Starting phenix.real_space_refine (version: dev) on Sat May 14 05:28:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/05_2022/7ojn_12956_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.024 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 16991 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 16142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2010, 16142 Classifications: {'peptide': 2010} Link IDs: {'PTRANS': 67, 'TRANS': 1942} Chain breaks: 7 Chain: "D" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'RNA': 11, 'DNA': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7, 'rna2p': 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 6, 'rna3p_pur': 4, 'rna2p_pyr': 1} Link IDs: {'rna3p': 9, 'rna2p': 1} Chain: "M" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'rna3p_pyr': 4, 'rna3p_pur': 5} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna3p_pyr': 1, 'rna3p_pur': 3, 'rna2p_pyr': 3} Link IDs: {'rna3p': 3, 'rna2p': 3} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Unusual residues: {' MN': 5, ' ZN': 1, '2KH': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2545 SG CYS L 321 17.609 80.693 96.895 1.00 62.90 S ATOM 2930 SG CYS L 366 16.328 77.352 98.420 1.00 65.25 S Time building chain proxies: 9.94, per 1000 atoms: 0.59 Number of scatterers: 16991 At special positions: 0 Unit cell: (110.5, 114.75, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 5 24.99 S 96 16.00 P 41 15.00 O 3304 8.00 N 2875 7.00 C 10669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.00 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN L2307 " pdb="ZN ZN L2307 " - pdb=" NE2 HIS L 316 " pdb="ZN ZN L2307 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2307 " - pdb=" SG CYS L 366 " pdb="ZN ZN L2307 " - pdb=" SG CYS L 321 " Number of angles added : 2 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 16 sheets defined 47.8% alpha, 8.9% beta 8 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 8.10 Creating SS restraints... Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 20 through 29 removed outlier: 4.706A pdb=" N ARG L 24 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN L 25 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 58 Processing helix chain 'L' and resid 69 through 75 Processing helix chain 'L' and resid 113 through 133 removed outlier: 3.819A pdb=" N LEU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL L 133 " --> pdb=" O ASP L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 171 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.903A pdb=" N GLU L 188 " --> pdb=" O SER L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 212 through 222 Processing helix chain 'L' and resid 231 through 251 Processing helix chain 'L' and resid 263 through 271 Processing helix chain 'L' and resid 285 through 294 removed outlier: 3.564A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG L 294 " --> pdb=" O TYR L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 Processing helix chain 'L' and resid 322 through 336 removed outlier: 3.755A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 364 Processing helix chain 'L' and resid 385 through 403 Processing helix chain 'L' and resid 413 through 433 Processing helix chain 'L' and resid 446 through 448 No H-bonds generated for 'chain 'L' and resid 446 through 448' Processing helix chain 'L' and resid 453 through 458 Processing helix chain 'L' and resid 476 through 478 No H-bonds generated for 'chain 'L' and resid 476 through 478' Processing helix chain 'L' and resid 492 through 509 removed outlier: 3.947A pdb=" N MET L 508 " --> pdb=" O LEU L 504 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS L 509 " --> pdb=" O VAL L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 522 through 526 Processing helix chain 'L' and resid 577 through 579 No H-bonds generated for 'chain 'L' and resid 577 through 579' Processing helix chain 'L' and resid 588 through 601 removed outlier: 4.028A pdb=" N VAL L 601 " --> pdb=" O MET L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 627 Processing helix chain 'L' and resid 633 through 647 removed outlier: 4.520A pdb=" N LEU L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN L 638 " --> pdb=" O GLN L 634 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 660 Processing helix chain 'L' and resid 667 through 683 Processing helix chain 'L' and resid 692 through 708 removed outlier: 3.648A pdb=" N MET L 705 " --> pdb=" O ASN L 701 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N CYS L 706 " --> pdb=" O ILE L 702 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS L 707 " --> pdb=" O SER L 703 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE L 708 " --> pdb=" O TYR L 704 " (cutoff:3.500A) Processing helix chain 'L' and resid 716 through 734 Proline residue: L 730 - end of helix Processing helix chain 'L' and resid 747 through 761 removed outlier: 3.673A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 781 through 793 Processing helix chain 'L' and resid 799 through 801 No H-bonds generated for 'chain 'L' and resid 799 through 801' Processing helix chain 'L' and resid 818 through 821 removed outlier: 3.597A pdb=" N LEU L 821 " --> pdb=" O ALA L 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 818 through 821' Processing helix chain 'L' and resid 843 through 861 removed outlier: 3.535A pdb=" N LYS L 861 " --> pdb=" O VAL L 857 " (cutoff:3.500A) Processing helix chain 'L' and resid 871 through 881 removed outlier: 3.780A pdb=" N ASN L 881 " --> pdb=" O GLN L 877 " (cutoff:3.500A) Processing helix chain 'L' and resid 911 through 924 removed outlier: 3.503A pdb=" N ASP L 923 " --> pdb=" O GLU L 919 " (cutoff:3.500A) Processing helix chain 'L' and resid 1061 through 1065 Processing helix chain 'L' and resid 1075 through 1085 removed outlier: 3.756A pdb=" N LEU L1085 " --> pdb=" O LYS L1081 " (cutoff:3.500A) Processing helix chain 'L' and resid 1093 through 1097 Processing helix chain 'L' and resid 1138 through 1157 removed outlier: 4.164A pdb=" N GLN L1157 " --> pdb=" O ALA L1153 " (cutoff:3.500A) Processing helix chain 'L' and resid 1166 through 1181 Processing helix chain 'L' and resid 1194 through 1197 No H-bonds generated for 'chain 'L' and resid 1194 through 1197' Processing helix chain 'L' and resid 1200 through 1209 removed outlier: 3.642A pdb=" N ASN L1209 " --> pdb=" O ALA L1205 " (cutoff:3.500A) Processing helix chain 'L' and resid 1219 through 1235 Processing helix chain 'L' and resid 1243 through 1257 Processing helix chain 'L' and resid 1268 through 1279 removed outlier: 3.870A pdb=" N ILE L1279 " --> pdb=" O SER L1275 " (cutoff:3.500A) Processing helix chain 'L' and resid 1298 through 1319 Processing helix chain 'L' and resid 1339 through 1347 Processing helix chain 'L' and resid 1349 through 1365 Processing helix chain 'L' and resid 1397 through 1405 Processing helix chain 'L' and resid 1413 through 1430 Processing helix chain 'L' and resid 1434 through 1450 removed outlier: 3.713A pdb=" N LEU L1439 " --> pdb=" O HIS L1435 " (cutoff:3.500A) Processing helix chain 'L' and resid 1466 through 1470 Processing helix chain 'L' and resid 1474 through 1485 Processing helix chain 'L' and resid 1490 through 1505 Processing helix chain 'L' and resid 1523 through 1532 Processing helix chain 'L' and resid 1540 through 1544 removed outlier: 3.604A pdb=" N GLU L1544 " --> pdb=" O GLU L1540 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1540 through 1544' Processing helix chain 'L' and resid 1579 through 1588 Processing helix chain 'L' and resid 1593 through 1612 removed outlier: 3.891A pdb=" N SER L1612 " --> pdb=" O ALA L1608 " (cutoff:3.500A) Processing helix chain 'L' and resid 1616 through 1623 Processing helix chain 'L' and resid 1639 through 1648 Processing helix chain 'L' and resid 1668 through 1670 No H-bonds generated for 'chain 'L' and resid 1668 through 1670' Processing helix chain 'L' and resid 1675 through 1680 removed outlier: 3.850A pdb=" N SER L1679 " --> pdb=" O GLU L1675 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR L1680 " --> pdb=" O GLY L1676 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1675 through 1680' Processing helix chain 'L' and resid 1684 through 1698 Processing helix chain 'L' and resid 1701 through 1704 Processing helix chain 'L' and resid 1734 through 1736 No H-bonds generated for 'chain 'L' and resid 1734 through 1736' Processing helix chain 'L' and resid 1740 through 1750 Processing helix chain 'L' and resid 1752 through 1758 Processing helix chain 'L' and resid 1760 through 1762 No H-bonds generated for 'chain 'L' and resid 1760 through 1762' Processing helix chain 'L' and resid 1767 through 1769 No H-bonds generated for 'chain 'L' and resid 1767 through 1769' Processing helix chain 'L' and resid 1778 through 1789 Processing helix chain 'L' and resid 1812 through 1817 removed outlier: 3.544A pdb=" N LEU L1817 " --> pdb=" O SER L1813 " (cutoff:3.500A) Processing helix chain 'L' and resid 1834 through 1851 removed outlier: 4.010A pdb=" N TYR L1850 " --> pdb=" O TYR L1846 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL L1851 " --> pdb=" O PHE L1847 " (cutoff:3.500A) Processing helix chain 'L' and resid 1858 through 1863 removed outlier: 3.683A pdb=" N GLY L1862 " --> pdb=" O THR L1858 " (cutoff:3.500A) Processing helix chain 'L' and resid 1883 through 1889 removed outlier: 4.021A pdb=" N SER L1887 " --> pdb=" O PRO L1884 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL L1889 " --> pdb=" O SER L1886 " (cutoff:3.500A) Processing helix chain 'L' and resid 1893 through 1895 No H-bonds generated for 'chain 'L' and resid 1893 through 1895' Processing helix chain 'L' and resid 1903 through 1906 Processing helix chain 'L' and resid 1924 through 1928 Processing helix chain 'L' and resid 1940 through 1948 Processing helix chain 'L' and resid 2007 through 2019 removed outlier: 5.224A pdb=" N SER L2011 " --> pdb=" O CYS L2008 " (cutoff:3.500A) Processing helix chain 'L' and resid 2036 through 2039 Processing helix chain 'L' and resid 2058 through 2061 Processing helix chain 'L' and resid 2103 through 2116 removed outlier: 3.744A pdb=" N ASP L2115 " --> pdb=" O LYS L2111 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER L2116 " --> pdb=" O GLU L2112 " (cutoff:3.500A) Processing helix chain 'L' and resid 2118 through 2134 Processing helix chain 'L' and resid 2144 through 2151 Processing helix chain 'L' and resid 2156 through 2167 Processing sheet with id= A, first strand: chain 'L' and resid 90 through 94 removed outlier: 6.109A pdb=" N ASN L 136 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU L 100 " --> pdb=" O ASN L 136 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE L 138 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLU L 102 " --> pdb=" O ILE L 138 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU L 140 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE L 104 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP L 142 " --> pdb=" O PHE L 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 258 through 260 Processing sheet with id= C, first strand: chain 'L' and resid 374 through 376 removed outlier: 3.670A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'L' and resid 826 through 830 Processing sheet with id= F, first strand: chain 'L' and resid 1238 through 1240 Processing sheet with id= G, first strand: chain 'L' and resid 1375 through 1377 Processing sheet with id= H, first strand: chain 'L' and resid 1380 through 1382 Processing sheet with id= I, first strand: chain 'L' and resid 1546 through 1548 Processing sheet with id= J, first strand: chain 'L' and resid 1653 through 1656 Processing sheet with id= K, first strand: chain 'L' and resid 1706 through 1709 removed outlier: 3.801A pdb=" N GLU L1706 " --> pdb=" O THR L1822 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR L1822 " --> pdb=" O GLU L1706 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 1723 through 1727 Processing sheet with id= M, first strand: chain 'L' and resid 1911 through 1917 removed outlier: 6.677A pdb=" N SER L1985 " --> pdb=" O VAL L1994 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL L1994 " --> pdb=" O SER L1985 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 2030 through 2032 Processing sheet with id= O, first strand: chain 'L' and resid 2178 through 2181 removed outlier: 3.740A pdb=" N LYS L2186 " --> pdb=" O SER L2181 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 2086 through 2089 removed outlier: 3.737A pdb=" N ALA L2095 " --> pdb=" O LEU L2087 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU L2089 " --> pdb=" O LYS L2093 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LYS L2093 " --> pdb=" O GLU L2089 " (cutoff:3.500A) 689 hydrogen bonds defined for protein. 1962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 8.19 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2724 1.31 - 1.43: 4724 1.43 - 1.56: 9726 1.56 - 1.68: 77 1.68 - 1.81: 148 Bond restraints: 17399 Sorted by residual: bond pdb=" C1' 2KH L2301 " pdb=" O4' 2KH L2301 " ideal model delta sigma weight residual 1.606 1.322 0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C1' 2KH L2301 " pdb=" C2' 2KH L2301 " ideal model delta sigma weight residual 1.350 1.605 -0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C4' 2KH L2301 " pdb=" O4' 2KH L2301 " ideal model delta sigma weight residual 1.312 1.530 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C2' 2KH L2301 " pdb=" C3' 2KH L2301 " ideal model delta sigma weight residual 1.520 1.307 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C3' 2KH L2301 " pdb=" O3' 2KH L2301 " ideal model delta sigma weight residual 1.353 1.513 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 17394 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.21: 671 107.21 - 113.91: 10000 113.91 - 120.60: 6919 120.60 - 127.29: 5873 127.29 - 133.99: 218 Bond angle restraints: 23681 Sorted by residual: angle pdb=" N GLU L2065 " pdb=" CA GLU L2065 " pdb=" CB GLU L2065 " ideal model delta sigma weight residual 113.65 109.26 4.39 1.47e+00 4.63e-01 8.93e+00 angle pdb=" C LYS L1263 " pdb=" N THR L1264 " pdb=" CA THR L1264 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.40e+00 angle pdb=" CA LEU L 339 " pdb=" CB LEU L 339 " pdb=" CG LEU L 339 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.80e+00 angle pdb=" C GLU L 180 " pdb=" N SER L 181 " pdb=" CA SER L 181 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.69e+00 angle pdb=" N PHE L 581 " pdb=" CA PHE L 581 " pdb=" C PHE L 581 " ideal model delta sigma weight residual 109.81 114.80 -4.99 2.21e+00 2.05e-01 5.11e+00 ... (remaining 23676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 10012 16.94 - 33.89: 369 33.89 - 50.83: 64 50.83 - 67.77: 13 67.77 - 84.72: 4 Dihedral angle restraints: 10462 sinusoidal: 4546 harmonic: 5916 Sorted by residual: dihedral pdb=" CA THR L2064 " pdb=" C THR L2064 " pdb=" N GLU L2065 " pdb=" CA GLU L2065 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA MET L1189 " pdb=" C MET L1189 " pdb=" N ASP L1190 " pdb=" CA ASP L1190 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CB GLU L 662 " pdb=" CG GLU L 662 " pdb=" CD GLU L 662 " pdb=" OE1 GLU L 662 " ideal model delta sinusoidal sigma weight residual 0.00 -84.72 84.72 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 10459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1860 0.031 - 0.062: 610 0.062 - 0.092: 135 0.092 - 0.123: 97 0.123 - 0.154: 5 Chirality restraints: 2707 Sorted by residual: chirality pdb=" C4' 2KH L2301 " pdb=" C3' 2KH L2301 " pdb=" C5' 2KH L2301 " pdb=" O4' 2KH L2301 " both_signs ideal model delta sigma weight residual False -2.52 -2.67 0.15 2.00e-01 2.50e+01 5.91e-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 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 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 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2704 not shown) Planarity restraints: 2857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE L 152 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO L 153 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO L 153 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 153 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G E 12 " -0.021 2.00e-02 2.50e+03 9.43e-03 2.67e+00 pdb=" N9 G E 12 " 0.024 2.00e-02 2.50e+03 pdb=" C8 G E 12 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G E 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G E 12 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G E 12 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G E 12 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G E 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G E 12 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G E 12 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G E 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G E 12 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU L1950 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO L1951 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO L1951 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L1951 " -0.022 5.00e-02 4.00e+02 ... (remaining 2854 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 53 2.47 - 3.08: 11368 3.08 - 3.68: 24312 3.68 - 4.29: 36672 4.29 - 4.90: 62232 Nonbonded interactions: 134637 Sorted by model distance: nonbonded pdb=" O2B 2KH L2301 " pdb="MN MN L2302 " model vdw 1.859 2.320 nonbonded pdb=" OD2 ASP L1190 " pdb="MN MN L2302 " model vdw 2.009 2.320 nonbonded pdb=" O2G 2KH L2301 " pdb="MN MN L2302 " model vdw 2.019 2.320 nonbonded pdb=" OD1 ASP L1332 " pdb="MN MN L2303 " model vdw 2.116 2.320 nonbonded pdb=" OD1 ASP L1190 " pdb="MN MN L2303 " model vdw 2.148 2.320 ... (remaining 134632 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 5 7.51 5 Zn 1 6.06 5 P 41 5.49 5 S 96 5.16 5 C 10669 2.51 5 N 2875 2.21 5 O 3304 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.560 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: 0.020 Extract box with map and model: 8.090 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.130 Process input model: 55.030 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 0.284 17399 Z= 0.258 Angle : 0.405 9.778 23681 Z= 0.221 Chirality : 0.036 0.154 2707 Planarity : 0.003 0.041 2857 Dihedral : 9.253 84.716 6618 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer Outliers : 0.93 % 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: 0.93 (0.19), residues: 1994 helix: 2.10 (0.17), residues: 971 sheet: 0.90 (0.40), residues: 166 loop : -1.27 (0.20), residues: 857 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 223 average time/residue: 1.5400 time to fit residues: 379.0841 Evaluate side-chains 112 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.7750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 340 ASN ** L 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1208 GLN L1234 HIS L1298 HIS L1597 GLN L1789 ASN ** L1807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 17399 Z= 0.273 Angle : 0.515 7.888 23681 Z= 0.273 Chirality : 0.040 0.167 2707 Planarity : 0.004 0.040 2857 Dihedral : 6.882 68.453 2623 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer Outliers : 2.08 % 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: 0.62 (0.19), residues: 1994 helix: 1.79 (0.17), residues: 991 sheet: 0.69 (0.40), residues: 162 loop : -1.40 (0.20), residues: 841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 12 residues processed: 140 average time/residue: 1.2888 time to fit residues: 203.9279 Evaluate side-chains 104 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.6623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 913 GLN L1234 HIS L1441 GLN L1554 HIS L1789 ASN ** L1807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 17399 Z= 0.307 Angle : 0.534 7.605 23681 Z= 0.282 Chirality : 0.041 0.185 2707 Planarity : 0.004 0.039 2857 Dihedral : 7.120 73.672 2623 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 2.35 % 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: 0.41 (0.19), residues: 1994 helix: 1.61 (0.17), residues: 990 sheet: 0.56 (0.38), residues: 172 loop : -1.50 (0.20), residues: 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 91 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 130 average time/residue: 1.2644 time to fit residues: 186.4549 Evaluate side-chains 104 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 2.6399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 17399 Z= 0.180 Angle : 0.464 7.996 23681 Z= 0.246 Chirality : 0.038 0.160 2707 Planarity : 0.003 0.039 2857 Dihedral : 6.962 72.756 2623 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.97 % 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: 0.62 (0.19), residues: 1994 helix: 1.83 (0.17), residues: 985 sheet: 0.60 (0.38), residues: 172 loop : -1.45 (0.20), residues: 837 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 124 average time/residue: 1.2516 time to fit residues: 177.7018 Evaluate side-chains 108 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 2.259 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 2.7468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 167 optimal weight: 0.1980 chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 17399 Z= 0.265 Angle : 0.505 8.085 23681 Z= 0.266 Chirality : 0.039 0.160 2707 Planarity : 0.004 0.044 2857 Dihedral : 7.066 75.948 2623 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 2.51 % 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: 0.48 (0.19), residues: 1994 helix: 1.69 (0.17), residues: 991 sheet: 0.56 (0.38), residues: 172 loop : -1.50 (0.20), residues: 831 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 86 time to evaluate : 2.013 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 125 average time/residue: 1.1806 time to fit residues: 168.7792 Evaluate side-chains 106 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 1.2254 time to fit residues: 4.0550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 103 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 17399 Z= 0.136 Angle : 0.445 7.741 23681 Z= 0.235 Chirality : 0.037 0.158 2707 Planarity : 0.003 0.044 2857 Dihedral : 6.920 74.644 2623 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 1.86 % 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: 0.69 (0.19), residues: 1994 helix: 1.88 (0.17), residues: 989 sheet: 0.69 (0.38), residues: 172 loop : -1.43 (0.20), residues: 833 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 86 time to evaluate : 2.077 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 119 average time/residue: 1.2879 time to fit residues: 176.6932 Evaluate side-chains 106 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 2.6860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 8.9990 chunk 22 optimal weight: 0.0470 chunk 111 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 overall best weight: 2.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17399 Z= 0.292 Angle : 0.520 10.686 23681 Z= 0.271 Chirality : 0.040 0.158 2707 Planarity : 0.004 0.055 2857 Dihedral : 7.061 77.653 2623 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1994 helix: 1.74 (0.17), residues: 987 sheet: 0.65 (0.38), residues: 172 loop : -1.48 (0.20), residues: 835 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 86 time to evaluate : 2.106 Fit side-chains outliers start: 41 outliers final: 27 residues processed: 122 average time/residue: 1.2409 time to fit residues: 173.1141 Evaluate side-chains 108 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 1 average time/residue: 1.1712 time to fit residues: 4.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17399 Z= 0.191 Angle : 0.485 7.943 23681 Z= 0.254 Chirality : 0.038 0.160 2707 Planarity : 0.003 0.056 2857 Dihedral : 7.017 77.566 2623 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.97 % 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: 0.58 (0.19), residues: 1994 helix: 1.80 (0.17), residues: 987 sheet: 0.66 (0.38), residues: 172 loop : -1.48 (0.20), residues: 835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 2.156 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 120 average time/residue: 1.2366 time to fit residues: 168.8734 Evaluate side-chains 110 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 1 average time/residue: 1.1455 time to fit residues: 3.9460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 164 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 17399 Z= 0.242 Angle : 0.508 8.809 23681 Z= 0.266 Chirality : 0.039 0.160 2707 Planarity : 0.004 0.061 2857 Dihedral : 7.051 78.775 2623 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 1.75 % 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: 0.51 (0.19), residues: 1994 helix: 1.73 (0.17), residues: 990 sheet: 0.63 (0.38), residues: 172 loop : -1.52 (0.20), residues: 832 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.998 Fit side-chains outliers start: 32 outliers final: 29 residues processed: 115 average time/residue: 1.2626 time to fit residues: 165.9442 Evaluate side-chains 110 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 1 average time/residue: 1.2916 time to fit residues: 4.0697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 17399 Z= 0.272 Angle : 0.531 9.983 23681 Z= 0.277 Chirality : 0.040 0.164 2707 Planarity : 0.004 0.060 2857 Dihedral : 7.132 80.708 2623 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.80 % 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: 0.45 (0.19), residues: 1994 helix: 1.67 (0.17), residues: 988 sheet: 0.58 (0.38), residues: 172 loop : -1.53 (0.20), residues: 834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 83 time to evaluate : 2.228 Fit side-chains outliers start: 33 outliers final: 28 residues processed: 114 average time/residue: 1.2347 time to fit residues: 161.1740 Evaluate side-chains 109 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.6830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.075810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.057171 restraints weight = 44449.351| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.38 r_work: 0.2913 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work: 0.2889 rms_B_bonded: 2.18 restraints_weight: 0.1250 r_work: 0.2877 rms_B_bonded: 2.25 restraints_weight: 0.0625 r_work: 0.2864 rms_B_bonded: 2.36 restraints_weight: 0.0312 r_work: 0.2850 rms_B_bonded: 2.50 restraints_weight: 0.0156 r_work: 0.2836 rms_B_bonded: 2.67 restraints_weight: 0.0078 r_work: 0.2821 rms_B_bonded: 2.87 restraints_weight: 0.0039 r_work: 0.2805 rms_B_bonded: 3.11 restraints_weight: 0.0020 r_work: 0.2788 rms_B_bonded: 3.38 restraints_weight: 0.0010 r_work: 0.2770 rms_B_bonded: 3.70 restraints_weight: 0.0005 r_work: 0.2751 rms_B_bonded: 4.06 restraints_weight: 0.0002 r_work: 0.2730 rms_B_bonded: 4.46 restraints_weight: 0.0001 r_work: 0.2708 rms_B_bonded: 4.93 restraints_weight: 0.0001 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17399 Z= 0.232 Angle : 0.505 8.551 23681 Z= 0.265 Chirality : 0.039 0.166 2707 Planarity : 0.003 0.040 2857 Dihedral : 7.106 81.016 2623 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 1.80 % 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: 0.49 (0.19), residues: 1994 helix: 1.70 (0.17), residues: 988 sheet: 0.61 (0.38), residues: 172 loop : -1.50 (0.20), residues: 834 =============================================================================== Job complete usr+sys time: 4044.33 seconds wall clock time: 73 minutes 48.45 seconds (4428.45 seconds total)