Starting phenix.real_space_refine on Fri Jan 19 22:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojl_12955/01_2024/7ojl_12955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojl_12955/01_2024/7ojl_12955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojl_12955/01_2024/7ojl_12955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojl_12955/01_2024/7ojl_12955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojl_12955/01_2024/7ojl_12955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojl_12955/01_2024/7ojl_12955.pdb" } resolution = 3.3 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= 0.004 sd= 0.029 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 Mn 1 7.51 5 P 31 5.49 5 S 67 5.16 5 C 8086 2.51 5 N 2182 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12842 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 12142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1498, 12142 Classifications: {'peptide': 1498} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 1450} Chain breaks: 12 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 5, 'rna3p': 14} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.20, per 1000 atoms: 0.56 Number of scatterers: 12842 At special positions: 0 Unit cell: (102, 115.6, 111.35, 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) Mn 1 24.99 S 67 16.00 P 31 15.00 O 2475 8.00 N 2182 7.00 C 8086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 321 " - pdb=" SG CYS L 366 " 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: 5.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2874 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 7 sheets defined 58.7% alpha, 4.9% beta 8 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.935A pdb=" N VAL L 205 " --> pdb=" O SER L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 221 removed outlier: 3.594A pdb=" N CYS L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 251 removed outlier: 3.757A pdb=" N LYS L 235 " --> pdb=" O ALA L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 Processing helix chain 'L' and resid 296 through 303 Processing helix chain 'L' and resid 321 through 336 removed outlier: 3.803A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 365 removed outlier: 3.515A pdb=" N ILE L 348 " --> pdb=" O LYS L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 404 Processing helix chain 'L' and resid 412 through 433 removed outlier: 3.780A pdb=" N MET L 420 " --> pdb=" O ILE L 416 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR L 424 " --> pdb=" O MET L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 442 Processing helix chain 'L' and resid 445 through 449 Processing helix chain 'L' and resid 453 through 459 Processing helix chain 'L' and resid 491 through 507 Processing helix chain 'L' and resid 521 through 527 removed outlier: 3.803A pdb=" N ALA L 524 " --> pdb=" O PHE L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 584 removed outlier: 3.509A pdb=" N TYR L 580 " --> pdb=" O PRO L 577 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE L 581 " --> pdb=" O LYS L 578 " (cutoff:3.500A) Proline residue: L 582 - end of helix Processing helix chain 'L' and resid 588 through 601 removed outlier: 3.907A pdb=" N VAL L 601 " --> pdb=" O MET L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 607 through 609 No H-bonds generated for 'chain 'L' and resid 607 through 609' Processing helix chain 'L' and resid 610 through 628 removed outlier: 3.629A pdb=" N ILE L 614 " --> pdb=" O GLN L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 631 through 649 removed outlier: 3.593A pdb=" N LYS L 635 " --> pdb=" O LYS L 631 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU L 636 " --> pdb=" O ARG L 632 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL L 648 " --> pdb=" O ILE L 644 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER L 649 " --> pdb=" O MET L 645 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 661 Processing helix chain 'L' and resid 666 through 684 Processing helix chain 'L' and resid 691 through 705 Processing helix chain 'L' and resid 706 through 709 Processing helix chain 'L' and resid 715 through 735 Proline residue: L 730 - end of helix removed outlier: 3.628A pdb=" N GLY L 735 " --> pdb=" O LYS L 731 " (cutoff:3.500A) Processing helix chain 'L' and resid 746 through 761 removed outlier: 3.509A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 798 through 803 removed outlier: 4.032A pdb=" N LYS L 803 " --> pdb=" O GLU L 799 " (cutoff:3.500A) Processing helix chain 'L' and resid 842 through 860 Processing helix chain 'L' and resid 862 through 866 removed outlier: 3.578A pdb=" N LEU L 865 " --> pdb=" O GLY L 862 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU L 866 " --> pdb=" O LYS L 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 862 through 866' Processing helix chain 'L' and resid 870 through 884 Processing helix chain 'L' and resid 906 through 925 removed outlier: 4.572A pdb=" N TYR L 910 " --> pdb=" O GLY L 906 " (cutoff:3.500A) Processing helix chain 'L' and resid 942 through 949 Processing helix chain 'L' and resid 952 through 966 removed outlier: 3.509A pdb=" N ILE L 956 " --> pdb=" O ASN L 952 " (cutoff:3.500A) Processing helix chain 'L' and resid 977 through 991 removed outlier: 4.015A pdb=" N TYR L 981 " --> pdb=" O PRO L 977 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU L 982 " --> pdb=" O GLY L 978 " (cutoff:3.500A) Processing helix chain 'L' and resid 991 through 999 Processing helix chain 'L' and resid 1014 through 1023 Processing helix chain 'L' and resid 1025 through 1038 Processing helix chain 'L' and resid 1059 through 1068 removed outlier: 4.128A pdb=" N ARG L1068 " --> pdb=" O SER L1064 " (cutoff:3.500A) Processing helix chain 'L' and resid 1074 through 1085 removed outlier: 3.528A pdb=" N ALA L1078 " --> pdb=" O SER L1074 " (cutoff:3.500A) Processing helix chain 'L' and resid 1093 through 1097 Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 3.592A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN L1157 " --> pdb=" O ALA L1153 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1165 through 1182 Processing helix chain 'L' and resid 1193 through 1198 Processing helix chain 'L' and resid 1199 through 1208 removed outlier: 3.520A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) Processing helix chain 'L' and resid 1218 through 1236 removed outlier: 4.024A pdb=" N LYS L1222 " --> pdb=" O GLN L1218 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP L1233 " --> pdb=" O THR L1229 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1259 Processing helix chain 'L' and resid 1267 through 1278 removed outlier: 3.699A pdb=" N ASN L1276 " --> pdb=" O PHE L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 removed outlier: 3.502A pdb=" N ASP L1302 " --> pdb=" O HIS L1298 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE L1311 " --> pdb=" O ILE L1307 " (cutoff:3.500A) Processing helix chain 'L' and resid 1338 through 1348 Processing helix chain 'L' and resid 1348 through 1366 Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.674A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1412 through 1429 removed outlier: 3.763A pdb=" N GLU L1418 " --> pdb=" O HIS L1414 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 3.523A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU L1439 " --> pdb=" O HIS L1435 " (cutoff:3.500A) removed outlier: 3.543A 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: 3.845A pdb=" N ILE L1478 " --> pdb=" O ARG L1474 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET L1479 " --> pdb=" O SER L1475 " (cutoff:3.500A) Processing helix chain 'L' and resid 1490 through 1507 removed outlier: 4.030A pdb=" N MET L1496 " --> pdb=" O ARG L1492 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS L1499 " --> pdb=" O SER L1495 " (cutoff:3.500A) Processing helix chain 'L' and resid 1511 through 1517 Processing helix chain 'L' and resid 1522 through 1533 removed outlier: 3.591A pdb=" N ASN L1528 " --> pdb=" O SER L1524 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU L1533 " --> pdb=" O LEU L1529 " (cutoff:3.500A) Processing helix chain 'L' and resid 1578 through 1589 Processing helix chain 'L' and resid 1612 through 1624 Processing helix chain 'L' and resid 1638 through 1649 removed outlier: 3.879A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1668 through 1672 removed outlier: 3.965A 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 1683 through 1697 Processing helix chain 'L' and resid 1700 through 1705 removed outlier: 3.867A pdb=" N VAL L1703 " --> pdb=" O GLY L1700 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) Processing helix chain 'L' and resid 1740 through 1745 Processing helix chain 'L' and resid 1751 through 1758 removed outlier: 3.548A pdb=" N PHE L1755 " --> pdb=" O TYR L1751 " (cutoff:3.500A) Processing helix chain 'L' and resid 1759 through 1763 removed outlier: 3.706A pdb=" N MET L1763 " --> pdb=" O LEU L1760 " (cutoff:3.500A) Processing helix chain 'L' and resid 1779 through 1787 removed outlier: 4.012A pdb=" N ALA L1785 " --> pdb=" O ASP L1781 " (cutoff:3.500A) Processing helix chain 'L' and resid 1796 through 1802 Processing helix chain 'L' and resid 1813 through 1818 Processing sheet with id=AA1, first strand: chain 'L' and resid 258 through 260 removed outlier: 3.597A pdb=" N VAL L1375 " --> pdb=" O SER L1188 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN L1333 " --> pdb=" O MET L1189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 374 through 376 removed outlier: 3.654A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 468 through 469 Processing sheet with id=AA4, first strand: chain 'L' and resid 738 through 739 Processing sheet with id=AA5, first strand: chain 'L' and resid 827 through 829 Processing sheet with id=AA6, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 8.389A pdb=" N GLN L1662 " --> pdb=" O LEU L1548 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU L1548 " --> pdb=" O GLN L1662 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1723 through 1726 602 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4012 1.34 - 1.46: 2641 1.46 - 1.58: 6344 1.58 - 1.70: 62 1.70 - 1.82: 100 Bond restraints: 13159 Sorted by residual: bond pdb=" CA PRO L 410 " pdb=" C PRO L 410 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.10e-02 2.27e+03 8.35e-01 bond pdb=" C ASN L 379 " pdb=" N ASP L 380 " ideal model delta sigma weight residual 1.331 1.314 0.017 2.22e-02 2.03e+03 5.89e-01 bond pdb=" CG LEU L 626 " pdb=" CD1 LEU L 626 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.26e-01 bond pdb=" CA THR L 710 " pdb=" CB THR L 710 " ideal model delta sigma weight residual 1.532 1.546 -0.013 2.01e-02 2.48e+03 4.30e-01 bond pdb=" C GLN L1333 " pdb=" N ILE L1334 " ideal model delta sigma weight residual 1.330 1.322 0.008 1.31e-02 5.83e+03 3.93e-01 ... (remaining 13154 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.82: 468 106.82 - 113.61: 7369 113.61 - 120.40: 4937 120.40 - 127.19: 4964 127.19 - 133.97: 170 Bond angle restraints: 17908 Sorted by residual: angle pdb=" C SER L1329 " pdb=" N SER L1330 " pdb=" CA SER L1330 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.31e+00 angle pdb=" N ASP L 380 " pdb=" CA ASP L 380 " pdb=" C ASP L 380 " ideal model delta sigma weight residual 114.16 110.50 3.66 1.48e+00 4.57e-01 6.11e+00 angle pdb=" C LEU L 541 " pdb=" N SER L 542 " pdb=" CA SER L 542 " ideal model delta sigma weight residual 121.54 125.97 -4.43 1.91e+00 2.74e-01 5.39e+00 angle pdb=" C TYR L 274 " pdb=" N VAL L 275 " pdb=" CA VAL L 275 " ideal model delta sigma weight residual 121.97 118.30 3.67 1.80e+00 3.09e-01 4.16e+00 angle pdb=" C MET L1189 " pdb=" N ASP L1190 " pdb=" CA ASP L1190 " ideal model delta sigma weight residual 121.87 126.42 -4.55 2.24e+00 1.99e-01 4.12e+00 ... (remaining 17903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.67: 7576 19.67 - 39.33: 319 39.33 - 59.00: 87 59.00 - 78.67: 40 78.67 - 98.34: 3 Dihedral angle restraints: 8025 sinusoidal: 3603 harmonic: 4422 Sorted by residual: dihedral pdb=" CA LEU L 541 " pdb=" C LEU L 541 " pdb=" N SER L 542 " pdb=" CA SER L 542 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+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 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA SER L1330 " pdb=" C SER L1330 " pdb=" N ASP L1331 " pdb=" CA ASP L1331 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 8022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1384 0.031 - 0.063: 487 0.063 - 0.094: 122 0.094 - 0.125: 43 0.125 - 0.156: 6 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CA ILE L1376 " pdb=" N ILE L1376 " pdb=" C ILE L1376 " pdb=" CB ILE L1376 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE L1809 " pdb=" N ILE L1809 " pdb=" C ILE L1809 " pdb=" CB ILE L1809 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE L 469 " pdb=" N ILE L 469 " pdb=" C ILE L 469 " pdb=" CB ILE L 469 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2039 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN L 720 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLN L 720 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN L 720 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE L 721 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 503 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ALA L 503 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA L 503 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU L 504 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 541 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C LEU L 541 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU L 541 " 0.014 2.00e-02 2.50e+03 pdb=" N SER L 542 " 0.013 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 72 2.44 - 3.06: 8647 3.06 - 3.67: 19062 3.67 - 4.29: 28996 4.29 - 4.90: 47475 Nonbonded interactions: 104252 Sorted by model distance: nonbonded pdb=" OD1 ASP L1332 " pdb="MN MN L2301 " model vdw 1.827 2.320 nonbonded pdb=" OE2 GLU L1382 " pdb="MN MN L2301 " model vdw 1.973 2.320 nonbonded pdb=" O ILE L 709 " pdb=" OG1 THR L 710 " model vdw 2.191 2.440 nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.195 2.440 nonbonded pdb=" O LEU L1083 " pdb=" OG1 THR L1086 " model vdw 2.203 2.440 ... (remaining 104247 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: 0.780 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: 4.110 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.430 Find NCS groups from input model: 0.310 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13159 Z= 0.162 Angle : 0.456 6.946 17908 Z= 0.242 Chirality : 0.036 0.156 2042 Planarity : 0.003 0.035 2144 Dihedral : 12.885 98.335 5148 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.15 % Favored : 91.78 % Rotamer: Outliers : 2.98 % Allowed : 4.80 % Favored : 92.21 % 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: -2.78 (0.19), residues: 1472 helix: -0.67 (0.17), residues: 793 sheet: -3.23 (0.45), residues: 92 loop : -3.29 (0.21), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1547 HIS 0.003 0.001 HIS L 652 PHE 0.011 0.001 PHE L 971 TYR 0.010 0.001 TYR L 642 ARG 0.003 0.000 ARG L 632 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 483 MET cc_start: 0.8050 (mmt) cc_final: 0.7816 (mmt) REVERT: L 1075 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7502 (m-40) REVERT: L 1085 LEU cc_start: 0.7510 (mm) cc_final: 0.6856 (pp) REVERT: L 1811 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8501 (mp) outliers start: 41 outliers final: 19 residues processed: 177 average time/residue: 0.3254 time to fit residues: 78.0518 Evaluate side-chains 100 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 658 ASP Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 828 VAL Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 1075 ASN Chi-restraints excluded: chain L residue 1230 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1456 ASP Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1811 LEU Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 57.9654 > 50: distance: 46 - 65: 20.566 distance: 60 - 65: 18.744 distance: 65 - 66: 31.916 distance: 66 - 67: 17.600 distance: 66 - 69: 27.469 distance: 67 - 68: 42.061 distance: 67 - 70: 17.506 distance: 70 - 71: 8.566 distance: 71 - 72: 12.093 distance: 71 - 74: 23.996 distance: 72 - 78: 18.309 distance: 74 - 75: 4.604 distance: 75 - 76: 34.030 distance: 75 - 77: 7.030 distance: 78 - 79: 17.271 distance: 80 - 81: 7.054 distance: 80 - 82: 13.251 distance: 82 - 83: 18.447 distance: 83 - 84: 15.731 distance: 83 - 86: 13.287 distance: 84 - 85: 10.170 distance: 84 - 89: 13.475 distance: 86 - 87: 14.461 distance: 86 - 88: 3.472 distance: 89 - 90: 44.788 distance: 90 - 91: 24.102 distance: 90 - 93: 7.214 distance: 91 - 92: 3.135 distance: 91 - 96: 43.533 distance: 93 - 94: 39.912 distance: 94 - 95: 26.848 distance: 96 - 97: 22.426 distance: 97 - 98: 18.917 distance: 97 - 100: 28.885 distance: 98 - 99: 25.064 distance: 98 - 103: 7.634 distance: 99 - 127: 32.793 distance: 100 - 101: 22.159 distance: 100 - 102: 13.034 distance: 103 - 104: 12.042 distance: 104 - 105: 26.823 distance: 105 - 106: 26.146 distance: 105 - 113: 42.129 distance: 107 - 108: 15.413 distance: 108 - 109: 7.172 distance: 108 - 110: 16.605 distance: 109 - 111: 16.388 distance: 110 - 112: 12.465 distance: 111 - 112: 14.830 distance: 113 - 114: 41.743 distance: 114 - 117: 10.518 distance: 115 - 116: 11.666 distance: 115 - 121: 17.469 distance: 116 - 143: 25.524 distance: 117 - 118: 17.850 distance: 118 - 119: 16.603 distance: 118 - 120: 12.954 distance: 121 - 122: 7.900 distance: 122 - 123: 13.374 distance: 122 - 125: 21.051 distance: 123 - 124: 12.208 distance: 123 - 127: 22.754 distance: 124 - 151: 22.924 distance: 125 - 126: 17.796 distance: 127 - 128: 8.477 distance: 128 - 129: 11.187 distance: 128 - 131: 11.589 distance: 129 - 130: 18.809 distance: 129 - 135: 12.800 distance: 130 - 160: 13.069 distance: 131 - 132: 39.885 distance: 132 - 133: 24.634 distance: 132 - 134: 34.016