Starting phenix.real_space_refine on Sun Mar 17 20:37:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orl_13041/03_2024/7orl_13041_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 51 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 11846 2.51 5 N 3157 2.21 5 O 3680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 18": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ASP 995": "OD1" <-> "OD2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A ASP 1207": "OD1" <-> "OD2" Residue "A GLU 1214": "OE1" <-> "OE2" Residue "A TYR 1307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A GLU 1469": "OE1" <-> "OE2" Residue "A GLU 1612": "OE1" <-> "OE2" Residue "A PHE 1613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1720": "OD1" <-> "OD2" Residue "A TYR 1740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1849": "OD1" <-> "OD2" Residue "A TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1913": "OE1" <-> "OE2" Residue "A TYR 1921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2022": "OE1" <-> "OE2" Residue "A GLU 2075": "OE1" <-> "OE2" Residue "A GLU 2140": "OE1" <-> "OE2" 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: 18852 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain breaks: 1 Chain: "A" Number of atoms: 17811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2183, 17811 Classifications: {'peptide': 2183} Link IDs: {'PTRANS': 72, 'TRANS': 2110} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'GTG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 1, ' ZN': 1, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16753 SG CYS A2064 49.307 100.427 49.634 1.00118.87 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O POP A2302 " occ=0.74 ... (7 atoms not shown) pdb=" P2 POP A2302 " occ=0.74 Time building chain proxies: 10.46, per 1000 atoms: 0.55 Number of scatterers: 18852 At special positions: 0 Unit cell: (113.52, 118.68, 148.995, 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 S 116 16.00 P 51 15.00 Mg 1 11.99 O 3680 8.00 N 3157 7.00 C 11846 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2182 " pdb="ZN ZN A2303 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2169 " 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 15 sheets defined 49.3% alpha, 8.2% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 12.74 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 19 through 45 Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 99 through 120 removed outlier: 4.808A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 176 through 183 removed outlier: 3.605A pdb=" N ALA A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 239 through 262 removed outlier: 4.642A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 291 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 476 through 488 removed outlier: 6.484A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 503 through 522 removed outlier: 3.508A pdb=" N SER A 522 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 607 through 619 Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 643 through 660 removed outlier: 3.562A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.068A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'A' and resid 681 through 699 removed outlier: 4.123A pdb=" N TYR A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 738 through 751 Proline residue: A 748 - end of helix removed outlier: 3.766A pdb=" N PHE A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 780 removed outlier: 4.231A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 881 through 884 No H-bonds generated for 'chain 'A' and resid 881 through 884' Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.922A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 984 removed outlier: 3.631A pdb=" N ARG A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1019 removed outlier: 3.767A pdb=" N LYS A 997 " --> pdb=" O GLY A 994 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A1014 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A1019 " --> pdb=" O THR A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1030 Processing helix chain 'A' and resid 1040 through 1047 Processing helix chain 'A' and resid 1071 through 1078 removed outlier: 3.753A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 3.547A pdb=" N ASP A1100 " --> pdb=" O CYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1115 Processing helix chain 'A' and resid 1124 through 1128 Processing helix chain 'A' and resid 1149 through 1173 Processing helix chain 'A' and resid 1202 through 1220 removed outlier: 3.731A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1260 Processing helix chain 'A' and resid 1268 through 1285 Processing helix chain 'A' and resid 1289 through 1306 Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1331 through 1333 No H-bonds generated for 'chain 'A' and resid 1331 through 1333' Processing helix chain 'A' and resid 1341 through 1346 Processing helix chain 'A' and resid 1351 through 1364 Processing helix chain 'A' and resid 1374 through 1380 removed outlier: 3.792A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1435 through 1440 Processing helix chain 'A' and resid 1442 through 1452 removed outlier: 3.704A pdb=" N LYS A1446 " --> pdb=" O TYR A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1466 Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1479 through 1490 removed outlier: 4.002A pdb=" N TYR A1489 " --> pdb=" O VAL A1485 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A1490 " --> pdb=" O ILE A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1497 No H-bonds generated for 'chain 'A' and resid 1494 through 1497' Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1551 through 1562 removed outlier: 3.519A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1577 Processing helix chain 'A' and resid 1582 through 1592 Processing helix chain 'A' and resid 1614 through 1616 No H-bonds generated for 'chain 'A' and resid 1614 through 1616' Processing helix chain 'A' and resid 1623 through 1631 Processing helix chain 'A' and resid 1645 through 1658 Processing helix chain 'A' and resid 1661 through 1676 removed outlier: 3.658A pdb=" N MET A1665 " --> pdb=" O LEU A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1702 Processing helix chain 'A' and resid 1718 through 1728 Processing helix chain 'A' and resid 1748 through 1752 removed outlier: 3.935A pdb=" N ILE A1752 " --> pdb=" O GLY A1748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1748 through 1752' Processing helix chain 'A' and resid 1757 through 1778 Processing helix chain 'A' and resid 1781 through 1794 removed outlier: 5.050A pdb=" N SER A1785 " --> pdb=" O LEU A1782 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A1787 " --> pdb=" O ARG A1784 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A1794 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1811 Processing helix chain 'A' and resid 1816 through 1824 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1832 through 1841 removed outlier: 4.528A pdb=" N LYS A1840 " --> pdb=" O TYR A1836 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER A1841 " --> pdb=" O ASP A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1904 Processing helix chain 'A' and resid 1944 through 1954 Processing helix chain 'A' and resid 1986 through 1990 Processing helix chain 'A' and resid 2015 through 2020 removed outlier: 3.806A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2038 Processing helix chain 'A' and resid 2047 through 2051 Processing helix chain 'A' and resid 2055 through 2061 removed outlier: 3.925A pdb=" N LYS A2060 " --> pdb=" O ILE A2056 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A2061 " --> pdb=" O SER A2057 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2076 removed outlier: 4.604A pdb=" N PHE A2076 " --> pdb=" O ASP A2072 " (cutoff:3.500A) Processing helix chain 'A' and resid 2110 through 2128 Processing helix chain 'A' and resid 2139 through 2154 Processing helix chain 'A' and resid 2161 through 2174 Processing helix chain 'A' and resid 2179 through 2182 No H-bonds generated for 'chain 'A' and resid 2179 through 2182' Processing helix chain 'A' and resid 2201 through 2210 Processing helix chain 'A' and resid 2218 through 2236 removed outlier: 3.688A pdb=" N VAL A2221 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A2223 " --> pdb=" O ASN A2220 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 80 through 84 Processing sheet with id= B, first strand: chain 'A' and resid 293 through 295 Processing sheet with id= C, first strand: chain 'A' and resid 308 through 310 Processing sheet with id= D, first strand: chain 'A' and resid 386 through 388 Processing sheet with id= E, first strand: chain 'A' and resid 398 through 400 Processing sheet with id= F, first strand: chain 'A' and resid 562 through 565 Processing sheet with id= G, first strand: chain 'A' and resid 842 through 846 Processing sheet with id= H, first strand: chain 'A' and resid 945 through 949 Processing sheet with id= I, first strand: chain 'A' and resid 1230 through 1232 Processing sheet with id= J, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id= K, first strand: chain 'A' and resid 1236 through 1238 removed outlier: 3.572A pdb=" N LEU A1241 " --> pdb=" O PHE A1238 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1606 through 1608 removed outlier: 3.525A pdb=" N PHE A1709 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1795 through 1797 Processing sheet with id= N, first strand: chain 'A' and resid 1844 through 1849 removed outlier: 6.754A pdb=" N ASN A1862 " --> pdb=" O ASN A1848 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A1871 " --> pdb=" O CYS A1887 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU A1877 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A1881 " --> pdb=" O GLU A1877 " (cutoff:3.500A) removed outlier: 12.578A pdb=" N LYS A1880 " --> pdb=" O THR A1966 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N VAL A1968 " --> pdb=" O LYS A1880 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR A1882 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A1970 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A1966 " --> pdb=" O TYR A1929 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A1929 " --> pdb=" O THR A1966 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1927 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 2084 through 2090 removed outlier: 3.507A pdb=" N PHE A2084 " --> pdb=" O LYS A2102 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3327 1.33 - 1.45: 5068 1.45 - 1.57: 10646 1.57 - 1.69: 96 1.69 - 1.82: 192 Bond restraints: 19329 Sorted by residual: bond pdb=" C2E GTG P 101 " pdb=" C3E GTG P 101 " ideal model delta sigma weight residual 1.254 1.483 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C5B GTG P 101 " pdb=" C6B GTG P 101 " ideal model delta sigma weight residual 1.538 1.328 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C5A GTG P 101 " pdb=" C6A GTG P 101 " ideal model delta sigma weight residual 1.539 1.335 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C3D GTG P 101 " pdb=" C4D GTG P 101 " ideal model delta sigma weight residual 1.298 1.487 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C4B GTG P 101 " pdb=" N3B GTG P 101 " ideal model delta sigma weight residual 1.499 1.337 0.162 2.00e-02 2.50e+03 6.56e+01 ... (remaining 19324 not shown) Histogram of bond angle deviations from ideal: 94.69 - 102.62: 163 102.62 - 110.54: 5252 110.54 - 118.46: 10362 118.46 - 126.38: 10188 126.38 - 134.31: 335 Bond angle restraints: 26300 Sorted by residual: angle pdb=" C1D GTG P 101 " pdb=" N9A GTG P 101 " pdb=" C4A GTG P 101 " ideal model delta sigma weight residual 93.21 126.21 -33.00 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C1D GTG P 101 " pdb=" N9A GTG P 101 " pdb=" C8A GTG P 101 " ideal model delta sigma weight residual 157.61 125.45 32.16 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C1E GTG P 101 " pdb=" N9B GTG P 101 " pdb=" C4B GTG P 101 " ideal model delta sigma weight residual 152.69 126.73 25.96 3.00e+00 1.11e-01 7.49e+01 angle pdb=" C1E GTG P 101 " pdb=" N9B GTG P 101 " pdb=" C8B GTG P 101 " ideal model delta sigma weight residual 99.21 124.87 -25.66 3.00e+00 1.11e-01 7.32e+01 angle pdb=" N PRO A2218 " pdb=" CA PRO A2218 " pdb=" C PRO A2218 " ideal model delta sigma weight residual 113.84 105.74 8.10 1.30e+00 5.92e-01 3.89e+01 ... (remaining 26295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 11499 35.09 - 70.19: 276 70.19 - 105.28: 30 105.28 - 140.38: 1 140.38 - 175.47: 3 Dihedral angle restraints: 11809 sinusoidal: 5330 harmonic: 6479 Sorted by residual: dihedral pdb=" O4' U P 9 " pdb=" C1' U P 9 " pdb=" N1 U P 9 " pdb=" C2 U P 9 " ideal model delta sinusoidal sigma weight residual 232.00 56.53 175.47 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U P 7 " pdb=" C1' U P 7 " pdb=" N1 U P 7 " pdb=" C2 U P 7 " ideal model delta sinusoidal sigma weight residual 232.00 58.73 173.27 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O2 POP A2302 " pdb=" O POP A2302 " pdb=" P1 POP A2302 " pdb=" P2 POP A2302 " ideal model delta sinusoidal sigma weight residual -88.77 59.07 -147.83 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 11806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2573 0.084 - 0.168: 316 0.168 - 0.252: 58 0.252 - 0.336: 11 0.336 - 0.420: 4 Chirality restraints: 2962 Sorted by residual: chirality pdb=" CA TYR A1364 " pdb=" N TYR A1364 " pdb=" C TYR A1364 " pdb=" CB TYR A1364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" C3E GTG P 101 " pdb=" C2E GTG P 101 " pdb=" C4E GTG P 101 " pdb=" O3E GTG P 101 " both_signs ideal model delta sigma weight residual False -2.43 -2.82 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA TYR A1576 " pdb=" N TYR A1576 " pdb=" C TYR A1576 " pdb=" CB TYR A1576 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 2959 not shown) Planarity restraints: 3157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1593 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C LEU A1593 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A1593 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A1594 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1655 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C PHE A1655 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A1655 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A1656 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1571 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLN A1571 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A1571 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A1572 " -0.014 2.00e-02 2.50e+03 ... (remaining 3154 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 396 2.69 - 3.24: 18843 3.24 - 3.79: 30634 3.79 - 4.35: 41710 4.35 - 4.90: 66353 Nonbonded interactions: 157936 Sorted by model distance: nonbonded pdb=" OD1 ASP A1188 " pdb="MG MG A2301 " model vdw 2.134 2.170 nonbonded pdb=" O ILE A2118 " pdb=" OG1 THR A2122 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR A2109 " pdb=" OD1 ASN A2112 " model vdw 2.271 2.440 nonbonded pdb=" OD2 ASP A1776 " pdb=" OG SER A1998 " model vdw 2.304 2.440 nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2303 " model vdw 2.312 2.230 ... (remaining 157931 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=0.74 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 17.580 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 63.530 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.007 0.229 19329 Z= 0.424 Angle : 0.915 32.999 26300 Z= 0.587 Chirality : 0.060 0.420 2962 Planarity : 0.004 0.059 3157 Dihedral : 15.412 175.469 7603 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 0.94 % Allowed : 2.19 % Favored : 96.87 % Cbeta Deviations : 0.10 % 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 (0.18), residues: 2169 helix: 1.79 (0.16), residues: 1088 sheet: 1.08 (0.42), residues: 169 loop : -0.95 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2219 HIS 0.005 0.001 HIS A 760 PHE 0.022 0.001 PHE A2207 TYR 0.019 0.001 TYR A1364 ARG 0.005 0.000 ARG A1829 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 CYS cc_start: 0.7754 (m) cc_final: 0.7480 (m) REVERT: A 58 ILE cc_start: 0.9156 (mt) cc_final: 0.8786 (mt) REVERT: A 765 ASP cc_start: 0.8377 (t70) cc_final: 0.8151 (t0) REVERT: A 779 GLU cc_start: 0.8150 (tt0) cc_final: 0.7880 (tp30) REVERT: A 995 ASP cc_start: 0.7844 (p0) cc_final: 0.7568 (p0) REVERT: A 1501 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: A 1613 PHE cc_start: 0.8121 (t80) cc_final: 0.7624 (t80) REVERT: A 2035 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7471 (mm-30) outliers start: 19 outliers final: 4 residues processed: 229 average time/residue: 0.3238 time to fit residues: 114.5205 Evaluate side-chains 164 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 1501 GLN Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1829 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.0050 chunk 89 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 397 GLN A 819 ASN A 932 GLN A 985 ASN A1280 GLN A1855 HIS A2179 HIS ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19329 Z= 0.150 Angle : 0.495 6.770 26300 Z= 0.265 Chirality : 0.039 0.154 2962 Planarity : 0.004 0.050 3157 Dihedral : 13.414 175.649 3088 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.29 % Allowed : 7.55 % Favored : 91.15 % 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: 0.84 (0.18), residues: 2169 helix: 1.69 (0.16), residues: 1090 sheet: 0.98 (0.42), residues: 166 loop : -0.94 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2160 HIS 0.009 0.001 HIS A2179 PHE 0.023 0.001 PHE A1787 TYR 0.021 0.001 TYR A 3 ARG 0.004 0.000 ARG A1784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8253 (ptp) cc_final: 0.7899 (ptm) REVERT: A 765 ASP cc_start: 0.8388 (t70) cc_final: 0.8163 (t0) REVERT: A 779 GLU cc_start: 0.8071 (tt0) cc_final: 0.7800 (tp30) REVERT: A 1350 GLU cc_start: 0.7749 (mp0) cc_final: 0.7545 (pm20) REVERT: A 1482 MET cc_start: 0.8579 (mmm) cc_final: 0.8344 (mtt) outliers start: 26 outliers final: 13 residues processed: 196 average time/residue: 0.2955 time to fit residues: 90.9039 Evaluate side-chains 168 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 2070 ILE Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2179 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 136 optimal weight: 0.0370 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 0.0270 chunk 217 optimal weight: 0.3980 chunk 179 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A1280 GLN A2179 HIS A2225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19329 Z= 0.169 Angle : 0.477 6.310 26300 Z= 0.254 Chirality : 0.039 0.140 2962 Planarity : 0.003 0.048 3157 Dihedral : 13.300 176.563 3081 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 1.44 % Allowed : 9.54 % Favored : 89.02 % 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: 0.84 (0.18), residues: 2169 helix: 1.70 (0.16), residues: 1090 sheet: 0.91 (0.42), residues: 166 loop : -0.95 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2160 HIS 0.019 0.001 HIS A2179 PHE 0.017 0.001 PHE A1787 TYR 0.015 0.001 TYR A 49 ARG 0.004 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 2.387 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8294 (ptp) cc_final: 0.7942 (ptm) REVERT: A 737 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 765 ASP cc_start: 0.8363 (t70) cc_final: 0.8131 (t0) REVERT: A 779 GLU cc_start: 0.8056 (tt0) cc_final: 0.7747 (tp30) REVERT: A 975 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7120 (mp0) REVERT: A 1858 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6346 (mmp) outliers start: 29 outliers final: 13 residues processed: 176 average time/residue: 0.3027 time to fit residues: 84.4117 Evaluate side-chains 166 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1858 MET Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN A1377 GLN A1842 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19329 Z= 0.150 Angle : 0.456 6.690 26300 Z= 0.242 Chirality : 0.038 0.138 2962 Planarity : 0.003 0.046 3157 Dihedral : 13.199 176.494 3079 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 1.69 % Allowed : 10.04 % Favored : 88.27 % 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: 0.89 (0.18), residues: 2169 helix: 1.75 (0.16), residues: 1089 sheet: 0.96 (0.43), residues: 166 loop : -0.94 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A2219 HIS 0.004 0.001 HIS A2179 PHE 0.014 0.001 PHE A1787 TYR 0.012 0.001 TYR A1576 ARG 0.002 0.000 ARG A1985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 2.293 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8318 (ptp) cc_final: 0.7952 (ptm) REVERT: A 765 ASP cc_start: 0.8370 (t70) cc_final: 0.8138 (t0) REVERT: A 779 GLU cc_start: 0.8036 (tt0) cc_final: 0.7695 (tp30) REVERT: A 975 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7090 (mp0) REVERT: A 1839 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7162 (pmm) outliers start: 34 outliers final: 17 residues processed: 184 average time/residue: 0.2814 time to fit residues: 84.1541 Evaluate side-chains 167 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1521 PHE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN A1693 GLN A1755 HIS A2049 ASN A2134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19329 Z= 0.295 Angle : 0.520 7.770 26300 Z= 0.275 Chirality : 0.041 0.142 2962 Planarity : 0.004 0.046 3157 Dihedral : 13.256 178.137 3079 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.69 % Allowed : 10.54 % 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: 0.74 (0.18), residues: 2169 helix: 1.66 (0.16), residues: 1097 sheet: 0.87 (0.43), residues: 159 loop : -1.06 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2219 HIS 0.004 0.001 HIS A1591 PHE 0.024 0.001 PHE A1768 TYR 0.016 0.001 TYR A1402 ARG 0.003 0.000 ARG A1829 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 2.402 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8357 (ptp) cc_final: 0.7977 (ptm) REVERT: A 61 ASP cc_start: 0.6536 (m-30) cc_final: 0.6326 (m-30) REVERT: A 737 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8649 (p) REVERT: A 765 ASP cc_start: 0.8433 (t70) cc_final: 0.8179 (t0) REVERT: A 779 GLU cc_start: 0.8126 (tt0) cc_final: 0.7727 (tp30) REVERT: A 975 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7309 (mp0) REVERT: A 1610 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7465 (tpt) REVERT: A 1839 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7389 (pmm) outliers start: 34 outliers final: 21 residues processed: 177 average time/residue: 0.2835 time to fit residues: 81.8525 Evaluate side-chains 174 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 MET Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1755 HIS Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 HIS A1621 HIS A1658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19329 Z= 0.228 Angle : 0.499 8.592 26300 Z= 0.263 Chirality : 0.040 0.137 2962 Planarity : 0.003 0.045 3157 Dihedral : 13.227 177.593 3079 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.54 % Allowed : 11.63 % Favored : 86.83 % 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: 0.74 (0.18), residues: 2169 helix: 1.66 (0.16), residues: 1094 sheet: 0.73 (0.43), residues: 165 loop : -1.04 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2219 HIS 0.007 0.001 HIS A1755 PHE 0.019 0.001 PHE A1768 TYR 0.018 0.001 TYR A 3 ARG 0.002 0.000 ARG A1829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 2.179 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8365 (ptp) cc_final: 0.7967 (ptm) REVERT: A 61 ASP cc_start: 0.6527 (m-30) cc_final: 0.6311 (m-30) REVERT: A 737 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8645 (p) REVERT: A 765 ASP cc_start: 0.8428 (t70) cc_final: 0.8178 (t0) REVERT: A 779 GLU cc_start: 0.8126 (tt0) cc_final: 0.7698 (tp30) REVERT: A 975 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7588 (mp0) REVERT: A 1214 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 1839 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7377 (pmm) outliers start: 31 outliers final: 20 residues processed: 177 average time/residue: 0.2908 time to fit residues: 82.5612 Evaluate side-chains 173 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2207 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2046 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19329 Z= 0.137 Angle : 0.459 7.038 26300 Z= 0.243 Chirality : 0.038 0.161 2962 Planarity : 0.003 0.045 3157 Dihedral : 13.126 176.588 3079 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.24 % Allowed : 12.28 % Favored : 86.48 % 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: 0.86 (0.18), residues: 2169 helix: 1.78 (0.16), residues: 1087 sheet: 0.69 (0.43), residues: 165 loop : -0.95 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1143 HIS 0.004 0.000 HIS A 760 PHE 0.015 0.001 PHE A2184 TYR 0.011 0.001 TYR A1163 ARG 0.002 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8367 (ptp) cc_final: 0.7968 (ptm) REVERT: A 61 ASP cc_start: 0.6580 (m-30) cc_final: 0.6336 (m-30) REVERT: A 737 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8652 (p) REVERT: A 765 ASP cc_start: 0.8376 (t70) cc_final: 0.8142 (t0) REVERT: A 779 GLU cc_start: 0.8096 (tt0) cc_final: 0.7674 (tp30) REVERT: A 975 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7525 (mp0) REVERT: A 1613 PHE cc_start: 0.8163 (t80) cc_final: 0.7728 (t80) REVERT: A 1839 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7249 (pmm) outliers start: 25 outliers final: 17 residues processed: 180 average time/residue: 0.2887 time to fit residues: 84.4025 Evaluate side-chains 174 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 2093 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19329 Z= 0.162 Angle : 0.473 9.344 26300 Z= 0.249 Chirality : 0.039 0.186 2962 Planarity : 0.003 0.044 3157 Dihedral : 13.099 177.232 3079 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.04 % Allowed : 12.92 % Favored : 86.03 % 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: 0.83 (0.18), residues: 2169 helix: 1.76 (0.16), residues: 1095 sheet: 0.59 (0.42), residues: 165 loop : -0.99 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2201 HIS 0.003 0.001 HIS A 760 PHE 0.015 0.001 PHE A1768 TYR 0.014 0.001 TYR A1402 ARG 0.002 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8383 (ptp) cc_final: 0.7972 (ptm) REVERT: A 61 ASP cc_start: 0.6565 (m-30) cc_final: 0.6321 (m-30) REVERT: A 231 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: A 737 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 765 ASP cc_start: 0.8381 (t70) cc_final: 0.8149 (t0) REVERT: A 779 GLU cc_start: 0.8113 (tt0) cc_final: 0.7674 (tp30) REVERT: A 1613 PHE cc_start: 0.8159 (t80) cc_final: 0.7696 (t80) REVERT: A 1839 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7243 (pmm) REVERT: A 2180 MET cc_start: 0.7380 (tpt) cc_final: 0.7100 (tpt) outliers start: 21 outliers final: 14 residues processed: 171 average time/residue: 0.2920 time to fit residues: 80.1002 Evaluate side-chains 168 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 2093 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 179 optimal weight: 0.1980 chunk 187 optimal weight: 0.9980 chunk 197 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19329 Z= 0.125 Angle : 0.464 7.927 26300 Z= 0.244 Chirality : 0.038 0.167 2962 Planarity : 0.003 0.043 3157 Dihedral : 13.028 176.584 3079 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.94 % Allowed : 13.07 % Favored : 85.98 % 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: 0.82 (0.19), residues: 2169 helix: 1.78 (0.16), residues: 1093 sheet: 0.60 (0.41), residues: 177 loop : -1.05 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1143 HIS 0.004 0.000 HIS A 760 PHE 0.012 0.001 PHE A1768 TYR 0.011 0.001 TYR A1402 ARG 0.002 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8378 (ptp) cc_final: 0.7981 (ptm) REVERT: A 61 ASP cc_start: 0.6512 (m-30) cc_final: 0.6272 (m-30) REVERT: A 231 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: A 737 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 765 ASP cc_start: 0.8369 (t70) cc_final: 0.8145 (t0) REVERT: A 1613 PHE cc_start: 0.8114 (t80) cc_final: 0.7666 (t80) REVERT: A 1839 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7108 (pmm) outliers start: 19 outliers final: 14 residues processed: 176 average time/residue: 0.2904 time to fit residues: 82.6765 Evaluate side-chains 167 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 2093 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19329 Z= 0.169 Angle : 0.478 8.379 26300 Z= 0.250 Chirality : 0.039 0.157 2962 Planarity : 0.003 0.043 3157 Dihedral : 13.021 177.429 3079 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 0.94 % Allowed : 13.17 % Favored : 85.88 % 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: 0.86 (0.18), residues: 2169 helix: 1.82 (0.16), residues: 1094 sheet: 0.58 (0.41), residues: 170 loop : -1.02 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2201 HIS 0.003 0.001 HIS A1944 PHE 0.014 0.001 PHE A1768 TYR 0.014 0.001 TYR A1402 ARG 0.002 0.000 ARG A1890 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8388 (ptp) cc_final: 0.8002 (ptm) REVERT: A 61 ASP cc_start: 0.6473 (m-30) cc_final: 0.6229 (m-30) REVERT: A 231 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: A 737 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8650 (p) REVERT: A 765 ASP cc_start: 0.8390 (t70) cc_final: 0.8156 (t0) REVERT: A 975 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7254 (mp0) REVERT: A 1613 PHE cc_start: 0.8128 (t80) cc_final: 0.7687 (t80) REVERT: A 1839 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7126 (pmm) outliers start: 19 outliers final: 15 residues processed: 168 average time/residue: 0.2907 time to fit residues: 79.0693 Evaluate side-chains 170 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1744 ILE Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 2093 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.0040 chunk 53 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 154 optimal weight: 0.4980 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.062168 restraints weight = 56588.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064141 restraints weight = 28509.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065440 restraints weight = 18754.059| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19329 Z= 0.122 Angle : 0.462 8.374 26300 Z= 0.242 Chirality : 0.038 0.153 2962 Planarity : 0.003 0.043 3157 Dihedral : 12.941 176.570 3079 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 0.89 % Allowed : 13.22 % Favored : 85.88 % 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: 0.86 (0.19), residues: 2169 helix: 1.81 (0.16), residues: 1095 sheet: 0.65 (0.41), residues: 177 loop : -1.05 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1143 HIS 0.004 0.000 HIS A1944 PHE 0.014 0.001 PHE A2184 TYR 0.010 0.001 TYR A1402 ARG 0.002 0.000 ARG A 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.09 seconds wall clock time: 63 minutes 7.52 seconds (3787.52 seconds total)