Starting phenix.real_space_refine on Sun Mar 17 07:04:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_12956_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_12956.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_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_12956/03_2024/7ojn_12956_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_12956_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_12956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_12956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_12956_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojn_12956/03_2024/7ojn_12956_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 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. 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-5265/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: {'DNA': 1, 'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 7} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 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: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "M" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} 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: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 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: 8.50, per 1000 atoms: 0.50 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: 6.09 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal 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: 9.76 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: 8.11 Time building geometry restraints manager: 6.64 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 1.561 1.322 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C4' 2KH L2301 " pdb=" O4' 2KH L2301 " ideal model delta sigma weight residual 1.310 1.530 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C1' 2KH L2301 " pdb=" N1 2KH L2301 " ideal model delta sigma weight residual 1.322 1.436 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C3' 2KH L2301 " pdb=" C4' 2KH L2301 " ideal model delta sigma weight residual 1.643 1.535 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C4' 2KH L2301 " pdb=" C5' 2KH L2301 " ideal model delta sigma weight residual 1.526 1.427 0.099 2.00e-02 2.50e+03 2.44e+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: 10078 16.94 - 33.89: 382 33.89 - 50.83: 89 50.83 - 67.77: 63 67.77 - 84.72: 16 Dihedral angle restraints: 10628 sinusoidal: 4712 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 10625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1896 0.032 - 0.064: 595 0.064 - 0.096: 126 0.096 - 0.128: 85 0.128 - 0.160: 5 Chirality restraints: 2707 Sorted by residual: chirality pdb=" C1' 2KH L2301 " pdb=" C2' 2KH L2301 " pdb=" N1 2KH L2301 " pdb=" O4' 2KH L2301 " both_signs ideal model delta sigma weight residual False 2.54 2.38 0.16 2.00e-01 2.50e+01 6.43e-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 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.520 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 52.710 Find NCS groups from input model: 0.450 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.239 17399 Z= 0.217 Angle : 0.406 9.778 23681 Z= 0.221 Chirality : 0.036 0.160 2707 Planarity : 0.003 0.041 2857 Dihedral : 11.330 84.716 6784 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 0.93 % Allowed : 3.00 % Favored : 96.07 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1547 HIS 0.002 0.000 HIS L1191 PHE 0.011 0.001 PHE L1272 TYR 0.010 0.001 TYR L 183 ARG 0.002 0.000 ARG L 632 *********************** 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 : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2152 MET cc_start: 0.6273 (mtm) cc_final: 0.6048 (mtm) outliers start: 17 outliers final: 8 residues processed: 223 average time/residue: 1.5850 time to fit residues: 386.5116 Evaluate side-chains 112 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 1137 ASP Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1650 GLN Chi-restraints excluded: chain L residue 1832 VAL 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: 0.8315 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17399 Z= 0.274 Angle : 0.531 8.871 23681 Z= 0.279 Chirality : 0.040 0.175 2707 Planarity : 0.004 0.039 2857 Dihedral : 12.358 73.951 2804 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 2.29 % Allowed : 7.81 % Favored : 89.90 % 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: 0.60 (0.19), residues: 1994 helix: 1.77 (0.17), residues: 991 sheet: 0.71 (0.40), residues: 162 loop : -1.41 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L2139 HIS 0.004 0.001 HIS L2190 PHE 0.019 0.002 PHE L1272 TYR 0.017 0.001 TYR L 183 ARG 0.009 0.001 ARG L 24 *********************** 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 152 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 110 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.6278 (ptp) cc_final: 0.6051 (ptm) REVERT: L 277 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: L 1674 ASN cc_start: 0.6452 (OUTLIER) cc_final: 0.6158 (p0) REVERT: L 1881 ARG cc_start: 0.7334 (mtp85) cc_final: 0.7121 (mtp180) outliers start: 42 outliers final: 13 residues processed: 145 average time/residue: 1.3525 time to fit residues: 220.3341 Evaluate side-chains 106 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 277 GLU Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 912 ASP Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1674 ASN Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1799 ILE Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP 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: 2.9990 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 913 GLN L1234 HIS L1294 GLN L1554 HIS L1789 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17399 Z= 0.145 Angle : 0.447 7.748 23681 Z= 0.235 Chirality : 0.037 0.166 2707 Planarity : 0.003 0.039 2857 Dihedral : 12.235 73.642 2797 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.80 % Allowed : 9.01 % Favored : 89.19 % 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: 0.82 (0.19), residues: 1994 helix: 1.99 (0.17), residues: 976 sheet: 0.76 (0.39), residues: 172 loop : -1.31 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L2139 HIS 0.002 0.000 HIS L2190 PHE 0.012 0.001 PHE L1400 TYR 0.010 0.001 TYR L1663 ARG 0.006 0.000 ARG L 530 *********************** 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 130 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 871 TYR cc_start: 0.5344 (OUTLIER) cc_final: 0.4487 (m-10) REVERT: L 1674 ASN cc_start: 0.6494 (OUTLIER) cc_final: 0.6192 (p0) outliers start: 33 outliers final: 17 residues processed: 127 average time/residue: 1.4366 time to fit residues: 203.2562 Evaluate side-chains 107 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 912 ASP Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1674 ASN Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2098 THR Chi-restraints excluded: chain L residue 2157 VAL 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: 6.9990 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 175 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 175 ASN L1234 HIS L1294 GLN L1789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17399 Z= 0.176 Angle : 0.463 9.694 23681 Z= 0.242 Chirality : 0.038 0.151 2707 Planarity : 0.003 0.040 2857 Dihedral : 12.201 73.748 2797 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.97 % Allowed : 9.12 % Favored : 88.91 % 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: 0.82 (0.19), residues: 1994 helix: 1.98 (0.17), residues: 985 sheet: 0.79 (0.38), residues: 172 loop : -1.34 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L2139 HIS 0.002 0.001 HIS L1191 PHE 0.014 0.001 PHE L1272 TYR 0.014 0.001 TYR L 183 ARG 0.010 0.000 ARG L 530 *********************** 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 129 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 871 TYR cc_start: 0.5701 (OUTLIER) cc_final: 0.4968 (m-10) REVERT: L 1674 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.6068 (p0) outliers start: 36 outliers final: 17 residues processed: 125 average time/residue: 1.3318 time to fit residues: 186.9328 Evaluate side-chains 104 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 912 ASP Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1674 ASN Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2098 THR Chi-restraints excluded: chain L residue 2154 SER Chi-restraints excluded: chain L residue 2157 VAL 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: 6.9990 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 135 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN L1441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2877 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= 0.209 Angle : 0.472 8.395 23681 Z= 0.248 Chirality : 0.038 0.155 2707 Planarity : 0.003 0.044 2857 Dihedral : 12.238 73.824 2797 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.29 % Allowed : 9.56 % Favored : 88.15 % 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: 0.71 (0.19), residues: 1994 helix: 1.83 (0.17), residues: 995 sheet: 0.76 (0.38), residues: 172 loop : -1.36 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L2139 HIS 0.004 0.001 HIS L1758 PHE 0.015 0.001 PHE L1272 TYR 0.014 0.001 TYR L 183 ARG 0.008 0.000 ARG L 530 *********************** 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: 42 poor density : 90 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 871 TYR cc_start: 0.5738 (OUTLIER) cc_final: 0.4490 (m-10) REVERT: L 1674 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.6029 (p0) outliers start: 42 outliers final: 19 residues processed: 127 average time/residue: 1.3949 time to fit residues: 198.3258 Evaluate side-chains 104 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 912 ASP Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1674 ASN Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2098 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 0.0270 overall best weight: 1.8046 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17399 Z= 0.210 Angle : 0.470 8.304 23681 Z= 0.246 Chirality : 0.038 0.156 2707 Planarity : 0.004 0.084 2857 Dihedral : 12.254 73.819 2797 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.80 % Allowed : 10.21 % Favored : 87.98 % 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: 1.83 (0.17), residues: 997 sheet: 0.74 (0.38), residues: 172 loop : -1.39 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L1547 HIS 0.002 0.001 HIS L1191 PHE 0.014 0.001 PHE L1272 TYR 0.015 0.001 TYR L 183 ARG 0.013 0.000 ARG L 530 *********************** 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: 33 poor density : 87 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 483 MET cc_start: 0.7856 (mmt) cc_final: 0.7576 (mmt) REVERT: L 871 TYR cc_start: 0.5702 (OUTLIER) cc_final: 0.4804 (m-10) REVERT: L 1848 GLU cc_start: 0.7029 (tp30) cc_final: 0.6707 (tp30) outliers start: 33 outliers final: 20 residues processed: 116 average time/residue: 1.3196 time to fit residues: 172.5452 Evaluate side-chains 103 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 912 ASP Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2009 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2098 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 143 optimal weight: 0.0070 chunk 165 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN L1597 GLN L1789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17399 Z= 0.107 Angle : 0.422 7.834 23681 Z= 0.220 Chirality : 0.036 0.143 2707 Planarity : 0.003 0.047 2857 Dihedral : 12.145 73.534 2797 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.47 % Allowed : 10.76 % Favored : 87.77 % 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: 2.07 (0.17), residues: 987 sheet: 0.89 (0.39), residues: 172 loop : -1.31 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L1773 HIS 0.001 0.000 HIS L1359 PHE 0.013 0.001 PHE L1400 TYR 0.011 0.001 TYR L 183 ARG 0.013 0.000 ARG L 530 *********************** 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 119 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 871 TYR cc_start: 0.5608 (OUTLIER) cc_final: 0.4813 (m-10) REVERT: L 1848 GLU cc_start: 0.6921 (tp30) cc_final: 0.6631 (tp30) outliers start: 27 outliers final: 14 residues processed: 117 average time/residue: 1.3893 time to fit residues: 182.2990 Evaluate side-chains 101 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2152 MET Chi-restraints excluded: chain L residue 2157 VAL 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: 0.6980 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN L1597 GLN L1789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3147 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= 0.182 Angle : 0.459 10.667 23681 Z= 0.238 Chirality : 0.038 0.147 2707 Planarity : 0.003 0.061 2857 Dihedral : 12.160 73.752 2797 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.64 % Allowed : 10.92 % Favored : 87.44 % 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: 0.88 (0.19), residues: 1994 helix: 1.99 (0.17), residues: 996 sheet: 0.93 (0.40), residues: 162 loop : -1.31 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1547 HIS 0.003 0.001 HIS L1191 PHE 0.026 0.001 PHE L 349 TYR 0.013 0.001 TYR L 183 ARG 0.013 0.000 ARG L 530 *********************** 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 115 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 871 TYR cc_start: 0.5689 (OUTLIER) cc_final: 0.4833 (m-10) REVERT: L 1848 GLU cc_start: 0.7013 (tp30) cc_final: 0.6673 (tp30) outliers start: 30 outliers final: 18 residues processed: 113 average time/residue: 1.3327 time to fit residues: 169.1108 Evaluate side-chains 106 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1516 ASN Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2098 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 182 optimal weight: 0.0870 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 0.0970 chunk 55 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1294 GLN L1597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17399 Z= 0.112 Angle : 0.430 8.593 23681 Z= 0.222 Chirality : 0.036 0.155 2707 Planarity : 0.003 0.054 2857 Dihedral : 12.106 73.552 2797 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.20 % Allowed : 11.41 % Favored : 87.38 % 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: 0.97 (0.19), residues: 1994 helix: 2.08 (0.17), residues: 990 sheet: 1.04 (0.40), residues: 162 loop : -1.27 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1773 HIS 0.002 0.000 HIS L1191 PHE 0.015 0.001 PHE L 349 TYR 0.012 0.001 TYR L 183 ARG 0.015 0.000 ARG L 530 *********************** 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 114 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 871 TYR cc_start: 0.5565 (OUTLIER) cc_final: 0.4857 (m-10) REVERT: L 1848 GLU cc_start: 0.6891 (tp30) cc_final: 0.6608 (tp30) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 1.3372 time to fit residues: 170.7707 Evaluate side-chains 103 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2098 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 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 L1597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17399 Z= 0.274 Angle : 0.520 9.072 23681 Z= 0.269 Chirality : 0.039 0.148 2707 Planarity : 0.004 0.068 2857 Dihedral : 12.223 73.946 2797 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.26 % Allowed : 11.69 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1994 helix: 1.88 (0.17), residues: 992 sheet: 0.81 (0.38), residues: 172 loop : -1.36 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L1233 HIS 0.006 0.001 HIS L1758 PHE 0.018 0.001 PHE L1272 TYR 0.016 0.001 TYR L 183 ARG 0.015 0.000 ARG L 530 ********************** 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 109 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 871 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.4865 (m-10) REVERT: L 1848 GLU cc_start: 0.6993 (tp30) cc_final: 0.6691 (tp30) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 1.3431 time to fit residues: 164.6894 Evaluate side-chains 99 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1103 SER Chi-restraints excluded: chain L residue 1268 ILE Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1389 VAL Chi-restraints excluded: chain L residue 1390 TRP Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2098 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.077729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.059070 restraints weight = 44151.891| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.45 r_work: 0.2849 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17399 Z= 0.142 Angle : 0.460 8.552 23681 Z= 0.238 Chirality : 0.037 0.142 2707 Planarity : 0.003 0.057 2857 Dihedral : 12.172 73.638 2797 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.31 % Allowed : 11.80 % Favored : 86.89 % 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: 0.87 (0.19), residues: 1994 helix: 2.00 (0.17), residues: 990 sheet: 0.93 (0.40), residues: 162 loop : -1.30 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L1773 HIS 0.006 0.001 HIS L1758 PHE 0.016 0.001 PHE L 349 TYR 0.013 0.001 TYR L1517 ARG 0.014 0.000 ARG L 530 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4461.64 seconds wall clock time: 80 minutes 50.22 seconds (4850.22 seconds total)