain 'L' and resid 1199 through 1208 removed outlier: 3.784A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) Processing helix chain 'L' and resid 1216 through 1236 removed outlier: 3.779A pdb=" N ASP L1220 " --> pdb=" O ASP L1216 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1259 removed outlier: 3.667A pdb=" N GLN L1257 " --> pdb=" O PHE L1253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) Processing helix chain 'L' and resid 1270 through 1278 removed outlier: 3.641A pdb=" N ASN L1276 " --> pdb=" O PHE L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 removed outlier: 3.522A pdb=" N SER L1301 " --> pdb=" O LEU L1297 " (cutoff:3.500A) Processing helix chain 'L' and resid 1338 through 1348 removed outlier: 3.719A pdb=" N GLN L1346 " --> pdb=" O THR L1342 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG L1347 " --> pdb=" O GLU L1343 " (cutoff:3.500A) Processing helix chain 'L' and resid 1348 through 1365 removed outlier: 3.851A pdb=" N THR L1354 " --> pdb=" O GLU L1350 " (cutoff:3.500A) Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.860A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1414 through 1429 removed outlier: 4.074A pdb=" N GLU L1418 " --> pdb=" O HIS L1414 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L1429 " --> pdb=" O ASP L1425 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 4.030A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA L1451 " --> pdb=" O LEU L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1466 through 1471 Processing helix chain 'L' and resid 1473 through 1486 removed outlier: 3.576A pdb=" N ARG L1477 " --> pdb=" O ASN L1473 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE L1478 " --> pdb=" O ARG L1474 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG L1484 " --> pdb=" O ARG L1480 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU L1485 " --> pdb=" O GLN L1481 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE L1486 " --> pdb=" O ILE L1482 " (cutoff:3.500A) Processing helix chain 'L' and resid 1492 through 1506 removed outlier: 4.371A pdb=" N ARG L1498 " --> pdb=" O ARG L1494 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) Processing helix chain 'L' and resid 1521 through 1533 removed outlier: 3.730A pdb=" N LEU L1533 " --> pdb=" O LEU L1529 " (cutoff:3.500A) Processing helix chain 'L' and resid 1539 through 1543 removed outlier: 3.878A pdb=" N LEU L1543 " --> pdb=" O GLU L1540 " (cutoff:3.500A) Processing helix chain 'L' and resid 1579 through 1589 Processing helix chain 'L' and resid 1592 through 1605 Processing helix chain 'L' and resid 1613 through 1624 Processing helix chain 'L' and resid 1639 through 1649 Processing helix chain 'L' and resid 1668 through 1672 removed outlier: 4.427A pdb=" N ASP L1672 " --> pdb=" O ASN L1669 " (cutoff:3.500A) Processing helix chain 'L' and resid 1677 through 1679 No H-bonds generated for 'chain 'L' and resid 1677 through 1679' Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1701 through 1705 removed outlier: 3.669A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) Processing helix chain 'L' and resid 1778 through 1790 removed outlier: 4.136A pdb=" N VAL L1788 " --> pdb=" O VAL L1784 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN L1789 " --> pdb=" O ALA L1785 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS L1790 " --> pdb=" O LEU L1786 " (cutoff:3.500A) Processing helix chain 'L' and resid 1794 through 1800 removed outlier: 3.585A pdb=" N HIS L1798 " --> pdb=" O SER L1794 " (cutoff:3.500A) Processing helix chain 'L' and resid 1812 through 1817 removed outlier: 3.690A pdb=" N ARG L1816 " --> pdb=" O SER L1812 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU L1817 " --> pdb=" O SER L1813 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1812 through 1817' Processing sheet with id=AA1, first strand: chain 'L' and resid 207 through 208 removed outlier: 6.631A pdb=" N LEU L 207 " --> pdb=" O TYR L1107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 259 through 260 Processing sheet with id=AA3, first strand: chain 'L' and resid 535 through 541 removed outlier: 3.950A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 826 through 828 removed outlier: 3.534A pdb=" N VAL L 827 " --> pdb=" O GLU L1073 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 1132 through 1136 removed outlier: 4.450A pdb=" N LEU L1121 " --> pdb=" O GLU L1240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 1333 through 1336 removed outlier: 3.949A pdb=" N GLN L1333 " --> pdb=" O MET L1189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1381 through 1382 Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1655 Processing sheet with id=AA9, first strand: chain 'L' and resid 1723 through 1726 removed outlier: 3.727A pdb=" N VAL L1810 " --> pdb=" O PHE L1724 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1371 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: 3.92 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3590 1.34 - 1.46: 2442 1.46 - 1.58: 5196 1.58 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 11322 Sorted by residual: bond pdb=" C PHE L 581 " pdb=" N PRO L 582 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.19e-02 7.06e+03 4.17e+00 bond pdb=" CA MET L 446 " pdb=" C MET L 446 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.38e-02 5.25e+03 1.62e+00 bond pdb=" CA ASP L1216 " pdb=" C ASP L1216 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.15e-01 bond pdb=" CA LYS L 635 " pdb=" C LYS L 635 " ideal model delta sigma weight residual 1.522 1.510 0.012 1.38e-02 5.25e+03 7.85e-01 bond pdb=" CA PRO L 410 " pdb=" C PRO L 410 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.43e-01 ... (remaining 11317 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.20: 293 107.20 - 113.89: 6429 113.89 - 120.58: 4413 120.58 - 127.28: 4047 127.28 - 133.97: 87 Bond angle restraints: 15269 Sorted by residual: angle pdb=" N ILE L1613 " pdb=" CA ILE L1613 " pdb=" C ILE L1613 " ideal model delta sigma weight residual 111.90 108.46 3.44 8.10e-01 1.52e+00 1.80e+01 angle pdb=" N ILE L 318 " pdb=" CA ILE L 318 " pdb=" C ILE L 318 " ideal model delta sigma weight residual 112.98 108.33 4.65 1.25e+00 6.40e-01 1.39e+01 angle pdb=" N ILE L1639 " pdb=" CA ILE L1639 " pdb=" C ILE L1639 " ideal model delta sigma weight residual 111.81 108.66 3.15 8.60e-01 1.35e+00 1.34e+01 angle pdb=" N SER L 211 " pdb=" CA SER L 211 " pdb=" C SER L 211 " ideal model delta sigma weight residual 110.97 114.81 -3.84 1.09e+00 8.42e-01 1.24e+01 angle pdb=" C ILE L1486 " pdb=" CA ILE L1486 " pdb=" CB ILE L1486 " ideal model delta sigma weight residual 111.08 114.21 -3.13 9.50e-01 1.11e+00 1.09e+01 ... (remaining 15264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 6055 16.94 - 33.87: 684 33.87 - 50.81: 126 50.81 - 67.74: 20 67.74 - 84.68: 10 Dihedral angle restraints: 6895 sinusoidal: 2827 harmonic: 4068 Sorted by residual: dihedral pdb=" CB CYS L1690 " pdb=" SG CYS L1690 " pdb=" SG CYS L1790 " pdb=" CB CYS L1790 " ideal model delta sinusoidal sigma weight residual -86.00 -131.89 45.89 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CA THR L 710 " pdb=" C THR L 710 " pdb=" N LYS L 711 " pdb=" CA LYS L 711 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA VAL L 275 " pdb=" C VAL L 275 " pdb=" N ASP L 276 " pdb=" CA ASP L 276 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1440 0.049 - 0.097: 253 0.097 - 0.146: 40 0.146 - 0.195: 1 0.195 - 0.244: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" CB THR L 710 " pdb=" CA THR L 710 " pdb=" OG1 THR L 710 " pdb=" CG2 THR L 710 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL L 601 " pdb=" CA VAL L 601 " pdb=" CG1 VAL L 601 " pdb=" CG2 VAL L 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ILE L1241 " pdb=" N ILE L1241 " pdb=" C ILE L1241 " pdb=" CB ILE L1241 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1732 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE L1486 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO L1487 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO L1487 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L1487 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L1412 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO L1413 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L1413 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L1413 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 709 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE L 709 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE L 709 " -0.010 2.00e-02 2.50e+03 pdb=" N THR L 710 " -0.009 2.00e-02 2.50e+03 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 100 2.65 - 3.21: 9785 3.21 - 3.77: 14997 3.77 - 4.34: 20108 4.34 - 4.90: 33890 Nonbonded interactions: 78880 Sorted by model distance: nonbonded pdb=" OD1 ASP L1332 " pdb="MG MG L2302 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP L1657 " pdb=" N SER L1658 " model vdw 2.125 2.520 nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.156 2.440 nonbonded pdb=" OG SER L 685 " pdb=" OD1 ASP L 687 " model vdw 2.158 2.440 nonbonded pdb=" OG SER L1161 " pdb=" OD2 ASP L1302 " model vdw 2.167 2.440 ... (remaining 78875 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 group one per residue 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.980 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.490 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11322 Z= 0.133 Angle : 0.528 7.276 15269 Z= 0.306 Chirality : 0.038 0.244 1735 Planarity : 0.003 0.044 1928 Dihedral : 14.332 84.676 4246 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.23), residues: 1358 helix: 0.92 (0.21), residues: 697 sheet: -1.94 (0.67), residues: 57 loop : -3.38 (0.20), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 395 HIS 0.002 0.001 HIS L 364 PHE 0.015 0.001 PHE L1303 TYR 0.018 0.001 TYR L 574 ARG 0.002 0.000 ARG L1665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2718 time to fit residues: 95.0983 Evaluate side-chains 106 residues out of total 1261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 35 optimal weight: 0.2980 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 0.0770 chunk 108 optimal weight: 0.0060 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.1110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 441 HIS L1126 GLN L1208 GLN L1508 GLN L1807 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11322 Z= 0.147 Angle : 0.591 12.393 15269 Z= 0.288 Chirality : 0.039 0.196 1735 Planarity : 0.003 0.036 1928 Dihedral : 3.801 17.386 1490 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.74 % Allowed : 9.20 % Favored : 89.06 % 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: -1.30 (0.23), residues: 1358 helix: 0.93 (0.21), residues: 714 sheet: -1.31 (0.70), residues: 53 loop : -3.28 (0.21), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L1664 HIS 0.004 0.001 HIS L1798 PHE 0.014 0.001 PHE L1303 TYR 0.017 0.001 TYR L 471 ARG 0.007 0.000 ARG L1131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 497 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7098 (tt) REVERT: L 750 LEU cc_start: 0.8084 (mp) cc_final: 0.7708 (mt) outliers start: 22 outliers final: 13 residues processed: 144 average time/residue: 0.2296 time to fit residues: 47.8072 Evaluate side-chains 105 residues out of total 1261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 390 ARG Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain L residue 667 ASP Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1319 ILE Chi-restraints excluded: chain L residue 1371 SER Chi-restraints excluded: chain L residue 1434 VAL Chi-restraints excluded: chain L residue 1468 ASP Chi-restraints excluded: chain L residue 1508 GLN Chi-restraints excluded: chain L residue 1524 SER Chi-restraints excluded: chain L residue 1550 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1709 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 65.4657 > 50: distance: 84 - 180: 26.670 distance: 87 - 177: 33.083 distance: 96 - 168: 23.037 distance: 112 - 118: 13.560 distance: 118 - 119: 12.607 distance: 119 - 120: 6.974 distance: 119 - 122: 20.663 distance: 120 - 121: 25.193 distance: 120 - 126: 27.165 distance: 122 - 123: 25.900 distance: 123 - 124: 28.884 distance: 123 - 125: 37.654 distance: 126 - 127: 13.032 distance: 127 - 128: 14.790 distance: 127 - 130: 31.490 distance: 128 - 129: 41.022 distance: 128 - 137: 17.987 distance: 130 - 131: 50.604 distance: 131 - 132: 13.817 distance: 133 - 134: 12.042 distance: 134 - 135: 17.908 distance: 134 - 136: 5.523 distance: 137 - 138: 32.010 distance: 138 - 139: 43.089 distance: 138 - 141: 15.612 distance: 139 - 140: 32.481 distance: 139 - 144: 16.098 distance: 141 - 142: 55.337 distance: 141 - 143: 42.662 distance: 144 - 145: 33.052 distance: 145 - 146: 55.330 distance: 146 - 147: 65.466 distance: 146 - 148: 21.616 distance: 148 - 149: 21.151 distance: 149 - 150: 38.550 distance: 149 - 152: 27.187 distance: 150 - 151: 18.032 distance: 150 - 157: 42.821 distance: 152 - 153: 36.375 distance: 153 - 154: 50.086 distance: 154 - 155: 17.011 distance: 154 - 156: 23.832 distance: 157 - 158: 11.768 distance: 158 - 159: 21.086 distance: 158 - 161: 34.255 distance: 159 - 160: 21.685 distance: 159 - 165: 15.014 distance: 161 - 162: 41.305 distance: 161 - 163: 32.050 distance: 162 - 164: 20.904 distance: 165 - 166: 26.581 distance: 166 - 167: 40.261 distance: 166 - 169: 26.204 distance: 167 - 168: 33.186 distance: 167 - 171: 23.498 distance: 169 - 170: 34.385 distance: 171 - 172: 23.176 distance: 172 - 173: 34.208 distance: 172 - 175: 28.231 distance: 173 - 174: 21.122 distance: 173 - 177: 56.666 distance: 175 - 176: 41.372 distance: 177 - 178: 22.137 distance: 178 - 179: 13.162 distance: 178 - 181: 30.773 distance: 179 - 180: 41.051 distance: 179 - 188: 5.676 distance: 181 - 182: 35.136 distance: 182 - 183: 26.303 distance: 182 - 184: 44.875 distance: 183 - 185: 29.098 distance: 184 - 186: 57.074 distance: 185 - 187: 28.554 distance: 186 - 187: 54.849 distance: 188 - 189: 22.687 distance: 189 - 190: 42.537 distance: 189 - 192: 21.729 distance: 190 - 191: 43.909 distance: 190 - 200: 30.550 distance: 192 - 193: 36.245 distance: 193 - 194: 34.024 distance: 193 - 195: 27.887 distance: 194 - 196: 13.259 distance: 195 - 197: 9.194 distance: 196 - 198: 11.548 distance: 197 - 198: 6.826 distance: 198 - 199: 12.761