Starting phenix.real_space_refine on Sun Jul 21 16:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/07_2024/8f5b_28864_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/07_2024/8f5b_28864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/07_2024/8f5b_28864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/07_2024/8f5b_28864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/07_2024/8f5b_28864_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5b_28864/07_2024/8f5b_28864_neut.cif" } resolution = 3.95 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 293 atoms to isotropic. 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 P 6 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 9121 2.51 5 N 2378 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1679": "OD1" <-> "OD2" Residue "A TYR 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1924, 13954 Classifications: {'peptide': 1924} Incomplete info: {'truncation_to_alanine': 350} Link IDs: {'PTRANS': 98, 'TRANS': 1825} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1440 Unresolved non-hydrogen angles: 1823 Unresolved non-hydrogen dihedrals: 1221 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 37, 'TYR:plan': 13, 'ASN:plan1': 21, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 22, 'GLU:plan': 54, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 998 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {' MG': 2, 'ANP': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.81, per 1000 atoms: 0.62 Number of scatterers: 14152 At special positions: 0 Unit cell: (80.7751, 94.4125, 217.149, 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) S 73 16.00 P 6 15.00 Mg 2 11.99 O 2572 8.00 N 2378 7.00 C 9121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.03 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 504 " " NAG A2303 " - " ASN A1662 " " NAG A2306 " - " ASN A 444 " " NAG B 1 " - " ASN A 415 " Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 2.8 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 11 sheets defined 57.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 21 through 45 Proline residue: A 32 - end of helix removed outlier: 4.175A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.974A pdb=" N SER A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 114 Processing helix chain 'A' and resid 116 through 137 removed outlier: 4.278A pdb=" N GLN A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 290 Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 342 through 349 removed outlier: 4.504A pdb=" N LYS A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 384 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 415 through 445 removed outlier: 3.969A pdb=" N LEU A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.831A pdb=" N PHE A 503 " --> pdb=" O TRP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 Processing helix chain 'A' and resid 530 through 544 removed outlier: 3.621A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 607 Processing helix chain 'A' and resid 607 through 623 Processing helix chain 'A' and resid 645 through 649 removed outlier: 3.921A pdb=" N ILE A 649 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 663 Proline residue: A 656 - end of helix removed outlier: 3.780A pdb=" N TRP A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 692 through 723 Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.553A pdb=" N PHE A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.591A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 787 through 795 Processing helix chain 'A' and resid 797 through 815 Processing helix chain 'A' and resid 835 through 861 removed outlier: 4.004A pdb=" N GLN A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 968 through 976 removed outlier: 3.627A pdb=" N LEU A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1004 removed outlier: 3.663A pdb=" N SER A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1030 Processing helix chain 'A' and resid 1034 through 1050 Processing helix chain 'A' and resid 1063 through 1077 Processing helix chain 'A' and resid 1093 through 1107 removed outlier: 3.786A pdb=" N SER A1099 " --> pdb=" O TYR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1143 through 1151 Processing helix chain 'A' and resid 1205 through 1216 Processing helix chain 'A' and resid 1241 through 1253 Processing helix chain 'A' and resid 1268 through 1281 removed outlier: 3.935A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1369 Processing helix chain 'A' and resid 1369 through 1392 removed outlier: 4.438A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 3.758A pdb=" N TYR A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1437 Processing helix chain 'A' and resid 1467 through 1477 Processing helix chain 'A' and resid 1530 through 1547 Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1573 through 1588 Processing helix chain 'A' and resid 1592 through 1600 Processing helix chain 'A' and resid 1601 through 1609 removed outlier: 3.700A pdb=" N HIS A1608 " --> pdb=" O ASP A1604 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1609 " --> pdb=" O PHE A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1639 Processing helix chain 'A' and resid 1668 through 1693 WARNING: missing atoms! Processing helix chain 'A' and resid 1694 through 1696 No H-bonds generated for 'chain 'A' and resid 1694 through 1696' Processing helix chain 'A' and resid 1697 through 1707 removed outlier: 4.076A pdb=" N LEU A1701 " --> pdb=" O PHE A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1715 Processing helix chain 'A' and resid 1719 through 1750 Processing helix chain 'A' and resid 1751 through 1756 Processing helix chain 'A' and resid 1759 through 1779 Proline residue: A1776 - end of helix Processing helix chain 'A' and resid 1780 through 1784 Processing helix chain 'A' and resid 1790 through 1817 Processing helix chain 'A' and resid 1822 through 1828 Processing helix chain 'A' and resid 1836 through 1862 Processing helix chain 'A' and resid 1875 through 1900 Processing helix chain 'A' and resid 1919 through 1931 Processing helix chain 'A' and resid 1977 through 1987 Processing helix chain 'A' and resid 2006 through 2012 Processing helix chain 'A' and resid 2028 through 2041 removed outlier: 3.970A pdb=" N GLY A2041 " --> pdb=" O ALA A2037 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2045 No H-bonds generated for 'chain 'A' and resid 2043 through 2045' Processing helix chain 'A' and resid 2046 through 2059 Processing helix chain 'A' and resid 2072 through 2085 Processing helix chain 'A' and resid 2102 through 2120 removed outlier: 3.826A pdb=" N ARG A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A2107 " --> pdb=" O PRO A2103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2137 removed outlier: 3.678A pdb=" N CYS A2133 " --> pdb=" O SER A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2161 Processing helix chain 'A' and resid 2186 through 2193 Processing helix chain 'A' and resid 2214 through 2226 removed outlier: 4.380A pdb=" N ILE A2218 " --> pdb=" O SER A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2253 Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 399 removed outlier: 5.828A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 550 through 552 removed outlier: 3.745A pdb=" N MET A 573 " --> pdb=" O GLN A1659 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 636 removed outlier: 3.562A pdb=" N VAL A1617 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 930 through 932 Processing sheet with id=AA5, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 3.501A pdb=" N MET A1115 " --> pdb=" O THR A 959 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA A 960 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE A1133 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 962 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1005 through 1006 Processing sheet with id=AA7, first strand: chain 'A' and resid 1155 through 1157 Processing sheet with id=AA8, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AA9, first strand: chain 'A' and resid 1961 through 1962 removed outlier: 3.590A pdb=" N VAL A1962 " --> pdb=" O LEU A1938 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A1938 " --> pdb=" O VAL A1962 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU A1942 " --> pdb=" O ASP A1995 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP A1995 " --> pdb=" O GLU A1942 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A1944 " --> pdb=" O SER A1993 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A1993 " --> pdb=" O THR A1944 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2091 through 2093 removed outlier: 9.042A pdb=" N ALA A2141 " --> pdb=" O CYS A1967 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY A1969 " --> pdb=" O ALA A2141 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N MET A2143 " --> pdb=" O GLY A1969 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A1971 " --> pdb=" O MET A2143 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A2150 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A2144 " --> pdb=" O PHE A2148 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE A2148 " --> pdb=" O VAL A2144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2205 through 2210 removed outlier: 4.084A pdb=" N ILE A2166 " --> pdb=" O THR A2237 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A2237 " --> pdb=" O ILE A2166 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2289 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: 5.46 Time building geometry restraints manager: 6.83 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: 4522 1.34 - 1.46: 3241 1.46 - 1.58: 6588 1.58 - 1.70: 7 1.70 - 1.82: 114 Bond restraints: 14472 Sorted by residual: bond pdb=" O3A ANP A2304 " pdb=" PB ANP A2304 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" O3A ANP A2305 " pdb=" PB ANP A2305 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" N3B ANP A2304 " pdb=" PG ANP A2304 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N3B ANP A2305 " pdb=" PG ANP A2305 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O5' ANP A2304 " pdb=" PA ANP A2304 " ideal model delta sigma weight residual 1.655 1.574 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 14467 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 399 105.89 - 112.93: 8061 112.93 - 119.96: 4680 119.96 - 127.00: 6453 127.00 - 134.04: 208 Bond angle restraints: 19801 Sorted by residual: angle pdb=" PB ANP A2304 " pdb=" N3B ANP A2304 " pdb=" PG ANP A2304 " ideal model delta sigma weight residual 126.95 108.46 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" PB ANP A2305 " pdb=" N3B ANP A2305 " pdb=" PG ANP A2305 " ideal model delta sigma weight residual 126.95 108.85 18.10 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C ASN A 444 " pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " ideal model delta sigma weight residual 110.09 101.94 8.15 1.67e+00 3.59e-01 2.38e+01 angle pdb=" C TYR A 97 " pdb=" CA TYR A 97 " pdb=" CB TYR A 97 " ideal model delta sigma weight residual 111.82 106.62 5.20 1.28e+00 6.10e-01 1.65e+01 angle pdb=" N ASN A 444 " pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " ideal model delta sigma weight residual 110.49 116.24 -5.75 1.48e+00 4.57e-01 1.51e+01 ... (remaining 19796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 8161 24.81 - 49.62: 421 49.62 - 74.44: 70 74.44 - 99.25: 26 99.25 - 124.06: 16 Dihedral angle restraints: 8694 sinusoidal: 3131 harmonic: 5563 Sorted by residual: dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 324 " pdb=" CB CYS A 324 " ideal model delta sinusoidal sigma weight residual -86.00 -8.32 -77.68 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CA ASN A 98 " pdb=" C ASN A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CB CYS A 370 " pdb=" SG CYS A 370 " pdb=" SG CYS A 519 " pdb=" CB CYS A 519 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 8691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2001 0.057 - 0.114: 355 0.114 - 0.170: 26 0.170 - 0.227: 3 0.227 - 0.284: 6 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.87e+00 chirality pdb=" C3' ANP A2304 " pdb=" C2' ANP A2304 " pdb=" C4' ANP A2304 " pdb=" O3' ANP A2304 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2388 not shown) Planarity restraints: 2499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 444 " -0.007 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN A 444 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 444 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 444 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A2306 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 444 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASN A 444 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 444 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 444 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.021 2.00e-02 2.50e+03 1.96e-02 4.81e+00 pdb=" CG ASN A 98 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.015 2.00e-02 2.50e+03 pdb=" C1 NAG A2301 " -0.018 2.00e-02 2.50e+03 ... (remaining 2496 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 178 2.57 - 3.16: 12686 3.16 - 3.74: 23880 3.74 - 4.32: 28498 4.32 - 4.90: 46837 Nonbonded interactions: 112079 Sorted by model distance: nonbonded pdb=" O1G ANP A2305 " pdb="MG MG A2307 " model vdw 1.993 2.170 nonbonded pdb=" OE1 GLN A2019 " pdb="MG MG A2307 " model vdw 2.007 2.170 nonbonded pdb=" N3B ANP A2304 " pdb="MG MG A2308 " model vdw 2.017 2.250 nonbonded pdb=" OG1 THR A 970 " pdb="MG MG A2308 " model vdw 2.025 2.170 nonbonded pdb=" O2A ANP A2304 " pdb="MG MG A2308 " model vdw 2.033 2.170 ... (remaining 112074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 42.520 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.004 0.152 14472 Z= 0.268 Angle : 0.715 18.492 19801 Z= 0.336 Chirality : 0.044 0.284 2391 Planarity : 0.004 0.041 2494 Dihedral : 16.735 124.061 5074 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1904 helix: 1.70 (0.17), residues: 1021 sheet: -0.24 (0.48), residues: 139 loop : -1.98 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 31 HIS 0.006 0.001 HIS A 52 PHE 0.023 0.001 PHE A 655 TYR 0.026 0.001 TYR A1735 ARG 0.002 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.712 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 1018 LEU cc_start: 0.8813 (tp) cc_final: 0.8547 (tp) REVERT: A 1115 MET cc_start: 0.6220 (ppp) cc_final: 0.5970 (ppp) REVERT: A 1679 ASP cc_start: 0.8855 (m-30) cc_final: 0.8591 (m-30) REVERT: A 1733 MET cc_start: 0.8877 (tmm) cc_final: 0.8367 (tmm) REVERT: A 1770 TYR cc_start: 0.9118 (t80) cc_final: 0.8764 (t80) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.2097 time to fit residues: 53.9028 Evaluate side-chains 126 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1670 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 0.0370 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1016 HIS ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN A1799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14472 Z= 0.206 Angle : 0.633 8.742 19801 Z= 0.305 Chirality : 0.042 0.204 2391 Planarity : 0.004 0.040 2494 Dihedral : 11.386 94.690 2288 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.19 % Allowed : 10.72 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1904 helix: 1.64 (0.16), residues: 1038 sheet: -0.67 (0.45), residues: 146 loop : -1.98 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 31 HIS 0.007 0.001 HIS A1023 PHE 0.021 0.001 PHE A1026 TYR 0.027 0.001 TYR A2016 ARG 0.003 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.673 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 659 MET cc_start: 0.8627 (mtt) cc_final: 0.8240 (mtm) REVERT: A 746 MET cc_start: 0.8627 (tpp) cc_final: 0.7976 (tpp) REVERT: A 1026 PHE cc_start: 0.7927 (m-80) cc_final: 0.7646 (m-80) REVERT: A 1115 MET cc_start: 0.6163 (ppp) cc_final: 0.5863 (ppp) REVERT: A 1690 MET cc_start: 0.8039 (mmt) cc_final: 0.7709 (mmt) REVERT: A 1731 ASP cc_start: 0.8596 (p0) cc_final: 0.8275 (p0) REVERT: A 1733 MET cc_start: 0.8907 (tmm) cc_final: 0.8339 (tmm) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 0.1942 time to fit residues: 47.7072 Evaluate side-chains 137 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 GLN A1727 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14472 Z= 0.256 Angle : 0.647 8.735 19801 Z= 0.315 Chirality : 0.042 0.196 2391 Planarity : 0.004 0.038 2494 Dihedral : 8.971 72.000 2288 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.86 % Allowed : 17.20 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1904 helix: 1.59 (0.16), residues: 1037 sheet: -0.79 (0.45), residues: 140 loop : -2.00 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 31 HIS 0.006 0.001 HIS A1711 PHE 0.015 0.001 PHE A 734 TYR 0.020 0.002 TYR A2036 ARG 0.003 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.555 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 659 MET cc_start: 0.8687 (mtt) cc_final: 0.8467 (mtm) REVERT: A 1115 MET cc_start: 0.6362 (ppp) cc_final: 0.6028 (ppp) REVERT: A 1690 MET cc_start: 0.8013 (mmt) cc_final: 0.7313 (mmt) REVERT: A 1733 MET cc_start: 0.8962 (tmm) cc_final: 0.8407 (tmm) REVERT: A 1770 TYR cc_start: 0.9226 (t80) cc_final: 0.8603 (t80) REVERT: A 2130 MET cc_start: 0.6823 (ptm) cc_final: 0.6623 (ptp) REVERT: A 2169 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8075 (mpp) outliers start: 25 outliers final: 17 residues processed: 145 average time/residue: 0.2018 time to fit residues: 48.8781 Evaluate side-chains 143 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14472 Z= 0.206 Angle : 0.633 9.790 19801 Z= 0.302 Chirality : 0.042 0.321 2391 Planarity : 0.004 0.038 2494 Dihedral : 7.875 74.645 2288 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.23 % Allowed : 19.21 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1904 helix: 1.64 (0.16), residues: 1039 sheet: -0.96 (0.45), residues: 142 loop : -1.98 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.005 0.001 HIS A1023 PHE 0.014 0.001 PHE A 734 TYR 0.019 0.001 TYR A1735 ARG 0.002 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.760 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.9048 (tpp) cc_final: 0.8793 (tpp) REVERT: A 746 MET cc_start: 0.8704 (tpp) cc_final: 0.8326 (tpp) REVERT: A 1026 PHE cc_start: 0.8195 (m-80) cc_final: 0.7983 (m-80) REVERT: A 1115 MET cc_start: 0.6349 (ppp) cc_final: 0.5976 (ppp) REVERT: A 1690 MET cc_start: 0.7986 (mmt) cc_final: 0.7613 (mmt) REVERT: A 1700 TYR cc_start: 0.8029 (t80) cc_final: 0.7550 (t80) REVERT: A 1733 MET cc_start: 0.9011 (tmm) cc_final: 0.8449 (tmm) REVERT: A 2143 MET cc_start: 0.9046 (ptm) cc_final: 0.8842 (ptm) REVERT: A 2169 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8131 (mpp) outliers start: 30 outliers final: 19 residues processed: 152 average time/residue: 0.1929 time to fit residues: 49.0188 Evaluate side-chains 149 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14472 Z= 0.176 Angle : 0.632 11.208 19801 Z= 0.298 Chirality : 0.042 0.285 2391 Planarity : 0.004 0.037 2494 Dihedral : 7.431 76.962 2288 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.86 % Allowed : 20.85 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1904 helix: 1.70 (0.16), residues: 1040 sheet: -1.16 (0.43), residues: 152 loop : -1.92 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.006 0.001 HIS A1016 PHE 0.013 0.001 PHE A 734 TYR 0.015 0.001 TYR A1779 ARG 0.001 0.000 ARG A2139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.637 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8767 (tpp) cc_final: 0.8355 (tpp) REVERT: A 1026 PHE cc_start: 0.8001 (m-80) cc_final: 0.7765 (m-80) REVERT: A 1115 MET cc_start: 0.6333 (ppp) cc_final: 0.5939 (ppp) REVERT: A 1690 MET cc_start: 0.8037 (mmt) cc_final: 0.7596 (mmt) REVERT: A 1700 TYR cc_start: 0.8057 (t80) cc_final: 0.7568 (t80) REVERT: A 1733 MET cc_start: 0.9004 (tmm) cc_final: 0.8484 (tmm) REVERT: A 2143 MET cc_start: 0.9047 (ptm) cc_final: 0.8845 (ptm) REVERT: A 2169 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8145 (mpp) outliers start: 25 outliers final: 21 residues processed: 150 average time/residue: 0.1997 time to fit residues: 50.4406 Evaluate side-chains 151 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.3946 > 50: distance: 9 - 24: 23.374 distance: 17 - 36: 22.530 distance: 20 - 24: 22.327 distance: 21 - 47: 11.936 distance: 24 - 25: 17.122 distance: 25 - 26: 8.423 distance: 25 - 28: 20.258 distance: 26 - 27: 17.398 distance: 26 - 31: 15.413 distance: 27 - 52: 27.973 distance: 28 - 29: 16.575 distance: 28 - 30: 16.308 distance: 32 - 33: 12.038 distance: 32 - 35: 18.772 distance: 33 - 34: 11.620 distance: 33 - 36: 12.973 distance: 34 - 57: 14.047 distance: 36 - 37: 20.023 distance: 37 - 38: 11.807 distance: 37 - 40: 14.004 distance: 38 - 39: 4.465 distance: 38 - 47: 16.271 distance: 39 - 62: 21.757 distance: 40 - 41: 6.431 distance: 41 - 42: 11.628 distance: 42 - 43: 8.868 distance: 44 - 46: 4.166 distance: 47 - 48: 17.011 distance: 48 - 49: 11.015 distance: 48 - 51: 27.919 distance: 49 - 50: 15.103 distance: 49 - 52: 14.457 distance: 50 - 70: 33.647 distance: 52 - 53: 5.011 distance: 53 - 54: 27.411 distance: 53 - 56: 23.592 distance: 54 - 55: 19.422 distance: 54 - 57: 14.394 distance: 55 - 78: 11.786 distance: 57 - 58: 7.222 distance: 58 - 59: 24.837 distance: 58 - 61: 24.999 distance: 59 - 60: 13.873 distance: 59 - 62: 8.586 distance: 62 - 63: 16.822 distance: 63 - 64: 19.801 distance: 63 - 66: 19.858 distance: 64 - 65: 9.472 distance: 64 - 70: 26.836 distance: 66 - 67: 14.824 distance: 67 - 68: 18.934 distance: 67 - 69: 23.385 distance: 70 - 71: 16.319 distance: 71 - 72: 28.225 distance: 71 - 74: 20.632 distance: 72 - 73: 22.323 distance: 72 - 78: 12.816 distance: 74 - 75: 28.881 distance: 75 - 76: 12.427 distance: 75 - 77: 14.827 distance: 78 - 79: 15.447 distance: 79 - 80: 26.560 distance: 79 - 82: 24.944 distance: 80 - 81: 15.613 distance: 80 - 83: 17.985 distance: 83 - 84: 10.905 distance: 84 - 85: 13.406 distance: 84 - 87: 7.737 distance: 85 - 86: 16.948 distance: 85 - 88: 14.425