Starting phenix.real_space_refine on Sat Sep 12 18:04:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ojn_12956/09_2026/7ojn_12956.cif" } 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 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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'RNAv2': 11} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 3.53, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 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: 1.51 Conformation dependent library (CDL) restraints added in 639.2 milliseconds 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... Secondary structure from input PDB file: 91 helices and 17 sheets defined 54.3% alpha, 11.6% beta 8 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 19 through 21 No H-bonds generated for 'chain 'L' and resid 19 through 21' Processing helix chain 'L' and resid 22 through 30 Processing helix chain 'L' and resid 34 through 59 Processing helix chain 'L' and resid 68 through 76 Processing helix chain 'L' and resid 112 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 153 through 172 removed outlier: 3.951A pdb=" N GLN L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 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 200 through 206 Processing helix chain 'L' and resid 211 through 222 Processing helix chain 'L' and resid 230 through 251 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 removed outlier: 3.564A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 303 Processing helix chain 'L' and resid 321 through 336 removed outlier: 3.693A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 341 through 365 Processing helix chain 'L' and resid 385 through 404 removed outlier: 3.908A pdb=" N ARG L 404 " --> pdb=" O GLN L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 434 removed outlier: 3.518A pdb=" N ILE L 416 " --> pdb=" O ASP L 412 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP L 434 " --> pdb=" O ALA L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.783A pdb=" N VAL L 448 " --> pdb=" O ASN L 445 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 459 removed outlier: 3.597A pdb=" N ASN L 459 " --> pdb=" O ASP L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 479 removed outlier: 4.169A pdb=" N LYS L 478 " --> pdb=" O GLU L 475 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE L 479 " --> pdb=" O ASP L 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 475 through 479' Processing helix chain 'L' and resid 491 through 507 Processing helix chain 'L' and resid 508 through 510 No H-bonds generated for 'chain 'L' and resid 508 through 510' Processing helix chain 'L' and resid 521 through 526 removed outlier: 3.691A pdb=" N ALA L 524 " --> pdb=" O PHE L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 580 removed outlier: 3.883A pdb=" N TYR L 580 " --> pdb=" O PRO L 577 " (cutoff:3.500A) Processing helix chain 'L' and resid 587 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 610 through 628 Processing helix chain 'L' and resid 632 through 648 removed outlier: 4.328A pdb=" N LEU L 636 " --> pdb=" O ARG L 632 " (cutoff:3.500A) 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) removed outlier: 3.766A pdb=" N VAL L 648 " --> pdb=" O ILE L 644 " (cutoff:3.500A) Processing helix chain 'L' and resid 655 through 661 Processing helix chain 'L' and resid 666 through 684 removed outlier: 3.529A pdb=" N PHE L 670 " --> pdb=" O THR L 666 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 704 Processing helix chain 'L' and resid 705 through 709 removed outlier: 3.571A pdb=" N ILE L 709 " --> pdb=" O CYS L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 715 through 735 Proline residue: L 730 - end of helix Processing helix chain 'L' and resid 746 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 780 through 793 Processing helix chain 'L' and resid 798 through 802 removed outlier: 3.900A pdb=" N VAL L 802 " --> pdb=" O GLU L 799 " (cutoff:3.500A) Processing helix chain 'L' and resid 817 through 822 removed outlier: 3.597A pdb=" N LEU L 821 " --> pdb=" O ALA L 818 " (cutoff:3.500A) Processing helix chain 'L' and resid 842 through 862 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 880 Processing helix chain 'L' and resid 911 through 925 removed outlier: 3.503A pdb=" N ASP L 923 " --> pdb=" O GLU L 919 " (cutoff:3.500A) Processing helix chain 'L' and resid 1060 through 1066 Processing helix chain 'L' and resid 1075 through 1084 Processing helix chain 'L' and resid 1092 through 1098 Processing helix chain 'L' and resid 1137 through 1156 Processing helix chain 'L' and resid 1165 through 1182 Processing helix chain 'L' and resid 1193 through 1198 Processing helix chain 'L' and resid 1199 through 1209 removed outlier: 3.586A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN L1209 " --> pdb=" O ALA L1205 " (cutoff:3.500A) Processing helix chain 'L' and resid 1218 through 1236 removed outlier: 3.880A pdb=" N LYS L1222 " --> pdb=" O GLN L1218 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1258 Processing helix chain 'L' and resid 1267 through 1280 removed outlier: 3.870A pdb=" N ILE L1279 " --> pdb=" O SER L1275 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY L1280 " --> pdb=" O ASN L1276 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 removed outlier: 3.842A pdb=" N SER L1301 " --> pdb=" O LEU L1297 " (cutoff:3.500A) Processing helix chain 'L' and resid 1338 through 1348 Processing helix chain 'L' and resid 1348 through 1366 Processing helix chain 'L' and resid 1396 through 1405 removed outlier: 4.169A pdb=" N PHE L1400 " --> pdb=" O LEU L1396 " (cutoff:3.500A) Processing helix chain 'L' and resid 1412 through 1430 Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 3.713A pdb=" N LEU L1439 " --> pdb=" O HIS L1435 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA L1451 " --> pdb=" O LEU L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1465 through 1471 removed outlier: 3.694A pdb=" N TRP L1469 " --> pdb=" O ASP L1465 " (cutoff:3.500A) Processing helix chain 'L' and resid 1473 through 1486 Processing helix chain 'L' and resid 1489 through 1506 removed outlier: 4.045A pdb=" N ILE L1493 " --> pdb=" O ALA L1489 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) Processing helix chain 'L' and resid 1522 through 1533 removed outlier: 3.670A pdb=" N LEU L1533 " --> pdb=" O LEU L1529 " (cutoff:3.500A) Processing helix chain 'L' and resid 1539 through 1544 removed outlier: 3.604A pdb=" N GLU L1544 " --> pdb=" O GLU L1540 " (cutoff:3.500A) Processing helix chain 'L' and resid 1578 through 1589 Processing helix chain 'L' and resid 1592 through 1611 Processing helix chain 'L' and resid 1615 through 1624 Processing helix chain 'L' and resid 1638 through 1648 Processing helix chain 'L' and resid 1667 through 1671 Processing helix chain 'L' and resid 1674 through 1679 removed outlier: 3.687A pdb=" N ILE L1678 " --> pdb=" O ASN L1674 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER L1679 " --> pdb=" O GLU L1675 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1674 through 1679' Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1700 through 1705 removed outlier: 3.632A pdb=" N VAL L1703 " --> pdb=" O GLY L1700 " (cutoff:3.500A) Processing helix chain 'L' and resid 1733 through 1737 removed outlier: 3.685A pdb=" N ARG L1737 " --> pdb=" O LEU L1734 " (cutoff:3.500A) Processing helix chain 'L' and resid 1739 through 1751 removed outlier: 3.696A pdb=" N ILE L1743 " --> pdb=" O GLY L1739 " (cutoff:3.500A) Processing helix chain 'L' and resid 1751 through 1759 Processing helix chain 'L' and resid 1760 through 1763 Processing helix chain 'L' and resid 1766 through 1770 Processing helix chain 'L' and resid 1777 through 1790 Processing helix chain 'L' and resid 1812 through 1816 Processing helix chain 'L' and resid 1833 through 1852 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 1857 through 1863 removed outlier: 3.673A pdb=" N LEU L1861 " --> pdb=" O THR L1857 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY L1862 " --> pdb=" O THR L1858 " (cutoff:3.500A) Processing helix chain 'L' and resid 1882 through 1884 No H-bonds generated for 'chain 'L' and resid 1882 through 1884' Processing helix chain 'L' and resid 1885 through 1890 removed outlier: 4.130A pdb=" N GLU L1890 " --> pdb=" O SER L1886 " (cutoff:3.500A) Processing helix chain 'L' and resid 1892 through 1896 removed outlier: 3.918A pdb=" N LYS L1895 " --> pdb=" O ALA L1892 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY L1896 " --> pdb=" O ILE L1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1892 through 1896' Processing helix chain 'L' and resid 1923 through 1929 Processing helix chain 'L' and resid 1939 through 1949 Processing helix chain 'L' and resid 2006 through 2008 No H-bonds generated for 'chain 'L' and resid 2006 through 2008' Processing helix chain 'L' and resid 2009 through 2020 removed outlier: 3.767A pdb=" N GLY L2020 " --> pdb=" O LEU L2016 " (cutoff:3.500A) Processing helix chain 'L' and resid 2035 through 2040 removed outlier: 3.502A pdb=" N LEU L2040 " --> pdb=" O ASN L2037 " (cutoff:3.500A) Processing helix chain 'L' and resid 2057 through 2062 Processing helix chain 'L' and resid 2102 through 2117 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 2135 Processing helix chain 'L' and resid 2143 through 2152 Processing helix chain 'L' and resid 2155 through 2168 Processing sheet with id=AA1, first strand: chain 'L' and resid 61 through 62 removed outlier: 3.556A pdb=" N GLU L 61 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR L 91 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU L 100 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 207 through 208 removed outlier: 6.505A pdb=" N LEU L 207 " --> pdb=" O TYR L1107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY L1111 " --> pdb=" O SER L1108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'L' and resid 370 through 371 removed outlier: 3.670A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 468 through 470 Processing sheet with id=AA6, first strand: chain 'L' and resid 738 through 739 Processing sheet with id=AA7, first strand: chain 'L' and resid 826 through 830 Processing sheet with id=AA8, first strand: chain 'L' and resid 1380 through 1382 Processing sheet with id=AA9, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 9.044A pdb=" N GLN L1662 " --> pdb=" O LEU L1548 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU L1548 " --> pdb=" O GLN L1662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 1629 through 1630 Processing sheet with id=AB2, 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=AB3, first strand: chain 'L' and resid 1723 through 1726 Processing sheet with id=AB4, first strand: chain 'L' and resid 1854 through 1855 removed outlier: 3.594A pdb=" N PHE L1854 " --> pdb=" O VAL L2082 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU L2087 " --> pdb=" O LEU L2094 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS L2092 " --> pdb=" O GLU L2089 " (cutoff:3.500A) Processing sheet with id=AB5, 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) removed outlier: 6.452A pdb=" N TYR L1992 " --> pdb=" O VAL L2055 " (cutoff:3.500A) Processing sheet with id=AB6, 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) removed outlier: 3.623A pdb=" N VAL L2069 " --> pdb=" O ALA L1999 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 2030 through 2032 Processing sheet with id=AB8, first strand: chain 'L' and resid 2171 through 2172 removed outlier: 5.490A pdb=" N ALA L2177 " --> pdb=" O HIS L2190 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS L2186 " --> pdb=" O SER L2181 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2388 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: 3.90 Time building geometry restraints manager: 2.00 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=" N3A 2KH L2301 " pdb=" PA 2KH L2301 " ideal model delta sigma weight residual 1.933 1.672 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C2' 2KH L2301 " pdb=" C3' 2KH L2301 " ideal model delta sigma weight residual 1.548 1.307 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" N3A 2KH L2301 " pdb=" PB 2KH L2301 " ideal model delta sigma weight residual 1.890 1.697 0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" O3G 2KH L2301 " pdb=" PG 2KH L2301 " ideal model delta sigma weight residual 1.669 1.497 0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" O2G 2KH L2301 " pdb=" PG 2KH L2301 " ideal model delta sigma weight residual 1.682 1.529 0.153 2.00e-02 2.50e+03 5.82e+01 ... (remaining 17394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.24: 23670 12.24 - 24.48: 6 24.48 - 36.72: 0 36.72 - 48.97: 0 48.97 - 61.21: 2 Bond angle restraints: 23678 Sorted by residual: angle pdb=" N3A 2KH L2301 " pdb=" PA 2KH L2301 " pdb=" O2A 2KH L2301 " ideal model delta sigma weight residual 48.17 109.38 -61.21 3.00e+00 1.11e-01 4.16e+02 angle pdb=" O2G 2KH L2301 " pdb=" PG 2KH L2301 " pdb=" O3G 2KH L2301 " ideal model delta sigma weight residual 53.94 109.62 -55.68 3.00e+00 1.11e-01 3.45e+02 angle pdb=" O1A 2KH L2301 " pdb=" PA 2KH L2301 " pdb=" O2A 2KH L2301 " ideal model delta sigma weight residual 130.82 109.25 21.57 3.00e+00 1.11e-01 5.17e+01 angle pdb=" O1B 2KH L2301 " pdb=" PB 2KH L2301 " pdb=" O2B 2KH L2301 " ideal model delta sigma weight residual 130.56 109.74 20.82 3.00e+00 1.11e-01 4.82e+01 angle pdb=" O1G 2KH L2301 " pdb=" PG 2KH L2301 " pdb=" O3G 2KH L2301 " ideal model delta sigma weight residual 130.17 109.50 20.67 3.00e+00 1.11e-01 4.75e+01 ... (remaining 23673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 10360 35.47 - 70.93: 123 70.93 - 106.40: 10 106.40 - 141.86: 1 141.86 - 177.33: 2 Dihedral angle restraints: 10496 sinusoidal: 4580 harmonic: 5916 Sorted by residual: dihedral pdb=" C4' G D 11 " pdb=" C3' G D 11 " pdb=" C2' G D 11 " pdb=" C1' G D 11 " ideal model delta sinusoidal sigma weight residual 36.34 -36.12 72.46 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' U E 11 " pdb=" C3' U E 11 " pdb=" C2' U E 11 " pdb=" C1' U E 11 " ideal model delta sinusoidal sigma weight residual 36.35 -35.47 71.81 1 3.10e+00 1.04e-01 6.87e+02 dihedral pdb=" C4' G D 1 " pdb=" C3' G D 1 " pdb=" C2' G D 1 " pdb=" C1' G D 1 " ideal model delta sinusoidal sigma weight residual 36.34 -35.38 71.73 1 3.10e+00 1.04e-01 6.86e+02 ... (remaining 10493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2511 0.080 - 0.160: 140 0.160 - 0.239: 35 0.239 - 0.319: 20 0.319 - 0.399: 1 Chirality restraints: 2707 Sorted by residual: chirality pdb=" C2' 2KH L2301 " pdb=" C1' 2KH L2301 " pdb=" C3' 2KH L2301 " pdb=" O2' 2KH L2301 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C2' U E 13 " pdb=" C3' U E 13 " pdb=" O2' U E 13 " pdb=" C1' U E 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' C R 16 " pdb=" C3' C R 16 " pdb=" O2' C R 16 " pdb=" C1' C R 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (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: 11324 3.08 - 3.68: 24203 3.68 - 4.29: 36388 4.29 - 4.90: 62157 Nonbonded interactions: 134125 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 134120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.090 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.760 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- 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 : 0.005 0.261 17403 Z= 0.244 Angle : 0.792 61.207 23680 Z= 0.318 Chirality : 0.051 0.399 2707 Planarity : 0.003 0.041 2857 Dihedral : 11.312 177.329 6652 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG L 632 TYR 0.010 0.001 TYR L 183 PHE 0.011 0.001 PHE L1272 TRP 0.008 0.001 TRP L1547 HIS 0.002 0.000 HIS L1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 (17399) covalent geometry : angle 0.79178 / 0.32 (23678) hydrogen bonds : bond 0.14119 / 9.72 ( 838) hydrogen bonds : angle 4.96840 / 3.39 ( 2430) metal coordination : bond 0.00177 / 0.09 ( 4) metal coordination : angle 0.89585 / 0.52 ( 2) *********************** 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 to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.694 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: 0.7238 time to fit residues: 176.5413 Evaluate side-chains 112 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 340 ASN L 913 GLN L1208 GLN L1234 HIS L1298 HIS L1441 GLN L1789 ASN ** L1807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.078053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059167 restraints weight = 44243.678| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.38 r_work: 0.2852 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17403 Z= 0.196 Angle : 0.679 17.181 23680 Z= 0.326 Chirality : 0.054 0.703 2707 Planarity : 0.004 0.045 2857 Dihedral : 11.141 141.252 2672 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 2.08 % Allowed : 7.65 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1994 helix: 1.96 (0.17), residues: 995 sheet: 0.67 (0.40), residues: 163 loop : -1.34 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L1962 TYR 0.017 0.001 TYR L 183 PHE 0.018 0.002 PHE L1272 TRP 0.016 0.001 TRP L2139 HIS 0.004 0.001 HIS L2190 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (17399) covalent geometry : angle 0.67878 / 0.33 (23678) hydrogen bonds : bond 0.05383 / 3.65 ( 838) hydrogen bonds : angle 4.07427 / 2.81 ( 2430) metal coordination : bond 0.00954 / 0.48 ( 4) metal coordination : angle 1.24970 / 0.69 ( 2) *********************** 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 149 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 277 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: L 1881 ARG cc_start: 0.8308 (mtp85) cc_final: 0.7994 (mmt180) REVERT: L 2152 MET cc_start: 0.7613 (mtm) cc_final: 0.7204 (mtp) outliers start: 38 outliers final: 15 residues processed: 143 average time/residue: 0.6120 time to fit residues: 97.5778 Evaluate side-chains 108 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 450 CYS 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 1390 TRP 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 Chi-restraints excluded: chain L residue 2058 MET Chi-restraints excluded: chain L residue 2098 THR Chi-restraints excluded: chain L residue 2154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 48 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 0.0770 chunk 161 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 126 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN L1481 GLN L1554 HIS L1789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.060478 restraints weight = 44652.116| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.41 r_work: 0.2886 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17403 Z= 0.111 Angle : 0.529 8.468 23680 Z= 0.265 Chirality : 0.045 0.361 2707 Planarity : 0.003 0.046 2857 Dihedral : 10.920 152.974 2663 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.24 % Allowed : 8.25 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1994 helix: 2.09 (0.17), residues: 1001 sheet: 0.74 (0.39), residues: 164 loop : -1.33 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 530 TYR 0.012 0.001 TYR L 183 PHE 0.014 0.001 PHE L1400 TRP 0.010 0.001 TRP L1194 HIS 0.002 0.000 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17399) covalent geometry : angle 0.52857 / 0.27 (23678) hydrogen bonds : bond 0.04096 / 2.77 ( 838) hydrogen bonds : angle 3.83411 / 2.65 ( 2430) metal coordination : bond 0.00203 / 0.10 ( 4) metal coordination : angle 1.25711 / 0.74 ( 2) *********************** 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 139 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1263 LYS cc_start: 0.6549 (mmtt) cc_final: 0.6316 (mmmm) REVERT: L 1848 GLU cc_start: 0.8627 (mp0) cc_final: 0.8362 (mp0) REVERT: L 1928 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9109 (tp) REVERT: L 2152 MET cc_start: 0.7660 (mtm) cc_final: 0.7385 (mtp) outliers start: 41 outliers final: 18 residues processed: 134 average time/residue: 0.6536 time to fit residues: 97.5918 Evaluate side-chains 109 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 912 ASP Chi-restraints excluded: chain L residue 914 LEU Chi-restraints excluded: chain L residue 1234 HIS 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 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 1928 ILE Chi-restraints excluded: chain L residue 2057 ASP Chi-restraints excluded: chain L residue 2058 MET Chi-restraints excluded: chain L residue 2069 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 186 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 110 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN L1789 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.079582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060966 restraints weight = 44363.935| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.40 r_work: 0.2900 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17403 Z= 0.099 Angle : 0.512 8.992 23680 Z= 0.256 Chirality : 0.044 0.319 2707 Planarity : 0.003 0.047 2857 Dihedral : 10.684 152.644 2663 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.18 % Allowed : 8.85 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 1994 helix: 2.19 (0.17), residues: 1000 sheet: 0.63 (0.39), residues: 174 loop : -1.32 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 530 TYR 0.012 0.001 TYR L 183 PHE 0.012 0.001 PHE L1400 TRP 0.010 0.001 TRP L1194 HIS 0.002 0.000 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (17399) covalent geometry : angle 0.51220 / 0.26 (23678) hydrogen bonds : bond 0.03735 / 2.54 ( 838) hydrogen bonds : angle 3.70730 / 2.57 ( 2430) metal coordination : bond 0.00210 / 0.10 ( 4) metal coordination : angle 0.95368 / 0.56 ( 2) *********************** 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 139 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 14 LYS cc_start: 0.9166 (pttp) cc_final: 0.8951 (pptt) REVERT: L 1263 LYS cc_start: 0.6735 (mmtt) cc_final: 0.6515 (mptm) REVERT: L 2152 MET cc_start: 0.7601 (mtm) cc_final: 0.7188 (mtp) REVERT: L 2185 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8817 (mtpt) outliers start: 40 outliers final: 18 residues processed: 137 average time/residue: 0.6441 time to fit residues: 97.9223 Evaluate side-chains 105 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 1712 VAL Chi-restraints excluded: chain L residue 1799 ILE Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 2069 VAL Chi-restraints excluded: chain L residue 2154 SER Chi-restraints excluded: chain L residue 2185 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 93 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN L1597 GLN L1758 HIS L1789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.075855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056980 restraints weight = 44636.294| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.40 r_work: 0.2797 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17403 Z= 0.221 Angle : 0.621 8.649 23680 Z= 0.311 Chirality : 0.049 0.468 2707 Planarity : 0.004 0.045 2857 Dihedral : 10.960 145.897 2663 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.35 % Allowed : 9.28 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1994 helix: 1.85 (0.17), residues: 1002 sheet: 0.67 (0.39), residues: 163 loop : -1.47 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 530 TYR 0.018 0.002 TYR L 183 PHE 0.019 0.002 PHE L1272 TRP 0.012 0.001 TRP L2139 HIS 0.004 0.001 HIS L1807 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (17399) covalent geometry : angle 0.62071 / 0.31 (23678) hydrogen bonds : bond 0.05698 / 3.89 ( 838) hydrogen bonds : angle 3.99687 / 2.79 ( 2430) metal coordination : bond 0.00552 / 0.27 ( 4) metal coordination : angle 2.00056 / 1.18 ( 2) *********************** 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 135 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1263 LYS cc_start: 0.6786 (mmtt) cc_final: 0.6551 (mptm) REVERT: L 1848 GLU cc_start: 0.8718 (mp0) cc_final: 0.8515 (mp0) REVERT: L 1928 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9154 (tp) REVERT: L 2152 MET cc_start: 0.7946 (mtm) cc_final: 0.7257 (ptp) REVERT: L 2174 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8732 (ttmm) outliers start: 43 outliers final: 17 residues processed: 131 average time/residue: 0.6149 time to fit residues: 90.1992 Evaluate side-chains 104 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 483 MET 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 1390 TRP Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 1928 ILE Chi-restraints excluded: chain L residue 2069 VAL Chi-restraints excluded: chain L residue 2078 VAL Chi-restraints excluded: chain L residue 2098 THR Chi-restraints excluded: chain L residue 2154 SER Chi-restraints excluded: chain L residue 2174 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 79 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.077302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058544 restraints weight = 44373.807| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.40 r_work: 0.2840 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17403 Z= 0.134 Angle : 0.544 8.955 23680 Z= 0.273 Chirality : 0.045 0.358 2707 Planarity : 0.003 0.045 2857 Dihedral : 10.822 146.770 2663 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.75 % Allowed : 10.16 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1994 helix: 2.00 (0.17), residues: 1000 sheet: 0.62 (0.39), residues: 163 loop : -1.45 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 530 TYR 0.014 0.001 TYR L 183 PHE 0.014 0.001 PHE L1400 TRP 0.013 0.001 TRP L1194 HIS 0.003 0.001 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (17399) covalent geometry : angle 0.54381 / 0.27 (23678) hydrogen bonds : bond 0.04423 / 3.01 ( 838) hydrogen bonds : angle 3.83531 / 2.67 ( 2430) metal coordination : bond 0.00283 / 0.14 ( 4) metal coordination : angle 1.37075 / 0.80 ( 2) *********************** 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 121 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1263 LYS cc_start: 0.6664 (mmtt) cc_final: 0.6454 (mptm) REVERT: L 1517 TYR cc_start: 0.7421 (m-10) cc_final: 0.7064 (m-10) REVERT: L 1848 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: L 1928 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9159 (tp) REVERT: L 2152 MET cc_start: 0.7782 (mtm) cc_final: 0.7368 (mtp) outliers start: 32 outliers final: 19 residues processed: 119 average time/residue: 0.6094 time to fit residues: 81.3122 Evaluate side-chains 105 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 512 SER 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 1234 HIS 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 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 1848 GLU Chi-restraints excluded: chain L residue 1928 ILE Chi-restraints excluded: chain L residue 2069 VAL Chi-restraints excluded: chain L residue 2154 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 0.0010 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.059811 restraints weight = 44119.343| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.40 r_work: 0.2875 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17403 Z= 0.105 Angle : 0.517 9.275 23680 Z= 0.259 Chirality : 0.044 0.328 2707 Planarity : 0.003 0.046 2857 Dihedral : 10.628 146.603 2663 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.47 % Allowed : 10.87 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.19), residues: 1994 helix: 2.11 (0.17), residues: 1002 sheet: 0.73 (0.39), residues: 164 loop : -1.35 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 530 TYR 0.014 0.001 TYR L 183 PHE 0.013 0.001 PHE L1400 TRP 0.013 0.001 TRP L1194 HIS 0.002 0.000 HIS L1758 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (17399) covalent geometry : angle 0.51659 / 0.26 (23678) hydrogen bonds : bond 0.03794 / 2.58 ( 838) hydrogen bonds : angle 3.69075 / 2.56 ( 2430) metal coordination : bond 0.00189 / 0.09 ( 4) metal coordination : angle 1.06750 / 0.63 ( 2) *********************** 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 117 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1060 MET cc_start: 0.8280 (ttt) cc_final: 0.8048 (tpp) REVERT: L 1517 TYR cc_start: 0.7351 (m-10) cc_final: 0.6984 (m-10) REVERT: L 1848 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: L 2152 MET cc_start: 0.7724 (mtm) cc_final: 0.7316 (mtp) outliers start: 27 outliers final: 18 residues processed: 116 average time/residue: 0.6109 time to fit residues: 78.9407 Evaluate side-chains 105 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 1234 HIS 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 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 1848 GLU Chi-restraints excluded: chain L residue 2069 VAL Chi-restraints excluded: chain L residue 2154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 158 optimal weight: 0.2980 chunk 198 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.078588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059922 restraints weight = 44468.628| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.41 r_work: 0.2877 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17403 Z= 0.104 Angle : 0.521 10.893 23680 Z= 0.259 Chirality : 0.043 0.327 2707 Planarity : 0.003 0.056 2857 Dihedral : 10.518 144.611 2663 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.47 % Allowed : 11.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1994 helix: 2.11 (0.17), residues: 1010 sheet: 0.90 (0.41), residues: 154 loop : -1.34 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 530 TYR 0.013 0.001 TYR L 183 PHE 0.024 0.001 PHE L 349 TRP 0.014 0.001 TRP L1194 HIS 0.002 0.000 HIS L1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (17399) covalent geometry : angle 0.52066 / 0.26 (23678) hydrogen bonds : bond 0.03789 / 2.58 ( 838) hydrogen bonds : angle 3.66120 / 2.55 ( 2430) metal coordination : bond 0.00208 / 0.10 ( 4) metal coordination : angle 1.00615 / 0.59 ( 2) *********************** 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 119 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 281 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8143 (m) REVERT: L 871 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5889 (m-10) REVERT: L 1060 MET cc_start: 0.8298 (ttt) cc_final: 0.8053 (tpp) REVERT: L 1517 TYR cc_start: 0.7398 (m-10) cc_final: 0.7023 (m-10) REVERT: L 1848 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: L 2152 MET cc_start: 0.7713 (mtm) cc_final: 0.7326 (mtp) outliers start: 27 outliers final: 18 residues processed: 117 average time/residue: 0.6106 time to fit residues: 79.8532 Evaluate side-chains 107 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 281 THR Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 512 SER 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 1234 HIS 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 1611 SER Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 1848 GLU Chi-restraints excluded: chain L residue 2069 VAL Chi-restraints excluded: chain L residue 2154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.074363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055588 restraints weight = 44598.831| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.39 r_work: 0.2765 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 17403 Z= 0.310 Angle : 0.700 9.116 23680 Z= 0.350 Chirality : 0.052 0.530 2707 Planarity : 0.005 0.066 2857 Dihedral : 11.038 139.824 2663 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.53 % Allowed : 11.31 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1994 helix: 1.65 (0.16), residues: 1002 sheet: 0.68 (0.41), residues: 153 loop : -1.61 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 530 TYR 0.021 0.002 TYR L 183 PHE 0.022 0.002 PHE L1272 TRP 0.017 0.002 TRP L1233 HIS 0.005 0.001 HIS L1758 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.31 (17399) covalent geometry : angle 0.70000 / 0.35 (23678) hydrogen bonds : bond 0.06413 / 4.37 ( 838) hydrogen bonds : angle 4.13829 / 2.89 ( 2430) metal coordination : bond 0.00774 / 0.38 ( 4) metal coordination : angle 2.21480 / 1.30 ( 2) *********************** 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 117 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: L 281 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8264 (m) REVERT: L 1517 TYR cc_start: 0.7448 (m-10) cc_final: 0.7118 (m-10) REVERT: L 1848 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8524 (mm-30) outliers start: 28 outliers final: 17 residues processed: 114 average time/residue: 0.5909 time to fit residues: 75.4866 Evaluate side-chains 101 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 CYS Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 450 CYS Chi-restraints excluded: chain L residue 512 SER 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 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 1848 GLU Chi-restraints excluded: chain L residue 2069 VAL Chi-restraints excluded: chain L residue 2078 VAL Chi-restraints excluded: chain L residue 2154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.077581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.059001 restraints weight = 44038.623| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.39 r_work: 0.2855 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17403 Z= 0.112 Angle : 0.556 8.953 23680 Z= 0.279 Chirality : 0.045 0.328 2707 Planarity : 0.003 0.053 2857 Dihedral : 10.763 141.607 2663 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.15 % Allowed : 11.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1994 helix: 1.93 (0.17), residues: 1005 sheet: 0.73 (0.41), residues: 154 loop : -1.47 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 530 TYR 0.014 0.001 TYR L 183 PHE 0.018 0.001 PHE L 349 TRP 0.015 0.001 TRP L1194 HIS 0.007 0.001 HIS L1758 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17399) covalent geometry : angle 0.55601 / 0.28 (23678) hydrogen bonds : bond 0.04087 / 2.77 ( 838) hydrogen bonds : angle 3.82582 / 2.66 ( 2430) metal coordination : bond 0.00214 / 0.11 ( 4) metal coordination : angle 1.14131 / 0.66 ( 2) ********************** 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 107 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 281 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8165 (m) REVERT: L 871 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.6032 (m-10) REVERT: L 1060 MET cc_start: 0.8318 (ttt) cc_final: 0.8073 (tpp) REVERT: L 1517 TYR cc_start: 0.7393 (m-10) cc_final: 0.7027 (m-10) REVERT: L 1734 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8596 (mt) outliers start: 21 outliers final: 12 residues processed: 104 average time/residue: 0.6564 time to fit residues: 75.7173 Evaluate side-chains 98 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 281 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 1390 TRP Chi-restraints excluded: chain L residue 1611 SER Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1734 LEU Chi-restraints excluded: chain L residue 1832 VAL Chi-restraints excluded: chain L residue 1848 GLU Chi-restraints excluded: chain L residue 2069 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 143 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1294 GLN ** L1758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.075633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056845 restraints weight = 44551.346| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.41 r_work: 0.2797 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17403 Z= 0.203 Angle : 0.612 9.186 23680 Z= 0.307 Chirality : 0.048 0.417 2707 Planarity : 0.004 0.043 2857 Dihedral : 10.866 139.616 2663 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.31 % Allowed : 11.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1994 helix: 1.82 (0.17), residues: 1001 sheet: 0.68 (0.41), residues: 153 loop : -1.52 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 530 TYR 0.018 0.001 TYR L 183 PHE 0.017 0.002 PHE L1272 TRP 0.008 0.001 TRP L1773 HIS 0.009 0.001 HIS L1758 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (17399) covalent geometry : angle 0.61141 / 0.31 (23678) hydrogen bonds : bond 0.05266 / 3.59 ( 838) hydrogen bonds : angle 3.96335 / 2.76 ( 2430) metal coordination : bond 0.00539 / 0.27 ( 4) metal coordination : angle 1.69711 / 1.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5034.22 seconds wall clock time: 86 minutes 40.14 seconds (5200.14 seconds total)