Starting phenix.real_space_refine on Wed Apr 10 03:23:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orm_13042/04_2024/7orm_13042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orm_13042/04_2024/7orm_13042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orm_13042/04_2024/7orm_13042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orm_13042/04_2024/7orm_13042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orm_13042/04_2024/7orm_13042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orm_13042/04_2024/7orm_13042.pdb" } resolution = 3.3 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= 0.002 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 Zn 1 6.06 5 P 40 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 11581 2.51 5 N 3077 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ASP 699": "OD1" <-> "OD2" Residue "A ASP 713": "OD1" <-> "OD2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "A GLU 783": "OE1" <-> "OE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 913": "OD1" <-> "OD2" Residue "A TYR 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A GLU 1002": "OE1" <-> "OE2" Residue "A GLU 1006": "OE1" <-> "OE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A GLU 1324": "OE1" <-> "OE2" Residue "A ASP 1388": "OD1" <-> "OD2" Residue "A GLU 1408": "OE1" <-> "OE2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A PHE 1432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1520": "OD1" <-> "OD2" Residue "A TYR 1528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1581": "OD1" <-> "OD2" Residue "A GLU 1612": "OE1" <-> "OE2" Residue "A GLU 1654": "OE1" <-> "OE2" Residue "A TYR 1696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1703": "OE1" <-> "OE2" Residue "A TYR 1813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1837": "OD1" <-> "OD2" Residue "A TYR 1925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2005": "OD1" <-> "OD2" Residue "A PHE 2096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2127": "OE1" <-> "OE2" Residue "A TYR 2181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2224": "OE1" <-> "OE2" Residue "A PHE 2238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18369 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 10} Chain: "A" Number of atoms: 17518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2147, 17518 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'peptide': 2145, 'undetermined': 2} Link IDs: {'PTRANS': 70, 'TRANS': 2074, None: 2} Not linked: pdbres="MET A2251 " pdbres=" ZN A2301 " Not linked: pdbres=" ZN A2301 " pdbres=" MG A2302 " Chain breaks: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16896 SG CYS A2064 61.779 37.228 30.093 1.00 92.99 S Time building chain proxies: 9.70, per 1000 atoms: 0.53 Number of scatterers: 18369 At special positions: 0 Unit cell: (106.485, 137.4, 139.69, 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 113 16.00 P 40 15.00 Mg 1 11.99 O 3556 8.00 N 3077 7.00 C 11581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4136 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 17 sheets defined 56.7% alpha, 10.0% beta 10 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 6.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 46 removed outlier: 3.956A pdb=" N LYS A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 99 through 121 removed outlier: 4.446A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.598A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.540A pdb=" N MET A 214 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 262 removed outlier: 3.704A pdb=" N LYS A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 6.104A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 502 through 523 removed outlier: 3.793A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 620 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 626 through 639 removed outlier: 3.690A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 3.983A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.055A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 680 through 700 removed outlier: 3.600A pdb=" N PHE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 758 through 780 removed outlier: 4.157A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 814 removed outlier: 3.580A pdb=" N HIS A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 830 through 838 removed outlier: 5.943A pdb=" N SER A 835 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 836 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.572A pdb=" N GLN A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 983 removed outlier: 3.807A pdb=" N ARG A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1020 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 4.011A pdb=" N PHE A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.554A pdb=" N ASP A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.886A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1267 through 1285 removed outlier: 3.509A pdb=" N ASP A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1317 through 1321 removed outlier: 3.852A pdb=" N PHE A1321 " --> pdb=" O ILE A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1340 through 1348 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1373 through 1380 removed outlier: 3.690A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1384 Processing helix chain 'A' and resid 1390 through 1403 Processing helix chain 'A' and resid 1418 through 1422 removed outlier: 3.522A pdb=" N ARG A1422 " --> pdb=" O SER A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1455 through 1467 removed outlier: 3.969A pdb=" N GLU A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1460 " --> pdb=" O GLY A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1472 removed outlier: 3.883A pdb=" N VAL A1472 " --> pdb=" O GLU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1491 through 1499 Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.555A pdb=" N LEU A1506 " --> pdb=" O ASN A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1528 removed outlier: 4.048A pdb=" N TYR A1528 " --> pdb=" O ILE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1563 removed outlier: 3.952A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1622 through 1632 removed outlier: 3.654A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1660 Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1680 through 1700 Processing helix chain 'A' and resid 1717 through 1729 Processing helix chain 'A' and resid 1760 through 1779 Processing helix chain 'A' and resid 1783 through 1795 Processing helix chain 'A' and resid 1802 through 1811 Processing helix chain 'A' and resid 1818 through 1825 Processing helix chain 'A' and resid 1830 through 1841 Processing helix chain 'A' and resid 1892 through 1904 Processing helix chain 'A' and resid 1944 through 1954 Processing helix chain 'A' and resid 1983 through 1991 Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.614A pdb=" N LYS A2017 " --> pdb=" O HIS A2014 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2046 through 2052 removed outlier: 3.519A pdb=" N ILE A2050 " --> pdb=" O ASN A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2059 Processing helix chain 'A' and resid 2060 through 2062 No H-bonds generated for 'chain 'A' and resid 2060 through 2062' Processing helix chain 'A' and resid 2069 through 2075 removed outlier: 3.591A pdb=" N GLY A2073 " --> pdb=" O ASN A2069 " (cutoff:3.500A) Processing helix chain 'A' and resid 2109 through 2127 Processing helix chain 'A' and resid 2138 through 2155 Processing helix chain 'A' and resid 2158 through 2175 Processing helix chain 'A' and resid 2177 through 2183 Processing helix chain 'A' and resid 2200 through 2210 Processing helix chain 'A' and resid 2216 through 2238 removed outlier: 4.679A pdb=" N VAL A2221 " --> pdb=" O PRO A2217 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A2238 " --> pdb=" O ILE A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2251 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.457A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS A 94 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 387 removed outlier: 6.975A pdb=" N VAL A 393 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET A 400 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A 395 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 387 removed outlier: 6.975A pdb=" N VAL A 393 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET A 400 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A 395 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 716 through 717 removed outlier: 6.586A pdb=" N ILE A 709 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N SER A2101 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LEU A 711 " --> pdb=" O SER A2101 " (cutoff:3.500A) removed outlier: 11.602A pdb=" N ARG A2103 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA7, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AA8, first strand: chain 'A' and resid 959 through 962 removed outlier: 6.259A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1177 through 1184 removed outlier: 3.665A pdb=" N GLN A1197 " --> pdb=" O LYS A1051 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1236 through 1237 Processing sheet with id=AB2, first strand: chain 'A' and resid 1519 through 1520 Processing sheet with id=AB3, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id=AB4, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id=AB5, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB6, first strand: chain 'A' and resid 1865 through 1867 removed outlier: 7.456A pdb=" N THR A1882 " --> pdb=" O VAL A1970 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASN A1972 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A1884 " --> pdb=" O ASN A1972 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA A1974 " --> pdb=" O ALA A1884 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A1886 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A1927 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1940 " --> pdb=" O THR A1928 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A1930 " --> pdb=" O VAL A1938 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A1938 " --> pdb=" O ARG A1930 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AB8, first strand: chain 'A' and resid 2027 through 2028 918 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 10.66 Time building geometry restraints manager: 7.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2942 1.30 - 1.43: 5094 1.43 - 1.56: 10520 1.56 - 1.69: 77 1.69 - 1.82: 187 Bond restraints: 18820 Sorted by residual: bond pdb=" C ASN A 826 " pdb=" O ASN A 826 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.30e-02 5.92e+03 1.85e+01 bond pdb=" C PRO A1288 " pdb=" O PRO A1288 " ideal model delta sigma weight residual 1.243 1.209 0.035 8.50e-03 1.38e+04 1.66e+01 bond pdb=" N ILE A1730 " pdb=" CA ILE A1730 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.31e+01 bond pdb=" N ILE A1637 " pdb=" CA ILE A1637 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.14e+01 bond pdb=" CA SER A1192 " pdb=" CB SER A1192 " ideal model delta sigma weight residual 1.531 1.480 0.051 1.52e-02 4.33e+03 1.12e+01 ... (remaining 18815 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.43: 487 105.43 - 112.63: 9864 112.63 - 119.83: 6521 119.83 - 127.03: 8447 127.03 - 134.23: 245 Bond angle restraints: 25564 Sorted by residual: angle pdb=" N TYR A 714 " pdb=" CA TYR A 714 " pdb=" C TYR A 714 " ideal model delta sigma weight residual 113.97 105.53 8.44 1.28e+00 6.10e-01 4.34e+01 angle pdb=" CA ILE A1057 " pdb=" C ILE A1057 " pdb=" O ILE A1057 " ideal model delta sigma weight residual 122.63 117.67 4.96 8.70e-01 1.32e+00 3.25e+01 angle pdb=" CA ASN A 826 " pdb=" C ASN A 826 " pdb=" O ASN A 826 " ideal model delta sigma weight residual 121.65 115.25 6.40 1.17e+00 7.31e-01 2.99e+01 angle pdb=" N LEU A1828 " pdb=" CA LEU A1828 " pdb=" C LEU A1828 " ideal model delta sigma weight residual 112.93 105.73 7.20 1.33e+00 5.65e-01 2.93e+01 angle pdb=" N PRO A2217 " pdb=" CA PRO A2217 " pdb=" C PRO A2217 " ideal model delta sigma weight residual 110.70 117.24 -6.54 1.22e+00 6.72e-01 2.87e+01 ... (remaining 25559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 11235 34.69 - 69.39: 256 69.39 - 104.08: 22 104.08 - 138.77: 0 138.77 - 173.47: 1 Dihedral angle restraints: 11514 sinusoidal: 5146 harmonic: 6368 Sorted by residual: 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 -128.00 45.47 -173.47 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" C5' A P 8 " pdb=" C4' A P 8 " pdb=" C3' A P 8 " pdb=" O3' A P 8 " ideal model delta sinusoidal sigma weight residual 147.00 112.47 34.53 1 8.00e+00 1.56e-02 2.64e+01 dihedral pdb=" CA TRP A1143 " pdb=" C TRP A1143 " pdb=" N LEU A1144 " pdb=" CA LEU A1144 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 11511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2410 0.059 - 0.117: 370 0.117 - 0.176: 66 0.176 - 0.234: 26 0.234 - 0.293: 5 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA ASP A 35 " pdb=" N ASP A 35 " pdb=" C ASP A 35 " pdb=" CB ASP A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE A1637 " pdb=" N ILE A1637 " pdb=" C ILE A1637 " pdb=" CB ILE A1637 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE A1706 " pdb=" CA ILE A1706 " pdb=" CG1 ILE A1706 " pdb=" CG2 ILE A1706 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2874 not shown) Planarity restraints: 3093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1368 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C MET A1368 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A1368 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A1369 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1826 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C GLY A1826 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY A1826 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP A1827 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A2118 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C ILE A2118 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE A2118 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A2119 " 0.016 2.00e-02 2.50e+03 ... (remaining 3090 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 81 2.58 - 3.16: 15299 3.16 - 3.74: 28822 3.74 - 4.32: 40977 4.32 - 4.90: 67783 Nonbonded interactions: 152962 Sorted by model distance: nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 2.004 2.230 nonbonded pdb=" OD1 ASP A1188 " pdb="MG MG A2302 " model vdw 2.041 2.170 nonbonded pdb=" OG SER A1443 " pdb=" OH TYR A1489 " model vdw 2.291 2.440 nonbonded pdb=" O ILE A1875 " pdb=" OG1 THR A1882 " model vdw 2.335 2.440 nonbonded pdb=" OD1 ASN A1924 " pdb=" OH TYR A1926 " model vdw 2.366 2.440 ... (remaining 152957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.030 Extract box with map and model: 4.730 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 61.570 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18820 Z= 0.275 Angle : 0.705 8.437 25564 Z= 0.478 Chirality : 0.049 0.293 2877 Planarity : 0.004 0.043 3093 Dihedral : 14.428 173.466 7378 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 0.20 % Allowed : 1.51 % Favored : 98.28 % Cbeta Deviations : 0.05 % 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: 0.73 (0.18), residues: 2127 helix: 1.72 (0.16), residues: 1109 sheet: 0.31 (0.43), residues: 149 loop : -1.15 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2160 HIS 0.003 0.001 HIS A1749 PHE 0.032 0.001 PHE A 511 TYR 0.013 0.001 TYR A1463 ARG 0.006 0.000 ARG A2205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 2.091 Fit side-chains REVERT: A 417 ASN cc_start: 0.8351 (m-40) cc_final: 0.8058 (m-40) REVERT: A 553 LYS cc_start: 0.8088 (mptt) cc_final: 0.7656 (mttp) REVERT: A 714 TYR cc_start: 0.6397 (m-80) cc_final: 0.6164 (m-80) REVERT: A 1430 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7528 (mmt-90) REVERT: A 2160 TRP cc_start: 0.7619 (m-10) cc_final: 0.7194 (m-10) outliers start: 4 outliers final: 3 residues processed: 232 average time/residue: 0.3410 time to fit residues: 119.4739 Evaluate side-chains 171 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1825 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 HIS A 823 ASN A 952 GLN A1007 GLN A1223 GLN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18820 Z= 0.268 Angle : 0.533 8.634 25564 Z= 0.285 Chirality : 0.042 0.170 2877 Planarity : 0.004 0.045 3093 Dihedral : 12.250 169.528 2929 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.76 % Allowed : 6.11 % Favored : 93.13 % 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: 0.92 (0.18), residues: 2127 helix: 1.90 (0.16), residues: 1127 sheet: 0.80 (0.41), residues: 158 loop : -1.29 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1143 HIS 0.007 0.001 HIS A2169 PHE 0.028 0.002 PHE A 511 TYR 0.016 0.001 TYR A 750 ARG 0.003 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 2.015 Fit side-chains REVERT: A 417 ASN cc_start: 0.8254 (m-40) cc_final: 0.7967 (m-40) REVERT: A 553 LYS cc_start: 0.8075 (mptt) cc_final: 0.7571 (mttp) REVERT: A 825 ASN cc_start: 0.8700 (m110) cc_final: 0.8314 (m110) REVERT: A 1430 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7540 (mmt-90) REVERT: A 2038 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8786 (mtpt) REVERT: A 2160 TRP cc_start: 0.7678 (m-10) cc_final: 0.7294 (m-10) REVERT: A 2180 MET cc_start: 0.6923 (tpt) cc_final: 0.6623 (tpt) outliers start: 15 outliers final: 11 residues processed: 184 average time/residue: 0.3360 time to fit residues: 93.6586 Evaluate side-chains 171 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 2041 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN A1112 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18820 Z= 0.169 Angle : 0.474 7.567 25564 Z= 0.253 Chirality : 0.039 0.178 2877 Planarity : 0.003 0.047 3093 Dihedral : 12.185 171.050 2926 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.01 % Allowed : 7.52 % Favored : 91.47 % 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: 1.06 (0.18), residues: 2127 helix: 1.99 (0.16), residues: 1133 sheet: 1.01 (0.41), residues: 158 loop : -1.24 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1143 HIS 0.005 0.001 HIS A2169 PHE 0.017 0.001 PHE A1768 TYR 0.012 0.001 TYR A 677 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.982 Fit side-chains REVERT: A 417 ASN cc_start: 0.8218 (m-40) cc_final: 0.7998 (m-40) REVERT: A 553 LYS cc_start: 0.8046 (mptt) cc_final: 0.7585 (mttp) REVERT: A 788 ASN cc_start: 0.8347 (p0) cc_final: 0.8018 (p0) REVERT: A 825 ASN cc_start: 0.8588 (m110) cc_final: 0.8338 (m-40) REVERT: A 1173 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 1430 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7524 (mmt-90) REVERT: A 2038 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8865 (mtpt) REVERT: A 2054 ASN cc_start: 0.7608 (t0) cc_final: 0.7369 (t0) REVERT: A 2160 TRP cc_start: 0.7700 (m-10) cc_final: 0.7231 (m-10) outliers start: 20 outliers final: 11 residues processed: 198 average time/residue: 0.3282 time to fit residues: 100.2995 Evaluate side-chains 178 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 2041 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A1112 ASN A1116 GLN ** A1334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 GLN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18820 Z= 0.237 Angle : 0.494 9.052 25564 Z= 0.263 Chirality : 0.040 0.209 2877 Planarity : 0.004 0.048 3093 Dihedral : 12.149 171.067 2926 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.26 % Allowed : 8.63 % Favored : 90.11 % 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: 1.09 (0.18), residues: 2127 helix: 2.04 (0.16), residues: 1127 sheet: 1.03 (0.41), residues: 158 loop : -1.23 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.005 0.001 HIS A2169 PHE 0.019 0.001 PHE A1768 TYR 0.014 0.001 TYR A 750 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 2.163 Fit side-chains REVERT: A 553 LYS cc_start: 0.7999 (mptt) cc_final: 0.7551 (mttp) REVERT: A 788 ASN cc_start: 0.8388 (p0) cc_final: 0.8031 (p0) REVERT: A 825 ASN cc_start: 0.8680 (m110) cc_final: 0.8430 (m-40) REVERT: A 1430 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7549 (mmt-90) REVERT: A 1645 MET cc_start: 0.8632 (tpp) cc_final: 0.8119 (tpp) REVERT: A 2054 ASN cc_start: 0.7617 (t0) cc_final: 0.7395 (t0) REVERT: A 2160 TRP cc_start: 0.7630 (m-10) cc_final: 0.7198 (m-10) outliers start: 25 outliers final: 19 residues processed: 189 average time/residue: 0.3343 time to fit residues: 96.5548 Evaluate side-chains 184 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2093 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A1334 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18820 Z= 0.257 Angle : 0.501 7.937 25564 Z= 0.267 Chirality : 0.041 0.165 2877 Planarity : 0.004 0.048 3093 Dihedral : 12.132 170.201 2926 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.87 % Allowed : 9.64 % Favored : 88.49 % 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: 1.03 (0.18), residues: 2127 helix: 1.96 (0.16), residues: 1132 sheet: 1.15 (0.41), residues: 156 loop : -1.26 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.005 0.001 HIS A2169 PHE 0.020 0.001 PHE A1768 TYR 0.015 0.001 TYR A 677 ARG 0.004 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 2.062 Fit side-chains REVERT: A 553 LYS cc_start: 0.7958 (mptt) cc_final: 0.7553 (mttp) REVERT: A 788 ASN cc_start: 0.8319 (p0) cc_final: 0.7923 (p0) REVERT: A 825 ASN cc_start: 0.8703 (m110) cc_final: 0.8449 (m-40) REVERT: A 1430 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7536 (mmt-90) REVERT: A 2080 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: A 2160 TRP cc_start: 0.7645 (m-10) cc_final: 0.7130 (m-10) outliers start: 37 outliers final: 27 residues processed: 196 average time/residue: 0.3369 time to fit residues: 101.2381 Evaluate side-chains 193 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2053 SER Chi-restraints excluded: chain A residue 2080 ASP Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 0.0470 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 174 optimal weight: 0.0970 chunk 97 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN A1334 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18820 Z= 0.160 Angle : 0.472 9.348 25564 Z= 0.250 Chirality : 0.039 0.158 2877 Planarity : 0.003 0.048 3093 Dihedral : 12.092 170.395 2926 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.51 % Allowed : 10.80 % Favored : 87.68 % 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: 1.14 (0.18), residues: 2127 helix: 2.07 (0.16), residues: 1129 sheet: 1.22 (0.41), residues: 156 loop : -1.24 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 PHE 0.019 0.001 PHE A1768 TYR 0.012 0.001 TYR A1230 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 2.256 Fit side-chains REVERT: A 526 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7536 (mtt-85) REVERT: A 553 LYS cc_start: 0.7991 (mptt) cc_final: 0.7580 (mttp) REVERT: A 788 ASN cc_start: 0.8329 (p0) cc_final: 0.7916 (p0) REVERT: A 825 ASN cc_start: 0.8605 (m110) cc_final: 0.8369 (m-40) REVERT: A 1661 LEU cc_start: 0.8804 (mt) cc_final: 0.8572 (mt) REVERT: A 2160 TRP cc_start: 0.7547 (m-10) cc_final: 0.7059 (m-10) outliers start: 30 outliers final: 21 residues processed: 196 average time/residue: 0.3257 time to fit residues: 98.9380 Evaluate side-chains 188 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18820 Z= 0.157 Angle : 0.463 10.216 25564 Z= 0.246 Chirality : 0.039 0.200 2877 Planarity : 0.003 0.049 3093 Dihedral : 12.029 170.867 2925 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.62 % Allowed : 10.95 % Favored : 87.43 % 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: 1.17 (0.18), residues: 2127 helix: 2.10 (0.16), residues: 1130 sheet: 1.25 (0.41), residues: 156 loop : -1.24 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.005 0.001 HIS A2169 PHE 0.019 0.001 PHE A1768 TYR 0.012 0.001 TYR A1230 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: A 526 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7494 (mtt-85) REVERT: A 553 LYS cc_start: 0.7898 (mptt) cc_final: 0.7493 (mttp) REVERT: A 717 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8518 (m) REVERT: A 825 ASN cc_start: 0.8574 (m110) cc_final: 0.8312 (m-40) REVERT: A 1309 MET cc_start: 0.8786 (mtt) cc_final: 0.8404 (mtt) REVERT: A 1661 LEU cc_start: 0.8770 (mt) cc_final: 0.8539 (mt) REVERT: A 2160 TRP cc_start: 0.7498 (m-10) cc_final: 0.6986 (m-10) outliers start: 32 outliers final: 20 residues processed: 206 average time/residue: 0.2587 time to fit residues: 81.0785 Evaluate side-chains 194 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18820 Z= 0.174 Angle : 0.479 10.377 25564 Z= 0.252 Chirality : 0.039 0.186 2877 Planarity : 0.003 0.048 3093 Dihedral : 11.993 170.981 2925 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.46 % Allowed : 11.51 % Favored : 87.03 % 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: 1.20 (0.18), residues: 2127 helix: 2.12 (0.16), residues: 1129 sheet: 1.27 (0.41), residues: 156 loop : -1.23 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 PHE 0.027 0.001 PHE A2226 TYR 0.011 0.001 TYR A1230 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 2.036 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: A 526 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7509 (mtt-85) REVERT: A 553 LYS cc_start: 0.7887 (mptt) cc_final: 0.7484 (mttp) REVERT: A 717 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8595 (m) REVERT: A 825 ASN cc_start: 0.8591 (m110) cc_final: 0.8348 (m-40) REVERT: A 1309 MET cc_start: 0.8809 (mtt) cc_final: 0.8601 (mtp) REVERT: A 1661 LEU cc_start: 0.8768 (mt) cc_final: 0.8536 (mt) REVERT: A 2160 TRP cc_start: 0.7475 (m-10) cc_final: 0.7027 (m-10) outliers start: 29 outliers final: 21 residues processed: 196 average time/residue: 0.3264 time to fit residues: 97.6612 Evaluate side-chains 195 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 194 optimal weight: 0.0870 chunk 117 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 127 optimal weight: 0.2980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1392 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18820 Z= 0.147 Angle : 0.472 10.352 25564 Z= 0.247 Chirality : 0.039 0.262 2877 Planarity : 0.003 0.048 3093 Dihedral : 11.959 171.432 2924 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.26 % Allowed : 11.86 % Favored : 86.88 % 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: 1.26 (0.18), residues: 2127 helix: 2.19 (0.16), residues: 1128 sheet: 1.16 (0.42), residues: 158 loop : -1.20 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 PHE 0.023 0.001 PHE A 363 TYR 0.015 0.001 TYR A1463 ARG 0.006 0.000 ARG A2103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: A 526 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7521 (mtt-85) REVERT: A 553 LYS cc_start: 0.7883 (mptt) cc_final: 0.7475 (mttp) REVERT: A 717 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8587 (m) REVERT: A 825 ASN cc_start: 0.8598 (m110) cc_final: 0.8343 (m-40) REVERT: A 1661 LEU cc_start: 0.8743 (mt) cc_final: 0.8514 (mt) REVERT: A 2160 TRP cc_start: 0.7453 (m-10) cc_final: 0.7039 (m-10) outliers start: 25 outliers final: 21 residues processed: 194 average time/residue: 0.3430 time to fit residues: 101.4488 Evaluate side-chains 191 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 0.0570 chunk 143 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 198 optimal weight: 0.2980 chunk 172 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18820 Z= 0.144 Angle : 0.475 11.025 25564 Z= 0.247 Chirality : 0.039 0.286 2877 Planarity : 0.003 0.048 3093 Dihedral : 11.930 171.874 2924 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.72 % 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: 1.33 (0.18), residues: 2127 helix: 2.23 (0.16), residues: 1130 sheet: 1.21 (0.42), residues: 158 loop : -1.14 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 PHE 0.031 0.001 PHE A 363 TYR 0.014 0.001 TYR A1463 ARG 0.007 0.000 ARG A2103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 2.284 Fit side-chains REVERT: A 7 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: A 526 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7529 (mtt-85) REVERT: A 553 LYS cc_start: 0.7912 (mptt) cc_final: 0.7481 (mttp) REVERT: A 717 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8489 (m) REVERT: A 763 MET cc_start: 0.8507 (mmm) cc_final: 0.8285 (mmt) REVERT: A 825 ASN cc_start: 0.8579 (m110) cc_final: 0.8349 (m-40) REVERT: A 1023 ILE cc_start: 0.7893 (mm) cc_final: 0.7618 (mm) REVERT: A 1661 LEU cc_start: 0.8687 (mt) cc_final: 0.8475 (mt) REVERT: A 2160 TRP cc_start: 0.7436 (m-10) cc_final: 0.7070 (m-10) outliers start: 24 outliers final: 18 residues processed: 190 average time/residue: 0.3492 time to fit residues: 100.6605 Evaluate side-chains 189 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2041 ASP Chi-restraints excluded: chain A residue 2216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089041 restraints weight = 27943.366| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.06 r_work: 0.2884 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18820 Z= 0.227 Angle : 0.503 10.780 25564 Z= 0.263 Chirality : 0.040 0.279 2877 Planarity : 0.004 0.047 3093 Dihedral : 11.936 171.038 2924 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.16 % Allowed : 12.42 % Favored : 86.42 % 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: 1.26 (0.18), residues: 2127 helix: 2.17 (0.16), residues: 1132 sheet: 1.14 (0.42), residues: 158 loop : -1.17 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 PHE 0.027 0.001 PHE A 363 TYR 0.015 0.001 TYR A1320 ARG 0.007 0.000 ARG A2103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.90 seconds wall clock time: 71 minutes 6.51 seconds (4266.51 seconds total)