Starting phenix.real_space_refine on Fri Aug 7 07:40:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vui_65364/08_2026/9vui_65364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vui_65364/08_2026/9vui_65364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vui_65364/08_2026/9vui_65364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vui_65364/08_2026/9vui_65364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vui_65364/08_2026/9vui_65364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vui_65364/08_2026/9vui_65364.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 111 5.16 5 C 12458 2.51 5 N 3331 2.21 5 O 3543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19446 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 988 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 3 Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 241 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain: "D" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 309 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "L" Number of atoms: 15713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1963, 15702 Classifications: {'peptide': 1963} Link IDs: {'PCIS': 1, 'PTRANS': 81, 'TRANS': 1880} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 1963, 15702 Classifications: {'peptide': 1963} Link IDs: {'PCIS': 1, 'PTRANS': 81, 'TRANS': 1880} Chain breaks: 10 bond proxies already assigned to first conformer: 16033 Chain: "X" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 1 Chain: "Y" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 896 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain breaks: 1 Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10374 SG CYS L1132 49.620 36.044 53.693 1.00 72.62 S ATOM 11855 SG CYS L1369 51.483 38.057 51.031 1.00 98.30 S ATOM 11861 SG CYS L1370 49.803 39.541 54.048 1.00 98.27 S ATOM 10740 SG CYS L1177 66.015 50.986 49.686 1.00 64.85 S ATOM 10761 SG CYS L1180 63.414 53.034 47.752 1.00 71.45 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE L 353 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE L 353 " occ=0.50 Time building chain proxies: 5.53, per 1000 atoms: 0.28 Number of scatterers: 19446 At special positions: 0 Unit cell: (107.226, 129.352, 144.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 111 16.00 O 3543 8.00 N 3331 7.00 C 12458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" NE2 HIS L 812 " pdb="ZN ZN L3001 " - pdb=" NE2 HIS L 817 " pdb=" ZN L3002 " pdb="ZN ZN L3002 " - pdb=" SG CYS L1132 " pdb="ZN ZN L3002 " - pdb=" SG CYS L1369 " pdb="ZN ZN L3002 " - pdb=" SG CYS L1370 " pdb=" ZN L3003 " pdb="ZN ZN L3003 " - pdb=" NE2 HIS L1364 " pdb="ZN ZN L3003 " - pdb=" ND1 HIS L1362 " pdb="ZN ZN L3003 " - pdb=" SG CYS L1180 " pdb="ZN ZN L3003 " - pdb=" SG CYS L1177 " Number of angles added : 1 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 11 sheets defined 64.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 342 through 370 removed outlier: 4.053A pdb=" N ILE A 370 " --> pdb=" O HIS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.741A pdb=" N ARG A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 490 through 506 removed outlier: 3.573A pdb=" N MET A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 371 Processing helix chain 'C' and resid 343 through 374 removed outlier: 3.788A pdb=" N ASN C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.885A pdb=" N ASP C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 400 removed outlier: 3.544A pdb=" N ILE C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 368 removed outlier: 3.565A pdb=" N ARG D 355 " --> pdb=" O LYS D 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 32 removed outlier: 3.536A pdb=" N ILE L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 56 Processing helix chain 'L' and resid 59 through 77 Processing helix chain 'L' and resid 90 through 95 Processing helix chain 'L' and resid 103 through 135 removed outlier: 3.871A pdb=" N VAL L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP L 122 " --> pdb=" O SER L 118 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 135 " --> pdb=" O THR L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 151 removed outlier: 3.544A pdb=" N LYS L 148 " --> pdb=" O ASP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 158 Processing helix chain 'L' and resid 161 through 182 removed outlier: 3.570A pdb=" N GLN L 182 " --> pdb=" O VAL L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 248 Processing helix chain 'L' and resid 251 through 273 removed outlier: 3.508A pdb=" N ARG L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG L 259 " --> pdb=" O LEU L 255 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE L 269 " --> pdb=" O ILE L 265 " (cutoff:3.500A) Proline residue: L 270 - end of helix Processing helix chain 'L' and resid 275 through 282 removed outlier: 3.964A pdb=" N ILE L 279 " --> pdb=" O PRO L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 292 removed outlier: 3.658A pdb=" N SER L 287 " --> pdb=" O LEU L 283 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU L 288 " --> pdb=" O GLU L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 295 No H-bonds generated for 'chain 'L' and resid 293 through 295' Processing helix chain 'L' and resid 302 through 319 removed outlier: 4.135A pdb=" N HIS L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN L 319 " --> pdb=" O VAL L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 339 removed outlier: 3.783A pdb=" N TYR L 327 " --> pdb=" O ASP L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 350 removed outlier: 3.582A pdb=" N THR L 346 " --> pdb=" O ASP L 342 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE L 350 " --> pdb=" O THR L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 355 removed outlier: 4.254A pdb=" N ARG L 354 " --> pdb=" O SER L 351 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 355 " --> pdb=" O PHE L 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 351 through 355' Processing helix chain 'L' and resid 362 through 375 removed outlier: 3.820A pdb=" N ALA L 366 " --> pdb=" O GLU L 362 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR L 373 " --> pdb=" O ASN L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 404 removed outlier: 3.639A pdb=" N ARG L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 418 through 428 Processing helix chain 'L' and resid 432 through 439 Processing helix chain 'L' and resid 440 through 444 Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.869A pdb=" N LEU L 464 " --> pdb=" O LEU L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 476 removed outlier: 3.725A pdb=" N TRP L 476 " --> pdb=" O GLN L 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 485 Processing helix chain 'L' and resid 497 through 504 Processing helix chain 'L' and resid 509 through 519 removed outlier: 3.741A pdb=" N VAL L 517 " --> pdb=" O VAL L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 520 through 524 removed outlier: 3.824A pdb=" N LEU L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 567 Processing helix chain 'L' and resid 568 through 571 Processing helix chain 'L' and resid 666 through 671 removed outlier: 3.650A pdb=" N ASN L 670 " --> pdb=" O LYS L 666 " (cutoff:3.500A) Processing helix chain 'L' and resid 672 through 688 removed outlier: 4.616A pdb=" N LEU L 678 " --> pdb=" O GLU L 674 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE L 679 " --> pdb=" O THR L 675 " (cutoff:3.500A) Processing helix chain 'L' and resid 694 through 701 Processing helix chain 'L' and resid 721 through 725 removed outlier: 3.727A pdb=" N VAL L 725 " --> pdb=" O LEU L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 743 through 763 removed outlier: 3.690A pdb=" N ILE L 752 " --> pdb=" O THR L 748 " (cutoff:3.500A) Proline residue: L 753 - end of helix Processing helix chain 'L' and resid 788 through 814 removed outlier: 3.549A pdb=" N ILE L 814 " --> pdb=" O ARG L 810 " (cutoff:3.500A) Processing helix chain 'L' and resid 819 through 823 removed outlier: 3.537A pdb=" N THR L 823 " --> pdb=" O ALA L 820 " (cutoff:3.500A) Processing helix chain 'L' and resid 846 through 851 removed outlier: 3.667A pdb=" N ILE L 850 " --> pdb=" O SER L 846 " (cutoff:3.500A) Processing helix chain 'L' and resid 863 through 881 Processing helix chain 'L' and resid 884 through 906 Processing helix chain 'L' and resid 913 through 923 Proline residue: L 919 - end of helix Processing helix chain 'L' and resid 923 through 933 removed outlier: 3.680A pdb=" N LEU L 927 " --> pdb=" O ASN L 923 " (cutoff:3.500A) Processing helix chain 'L' and resid 934 through 938 removed outlier: 3.566A pdb=" N ILE L 937 " --> pdb=" O PRO L 934 " (cutoff:3.500A) Processing helix chain 'L' and resid 945 through 949 Processing helix chain 'L' and resid 955 through 969 Processing helix chain 'L' and resid 975 through 983 removed outlier: 3.987A pdb=" N HIS L 979 " --> pdb=" O GLU L 975 " (cutoff:3.500A) Processing helix chain 'L' and resid 990 through 996 Processing helix chain 'L' and resid 1008 through 1024 removed outlier: 3.708A pdb=" N HIS L1024 " --> pdb=" O PHE L1020 " (cutoff:3.500A) Processing helix chain 'L' and resid 1027 through 1031 Processing helix chain 'L' and resid 1037 through 1051 Processing helix chain 'L' and resid 1056 through 1067 removed outlier: 3.610A pdb=" N ALA L1060 " --> pdb=" O VAL L1056 " (cutoff:3.500A) Processing helix chain 'L' and resid 1067 through 1079 removed outlier: 3.577A pdb=" N LEU L1079 " --> pdb=" O ILE L1075 " (cutoff:3.500A) Processing helix chain 'L' and resid 1082 through 1092 Processing helix chain 'L' and resid 1096 through 1105 Processing helix chain 'L' and resid 1105 through 1119 Processing helix chain 'L' and resid 1132 through 1145 Processing helix chain 'L' and resid 1145 through 1150 Processing helix chain 'L' and resid 1162 through 1164 No H-bonds generated for 'chain 'L' and resid 1162 through 1164' Processing helix chain 'L' and resid 1177 through 1183 Processing helix chain 'L' and resid 1232 through 1250 Processing helix chain 'L' and resid 1252 through 1264 Processing helix chain 'L' and resid 1270 through 1278 Processing helix chain 'L' and resid 1307 through 1311 removed outlier: 3.572A pdb=" N THR L1311 " --> pdb=" O ALA L1308 " (cutoff:3.500A) Processing helix chain 'L' and resid 1318 through 1323 Processing helix chain 'L' and resid 1329 through 1348 removed outlier: 4.129A pdb=" N MET L1337 " --> pdb=" O TYR L1333 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU L1338 " --> pdb=" O GLN L1334 " (cutoff:3.500A) Processing helix chain 'L' and resid 1428 through 1455 Processing helix chain 'L' and resid 1471 through 1478 removed outlier: 3.659A pdb=" N VAL L1477 " --> pdb=" O THR L1473 " (cutoff:3.500A) Processing helix chain 'L' and resid 1479 through 1495 Processing helix chain 'L' and resid 1495 through 1503 removed outlier: 3.901A pdb=" N HIS L1502 " --> pdb=" O ASP L1498 " (cutoff:3.500A) Processing helix chain 'L' and resid 1506 through 1521 Processing helix chain 'L' and resid 1526 through 1535 removed outlier: 4.065A pdb=" N HIS L1535 " --> pdb=" O ASN L1531 " (cutoff:3.500A) Processing helix chain 'L' and resid 1535 through 1545 removed outlier: 3.802A pdb=" N CYS L1545 " --> pdb=" O LYS L1541 " (cutoff:3.500A) Processing helix chain 'L' and resid 1561 through 1582 removed outlier: 3.690A pdb=" N ASN L1582 " --> pdb=" O ASP L1578 " (cutoff:3.500A) Processing helix chain 'L' and resid 1599 through 1620 removed outlier: 3.610A pdb=" N ARG L1603 " --> pdb=" O VAL L1599 " (cutoff:3.500A) Processing helix chain 'L' and resid 1632 through 1651 removed outlier: 3.557A pdb=" N ASP L1642 " --> pdb=" O ALA L1638 " (cutoff:3.500A) Processing helix chain 'L' and resid 1653 through 1657 Processing helix chain 'L' and resid 1670 through 1686 Processing helix chain 'L' and resid 1715 through 1719 removed outlier: 3.963A pdb=" N ARG L1719 " --> pdb=" O LYS L1716 " (cutoff:3.500A) Processing helix chain 'L' and resid 1725 through 1735 removed outlier: 3.707A pdb=" N LYS L1730 " --> pdb=" O ALA L1726 " (cutoff:3.500A) Processing helix chain 'L' and resid 1749 through 1754 Processing helix chain 'L' and resid 1763 through 1775 removed outlier: 3.740A pdb=" N LEU L1773 " --> pdb=" O GLU L1769 " (cutoff:3.500A) Processing helix chain 'L' and resid 1792 through 1803 Processing helix chain 'L' and resid 1828 through 1839 Processing helix chain 'L' and resid 1851 through 1856 removed outlier: 3.852A pdb=" N TRP L1856 " --> pdb=" O GLU L1853 " (cutoff:3.500A) Processing helix chain 'L' and resid 1859 through 1870 Processing helix chain 'L' and resid 1889 through 1907 Processing helix chain 'L' and resid 1925 through 1934 removed outlier: 4.078A pdb=" N GLY L1934 " --> pdb=" O ILE L1930 " (cutoff:3.500A) Processing helix chain 'L' and resid 1969 through 1981 removed outlier: 3.607A pdb=" N SER L1981 " --> pdb=" O ILE L1977 " (cutoff:3.500A) Processing helix chain 'L' and resid 1985 through 2000 removed outlier: 3.632A pdb=" N ILE L1989 " --> pdb=" O SER L1985 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU L1998 " --> pdb=" O SER L1994 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS L2000 " --> pdb=" O LYS L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2000 through 2005 Processing helix chain 'L' and resid 2016 through 2020 removed outlier: 3.898A pdb=" N LYS L2020 " --> pdb=" O THR L2017 " (cutoff:3.500A) Processing helix chain 'L' and resid 2022 through 2031 removed outlier: 3.528A pdb=" N CYS L2031 " --> pdb=" O VAL L2027 " (cutoff:3.500A) Processing helix chain 'L' and resid 2036 through 2045 Processing helix chain 'L' and resid 2051 through 2069 removed outlier: 3.659A pdb=" N GLY L2055 " --> pdb=" O SER L2051 " (cutoff:3.500A) Processing helix chain 'L' and resid 2084 through 2111 removed outlier: 3.620A pdb=" N SER L2111 " --> pdb=" O ILE L2107 " (cutoff:3.500A) Processing helix chain 'L' and resid 2113 through 2127 Processing helix chain 'L' and resid 2137 through 2142 removed outlier: 3.694A pdb=" N LYS L2140 " --> pdb=" O ILE L2137 " (cutoff:3.500A) Processing helix chain 'L' and resid 2143 through 2153 Processing helix chain 'L' and resid 2164 through 2182 removed outlier: 3.701A pdb=" N ALA L2179 " --> pdb=" O VAL L2175 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU L2180 " --> pdb=" O GLY L2176 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 85 removed outlier: 4.215A pdb=" N LEU X 85 " --> pdb=" O THR X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 115 Processing helix chain 'X' and resid 120 through 131 Processing helix chain 'X' and resid 134 through 152 removed outlier: 3.762A pdb=" N THR X 138 " --> pdb=" O TYR X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 160 removed outlier: 3.980A pdb=" N SER X 158 " --> pdb=" O ASP X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 167 Processing helix chain 'Y' and resid 53 through 87 removed outlier: 3.576A pdb=" N GLU Y 87 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 115 removed outlier: 3.550A pdb=" N PHE Y 105 " --> pdb=" O SER Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 131 Processing helix chain 'Y' and resid 134 through 152 removed outlier: 3.554A pdb=" N THR Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 160 Processing helix chain 'Y' and resid 162 through 168 Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA2, first strand: chain 'L' and resid 20 through 21 removed outlier: 6.842A pdb=" N ILE L 20 " --> pdb=" O LEU L 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 83 through 84 removed outlier: 6.447A pdb=" N SER L 83 " --> pdb=" O VAL L 220 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR L 222 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS L 219 " --> pdb=" O SER L 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 545 through 549 removed outlier: 5.489A pdb=" N LEU L 530 " --> pdb=" O VAL L 704 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR L 706 " --> pdb=" O LEU L 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 765 through 771 Processing sheet with id=AA6, first strand: chain 'L' and resid 831 through 832 Processing sheet with id=AA7, first strand: chain 'L' and resid 1166 through 1171 Processing sheet with id=AA8, first strand: chain 'L' and resid 1590 through 1593 removed outlier: 6.610A pdb=" N PHE L1590 " --> pdb=" O ASP L1665 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR L1667 " --> pdb=" O PHE L1590 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU L1592 " --> pdb=" O TYR L1667 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 1722 through 1724 removed outlier: 6.873A pdb=" N TYR L1937 " --> pdb=" O LEU L1962 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU L1962 " --> pdb=" O TYR L1937 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N SER L1912 " --> pdb=" O ASP L1961 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLY L1876 " --> pdb=" O GLY L1911 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP L1783 " --> pdb=" O PHE L1877 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS L1879 " --> pdb=" O ASP L1783 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU L1785 " --> pdb=" O HIS L1879 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 2009 through 2010 Processing sheet with id=AB2, first strand: chain 'L' and resid 2128 through 2132 1119 hydrogen bonds defined for protein. 3219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6245 1.34 - 1.46: 3746 1.46 - 1.58: 9658 1.58 - 1.70: 0 1.70 - 1.82: 182 Bond restraints: 19831 Sorted by residual: bond pdb=" N ALA Y 132 " pdb=" CA ALA Y 132 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.35e+00 bond pdb=" N ILE Y 131 " pdb=" CA ILE Y 131 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.35e-02 5.49e+03 7.31e+00 bond pdb=" N GLU Y 115 " pdb=" CA GLU Y 115 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.10e-02 8.26e+03 7.09e+00 bond pdb=" N MET Y 118 " pdb=" CA MET Y 118 " ideal model delta sigma weight residual 1.453 1.486 -0.032 1.22e-02 6.72e+03 7.01e+00 bond pdb=" N VAL Y 130 " pdb=" CA VAL Y 130 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.41e-02 5.03e+03 6.54e+00 ... (remaining 19826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 26302 1.86 - 3.72: 451 3.72 - 5.59: 56 5.59 - 7.45: 10 7.45 - 9.31: 2 Bond angle restraints: 26821 Sorted by residual: angle pdb=" CA GLY Y 99 " pdb=" C GLY Y 99 " pdb=" O GLY Y 99 " ideal model delta sigma weight residual 121.18 117.64 3.54 8.80e-01 1.29e+00 1.62e+01 angle pdb=" N GLU L 143 " pdb=" CA GLU L 143 " pdb=" CB GLU L 143 " ideal model delta sigma weight residual 114.17 109.79 4.38 1.14e+00 7.69e-01 1.48e+01 angle pdb=" N GLU Y 115 " pdb=" CA GLU Y 115 " pdb=" C GLU Y 115 " ideal model delta sigma weight residual 112.57 108.60 3.97 1.13e+00 7.83e-01 1.24e+01 angle pdb=" CA ARG X 74 " pdb=" CB ARG X 74 " pdb=" CG ARG X 74 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA THR Y 138 " pdb=" CB THR Y 138 " pdb=" OG1 THR Y 138 " ideal model delta sigma weight residual 109.60 104.59 5.01 1.50e+00 4.44e-01 1.12e+01 ... (remaining 26816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 11010 17.13 - 34.25: 848 34.25 - 51.38: 131 51.38 - 68.50: 21 68.50 - 85.63: 11 Dihedral angle restraints: 12021 sinusoidal: 4900 harmonic: 7121 Sorted by residual: dihedral pdb=" CA LEU Y 119 " pdb=" C LEU Y 119 " pdb=" N THR Y 120 " pdb=" CA THR Y 120 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA LYS X 117 " pdb=" C LYS X 117 " pdb=" N MET X 118 " pdb=" CA MET X 118 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ASN L 727 " pdb=" C ASN L 727 " pdb=" N ASP L 728 " pdb=" CA ASP L 728 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 12018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2287 0.043 - 0.086: 610 0.086 - 0.129: 156 0.129 - 0.171: 16 0.171 - 0.214: 5 Chirality restraints: 3074 Sorted by residual: chirality pdb=" CA GLU Y 137 " pdb=" N GLU Y 137 " pdb=" C GLU Y 137 " pdb=" CB GLU Y 137 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA VAL Y 130 " pdb=" N VAL Y 130 " pdb=" C VAL Y 130 " pdb=" CB VAL Y 130 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CB ILE L1741 " pdb=" CA ILE L1741 " pdb=" CG1 ILE L1741 " pdb=" CG2 ILE L1741 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 3071 not shown) Planarity restraints: 3368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 114 " -0.400 9.50e-02 1.11e+02 1.79e-01 1.97e+01 pdb=" NE ARG Y 114 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG Y 114 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 114 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 114 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU L1779 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO L1780 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO L1780 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO L1780 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L1503 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO L1504 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO L1504 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L1504 " -0.028 5.00e-02 4.00e+02 ... (remaining 3365 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 344 2.70 - 3.25: 19246 3.25 - 3.80: 29663 3.80 - 4.35: 38781 4.35 - 4.90: 65797 Nonbonded interactions: 153831 Sorted by model distance: nonbonded pdb=" OD2 ASP L 42 " pdb=" NE2 GLN L 729 " model vdw 2.151 3.120 nonbonded pdb=" OG SER L 427 " pdb=" OE1 GLU L 429 " model vdw 2.159 3.040 nonbonded pdb=" O PHE L1921 " pdb=" OG1 THR L1984 " model vdw 2.189 3.040 nonbonded pdb=" NE2 GLN A 352 " pdb=" OD1 ASN B 354 " model vdw 2.190 3.120 nonbonded pdb=" NH2 ARG L1306 " pdb=" O GLU L1351 " model vdw 2.194 3.120 ... (remaining 153826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'X' and (resid 59 through 87 or resid 100 through 173)) selection = (chain 'Y' and (resid 59 through 87 or resid 100 through 173)) } 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=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 0.044 19840 Z= 0.190 Angle : 0.608 9.310 26822 Z= 0.351 Chirality : 0.042 0.214 3074 Planarity : 0.005 0.179 3368 Dihedral : 12.488 85.627 7411 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.17), residues: 2399 helix: 1.71 (0.14), residues: 1375 sheet: 0.68 (0.42), residues: 166 loop : -0.89 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG X 74 TYR 0.014 0.001 TYR L 382 PHE 0.016 0.001 PHE X 124 TRP 0.016 0.001 TRP L1189 HIS 0.010 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (19831) covalent geometry : angle 0.60776 / 0.35 (26821) hydrogen bonds : bond 0.14887 / 10.10 ( 1119) hydrogen bonds : angle 5.40674 / 3.90 ( 3219) metal coordination : bond 0.01379 / 0.60 ( 9) metal coordination : angle 3.79355 / 2.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.510 Fit side-chains REVERT: A 461 ARG cc_start: 0.5841 (ttm-80) cc_final: 0.5482 (ttt90) REVERT: D 379 LYS cc_start: 0.5907 (tttm) cc_final: 0.5183 (ttmt) REVERT: L 108 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6524 (pt0) REVERT: L 119 LYS cc_start: 0.7582 (mtpt) cc_final: 0.7223 (mttm) REVERT: L 123 LYS cc_start: 0.6985 (mttt) cc_final: 0.6752 (mtpt) REVERT: L 174 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6955 (mm-30) REVERT: L 240 MET cc_start: 0.7656 (mmm) cc_final: 0.7435 (mmm) REVERT: L 329 GLU cc_start: 0.6837 (mp0) cc_final: 0.6131 (mm-30) REVERT: L 332 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6899 (mm-30) REVERT: L 402 ASP cc_start: 0.6704 (t70) cc_final: 0.6415 (m-30) REVERT: L 463 TYR cc_start: 0.6050 (m-80) cc_final: 0.5769 (m-80) REVERT: L 491 LYS cc_start: 0.8105 (mppt) cc_final: 0.7860 (tppt) REVERT: L 527 GLU cc_start: 0.6356 (pp20) cc_final: 0.6047 (pp20) REVERT: L 562 ASN cc_start: 0.7426 (t0) cc_final: 0.7203 (t0) REVERT: L 657 SER cc_start: 0.8184 (p) cc_final: 0.7883 (t) REVERT: L 911 THR cc_start: 0.8075 (t) cc_final: 0.7674 (p) REVERT: L 925 ASP cc_start: 0.7230 (m-30) cc_final: 0.7016 (m-30) REVERT: L 967 MET cc_start: 0.8146 (mtt) cc_final: 0.7726 (mtm) REVERT: L 982 MET cc_start: 0.8475 (mmm) cc_final: 0.8176 (mmt) REVERT: L 988 ASP cc_start: 0.7131 (t0) cc_final: 0.6617 (p0) REVERT: L 1014 LYS cc_start: 0.6367 (mttp) cc_final: 0.5969 (mttt) REVERT: L 1019 ARG cc_start: 0.6443 (ttp80) cc_final: 0.5775 (tpp80) REVERT: L 1024 HIS cc_start: 0.7745 (m90) cc_final: 0.7426 (m90) REVERT: L 1109 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6240 (mm-30) REVERT: L 1128 ASP cc_start: 0.7642 (p0) cc_final: 0.7130 (t70) REVERT: L 1129 LYS cc_start: 0.7108 (pttt) cc_final: 0.6653 (pttp) REVERT: L 1130 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7012 (mm-30) REVERT: L 1150 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7260 (mtm180) REVERT: L 1334 GLN cc_start: 0.7229 (tt0) cc_final: 0.6730 (tm-30) REVERT: L 1523 LYS cc_start: 0.7811 (tttp) cc_final: 0.7292 (tttm) REVERT: L 1676 ARG cc_start: 0.5601 (mtm-85) cc_final: 0.5361 (mtm-85) REVERT: L 1727 LYS cc_start: 0.6601 (tmmt) cc_final: 0.6345 (tmmt) REVERT: L 1783 ASP cc_start: 0.7708 (m-30) cc_final: 0.7050 (m-30) REVERT: L 1803 LYS cc_start: 0.8260 (mttm) cc_final: 0.8048 (mptp) REVERT: L 1881 ASP cc_start: 0.7406 (t70) cc_final: 0.7107 (t70) REVERT: L 1939 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6522 (mm-30) REVERT: L 1969 ASN cc_start: 0.7611 (p0) cc_final: 0.7250 (p0) REVERT: L 1979 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6271 (pt0) REVERT: L 2059 SER cc_start: 0.6533 (m) cc_final: 0.6321 (p) REVERT: L 2114 ARG cc_start: 0.5682 (mtp-110) cc_final: 0.5472 (mmm160) REVERT: L 2166 LYS cc_start: 0.7039 (ttmt) cc_final: 0.6646 (ttmp) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.6020 time to fit residues: 249.1080 Evaluate side-chains 300 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN L 375 ASN L 562 ASN L 775 GLN L1608 GLN L1965 ASN L2113 ASN L2122 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134893 restraints weight = 24803.560| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.29 r_work: 0.3390 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19840 Z= 0.150 Angle : 0.594 9.413 26822 Z= 0.303 Chirality : 0.041 0.178 3074 Planarity : 0.005 0.054 3368 Dihedral : 4.366 25.142 2646 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.80 % Allowed : 8.25 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2399 helix: 2.08 (0.14), residues: 1390 sheet: 0.86 (0.44), residues: 166 loop : -0.81 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 114 TYR 0.017 0.001 TYR L 277 PHE 0.023 0.002 PHE L 546 TRP 0.013 0.002 TRP X 86 HIS 0.007 0.001 HIS D 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (19831) covalent geometry : angle 0.59313 / 0.30 (26821) hydrogen bonds : bond 0.05477 / 3.64 ( 1119) hydrogen bonds : angle 4.06313 / 2.89 ( 3219) metal coordination : bond 0.02091 / 0.92 ( 9) metal coordination : angle 4.90237 / 2.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 0.641 Fit side-chains REVERT: A 371 MET cc_start: 0.6935 (mtt) cc_final: 0.6445 (mmm) REVERT: D 379 LYS cc_start: 0.6549 (tttm) cc_final: 0.6050 (ttmt) REVERT: L 50 LYS cc_start: 0.8536 (tttt) cc_final: 0.7539 (tppt) REVERT: L 108 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7732 (pt0) REVERT: L 123 LYS cc_start: 0.8339 (mttt) cc_final: 0.8043 (mmtt) REVERT: L 174 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8078 (mm-30) REVERT: L 175 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8771 (ttt) REVERT: L 311 GLU cc_start: 0.8141 (tp30) cc_final: 0.7930 (tp30) REVERT: L 329 GLU cc_start: 0.7898 (mp0) cc_final: 0.7243 (mm-30) REVERT: L 332 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8037 (mm-30) REVERT: L 402 ASP cc_start: 0.6993 (t70) cc_final: 0.6741 (m-30) REVERT: L 463 TYR cc_start: 0.7042 (m-80) cc_final: 0.6798 (m-80) REVERT: L 491 LYS cc_start: 0.8394 (mppt) cc_final: 0.8182 (tppt) REVERT: L 570 LYS cc_start: 0.7985 (mttt) cc_final: 0.7703 (mmtm) REVERT: L 657 SER cc_start: 0.8823 (p) cc_final: 0.8518 (t) REVERT: L 666 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8454 (mmtp) REVERT: L 911 THR cc_start: 0.8579 (t) cc_final: 0.8200 (p) REVERT: L 967 MET cc_start: 0.8949 (mtt) cc_final: 0.8631 (mtm) REVERT: L 988 ASP cc_start: 0.7742 (t0) cc_final: 0.7210 (p0) REVERT: L 1019 ARG cc_start: 0.7370 (ttp80) cc_final: 0.6648 (tpp80) REVERT: L 1024 HIS cc_start: 0.8126 (m90) cc_final: 0.7837 (m90) REVERT: L 1112 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7543 (ttp80) REVERT: L 1128 ASP cc_start: 0.8053 (p0) cc_final: 0.7586 (t70) REVERT: L 1129 LYS cc_start: 0.7439 (pttt) cc_final: 0.7046 (pttp) REVERT: L 1334 GLN cc_start: 0.8239 (tt0) cc_final: 0.7820 (tm-30) REVERT: L 1676 ARG cc_start: 0.6525 (mtm-85) cc_final: 0.6182 (mtm-85) REVERT: L 1783 ASP cc_start: 0.8028 (m-30) cc_final: 0.7580 (m-30) REVERT: L 1881 ASP cc_start: 0.8058 (t70) cc_final: 0.7835 (t70) REVERT: L 1939 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7276 (mm-30) REVERT: L 1979 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6568 (pt0) REVERT: L 2059 SER cc_start: 0.7378 (m) cc_final: 0.7148 (p) REVERT: L 2157 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6946 (ttt-90) outliers start: 39 outliers final: 17 residues processed: 320 average time/residue: 0.5566 time to fit residues: 199.8589 Evaluate side-chains 304 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 666 LYS Chi-restraints excluded: chain L residue 769 LEU Chi-restraints excluded: chain L residue 873 THR Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1472 ILE Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1772 THR Chi-restraints excluded: chain L residue 1968 MET Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2157 ARG Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain X residue 104 MET Chi-restraints excluded: chain Y residue 53 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 179 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 146 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 175 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 771 GLN L 775 GLN L1315 ASN L1976 GLN L2113 ASN L2122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130432 restraints weight = 26340.152| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.31 r_work: 0.3360 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19840 Z= 0.163 Angle : 0.589 9.631 26822 Z= 0.301 Chirality : 0.041 0.149 3074 Planarity : 0.005 0.054 3368 Dihedral : 4.369 27.424 2646 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.93 % Allowed : 10.04 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2399 helix: 2.05 (0.14), residues: 1397 sheet: 1.30 (0.46), residues: 151 loop : -0.84 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 78 TYR 0.025 0.002 TYR L 400 PHE 0.018 0.002 PHE L 659 TRP 0.014 0.002 TRP L1427 HIS 0.007 0.001 HIS D 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (19831) covalent geometry : angle 0.58819 / 0.30 (26821) hydrogen bonds : bond 0.05542 / 3.67 ( 1119) hydrogen bonds : angle 3.92549 / 2.79 ( 3219) metal coordination : bond 0.01732 / 0.76 ( 9) metal coordination : angle 4.45732 / 2.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: D 379 LYS cc_start: 0.6530 (tttm) cc_final: 0.6075 (ttmt) REVERT: L 50 LYS cc_start: 0.8447 (tttt) cc_final: 0.7435 (tppt) REVERT: L 108 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7699 (pt0) REVERT: L 123 LYS cc_start: 0.8412 (mttt) cc_final: 0.8080 (mmtt) REVERT: L 174 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8078 (mm-30) REVERT: L 175 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8784 (ttt) REVERT: L 332 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8095 (mm-30) REVERT: L 368 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: L 402 ASP cc_start: 0.7026 (t70) cc_final: 0.6778 (m-30) REVERT: L 491 LYS cc_start: 0.8393 (mppt) cc_final: 0.8176 (tppt) REVERT: L 570 LYS cc_start: 0.7990 (mttt) cc_final: 0.7721 (mmtm) REVERT: L 666 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8454 (mmtp) REVERT: L 911 THR cc_start: 0.8693 (t) cc_final: 0.8267 (p) REVERT: L 967 MET cc_start: 0.8932 (mtt) cc_final: 0.8600 (mtm) REVERT: L 988 ASP cc_start: 0.7807 (t0) cc_final: 0.7271 (p0) REVERT: L 1014 LYS cc_start: 0.7371 (mtpp) cc_final: 0.7133 (mmtt) REVERT: L 1019 ARG cc_start: 0.7512 (ttp80) cc_final: 0.6751 (tpp80) REVERT: L 1031 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6980 (mmmm) REVERT: L 1128 ASP cc_start: 0.8022 (p0) cc_final: 0.7554 (t70) REVERT: L 1129 LYS cc_start: 0.7443 (pttt) cc_final: 0.6972 (pttp) REVERT: L 1334 GLN cc_start: 0.8238 (tt0) cc_final: 0.7827 (tm-30) REVERT: L 1388 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7513 (mm) REVERT: L 1676 ARG cc_start: 0.6574 (mtm-85) cc_final: 0.6232 (mtm-85) REVERT: L 1783 ASP cc_start: 0.8056 (m-30) cc_final: 0.7851 (m-30) REVERT: L 1881 ASP cc_start: 0.8074 (t70) cc_final: 0.7869 (t70) REVERT: L 1939 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7286 (mm-30) REVERT: L 1979 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6535 (pt0) REVERT: L 2170 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7402 (mt-10) outliers start: 42 outliers final: 15 residues processed: 309 average time/residue: 0.5514 time to fit residues: 190.8709 Evaluate side-chains 304 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 666 LYS Chi-restraints excluded: chain L residue 769 LEU Chi-restraints excluded: chain L residue 873 THR Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1101 THR Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1472 ILE Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1772 THR Chi-restraints excluded: chain L residue 1796 ILE Chi-restraints excluded: chain L residue 1873 SER Chi-restraints excluded: chain L residue 2113 ASN Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2170 GLU Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 109 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 172 optimal weight: 0.0470 chunk 237 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 771 GLN L 775 GLN L1760 ASN L1976 GLN L2122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138014 restraints weight = 31704.643| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.68 r_work: 0.3363 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19840 Z= 0.133 Angle : 0.553 9.683 26822 Z= 0.281 Chirality : 0.040 0.148 3074 Planarity : 0.004 0.059 3368 Dihedral : 4.236 27.613 2646 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.52 % Allowed : 11.42 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.17), residues: 2399 helix: 2.21 (0.14), residues: 1396 sheet: 0.97 (0.45), residues: 161 loop : -0.73 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 78 TYR 0.014 0.001 TYR L 382 PHE 0.024 0.001 PHE L 546 TRP 0.015 0.001 TRP L1256 HIS 0.007 0.001 HIS L1643 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (19831) covalent geometry : angle 0.55198 / 0.28 (26821) hydrogen bonds : bond 0.04910 / 3.24 ( 1119) hydrogen bonds : angle 3.81629 / 2.72 ( 3219) metal coordination : bond 0.01723 / 0.75 ( 9) metal coordination : angle 4.42900 / 2.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 296 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: D 363 LEU cc_start: 0.6705 (tt) cc_final: 0.6496 (tp) REVERT: D 379 LYS cc_start: 0.6586 (tttm) cc_final: 0.6195 (ttmt) REVERT: L 50 LYS cc_start: 0.8399 (tttt) cc_final: 0.7409 (tppt) REVERT: L 77 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7401 (mtp180) REVERT: L 108 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7779 (pt0) REVERT: L 123 LYS cc_start: 0.8450 (mttt) cc_final: 0.8137 (mmtt) REVERT: L 174 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8134 (mm-30) REVERT: L 332 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8167 (mm-30) REVERT: L 350 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6259 (m-80) REVERT: L 368 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: L 402 ASP cc_start: 0.7037 (t70) cc_final: 0.6792 (m-30) REVERT: L 491 LYS cc_start: 0.8456 (mppt) cc_final: 0.8204 (tppt) REVERT: L 496 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7419 (mmm-85) REVERT: L 570 LYS cc_start: 0.8014 (mttt) cc_final: 0.7741 (mmtm) REVERT: L 666 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8452 (mmtp) REVERT: L 911 THR cc_start: 0.8700 (t) cc_final: 0.8274 (p) REVERT: L 967 MET cc_start: 0.8946 (mtt) cc_final: 0.8622 (mtm) REVERT: L 975 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: L 988 ASP cc_start: 0.7849 (t0) cc_final: 0.7270 (p0) REVERT: L 1014 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7214 (mmtt) REVERT: L 1019 ARG cc_start: 0.7646 (ttp80) cc_final: 0.6821 (tpp80) REVERT: L 1031 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7074 (mmmm) REVERT: L 1073 GLU cc_start: 0.7706 (pp20) cc_final: 0.7119 (tm-30) REVERT: L 1128 ASP cc_start: 0.8041 (p0) cc_final: 0.7560 (t70) REVERT: L 1129 LYS cc_start: 0.7427 (pttt) cc_final: 0.6983 (pttp) REVERT: L 1334 GLN cc_start: 0.8206 (tt0) cc_final: 0.7373 (tp-100) REVERT: L 1388 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7500 (mm) REVERT: L 1586 GLU cc_start: 0.7763 (tt0) cc_final: 0.7190 (tp30) REVERT: L 1676 ARG cc_start: 0.6664 (mtm-85) cc_final: 0.6323 (mtm-85) REVERT: L 1783 ASP cc_start: 0.8080 (m-30) cc_final: 0.7870 (m-30) REVERT: L 1881 ASP cc_start: 0.8126 (t70) cc_final: 0.7916 (t70) REVERT: L 1939 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7310 (mm-30) REVERT: L 1979 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6470 (pt0) REVERT: L 2011 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7280 (mtm180) REVERT: L 2157 ARG cc_start: 0.7282 (mtp85) cc_final: 0.7076 (mmm-85) REVERT: L 2170 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: Y 129 MET cc_start: 0.7225 (mmp) cc_final: 0.6990 (mmm) outliers start: 33 outliers final: 15 residues processed: 309 average time/residue: 0.5524 time to fit residues: 190.5947 Evaluate side-chains 305 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 666 LYS Chi-restraints excluded: chain L residue 769 LEU Chi-restraints excluded: chain L residue 975 GLU Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1101 THR Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1472 ILE Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1796 ILE Chi-restraints excluded: chain L residue 1873 SER Chi-restraints excluded: chain L residue 2113 ASN Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2170 GLU Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 8 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1315 ASN L1887 ASN L1976 GLN L2113 ASN L2122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132511 restraints weight = 21747.664| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.08 r_work: 0.3382 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19840 Z= 0.143 Angle : 0.563 9.915 26822 Z= 0.285 Chirality : 0.040 0.150 3074 Planarity : 0.004 0.060 3368 Dihedral : 4.234 27.990 2646 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.89 % Allowed : 12.30 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.17), residues: 2399 helix: 2.21 (0.14), residues: 1399 sheet: 1.34 (0.45), residues: 151 loop : -0.76 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 78 TYR 0.014 0.001 TYR L 382 PHE 0.015 0.001 PHE L 659 TRP 0.016 0.001 TRP L1427 HIS 0.006 0.001 HIS L1643 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (19831) covalent geometry : angle 0.56284 / 0.29 (26821) hydrogen bonds : bond 0.05005 / 3.31 ( 1119) hydrogen bonds : angle 3.79972 / 2.70 ( 3219) metal coordination : bond 0.01637 / 0.71 ( 9) metal coordination : angle 4.32981 / 2.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.511 Fit side-chains REVERT: D 379 LYS cc_start: 0.6466 (tttm) cc_final: 0.6111 (ttmt) REVERT: L 50 LYS cc_start: 0.8198 (tttt) cc_final: 0.7213 (tppt) REVERT: L 77 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7366 (mtp180) REVERT: L 108 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7666 (pt0) REVERT: L 123 LYS cc_start: 0.8372 (mttt) cc_final: 0.8047 (mmtt) REVERT: L 174 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8051 (mm-30) REVERT: L 332 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8054 (mm-30) REVERT: L 350 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.6230 (m-80) REVERT: L 354 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7667 (mmt180) REVERT: L 368 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: L 402 ASP cc_start: 0.7024 (t70) cc_final: 0.6750 (m-30) REVERT: L 491 LYS cc_start: 0.8434 (mppt) cc_final: 0.8187 (tppt) REVERT: L 496 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: L 570 LYS cc_start: 0.7970 (mttt) cc_final: 0.7694 (mmtm) REVERT: L 666 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8449 (mmtp) REVERT: L 911 THR cc_start: 0.8669 (t) cc_final: 0.8245 (p) REVERT: L 967 MET cc_start: 0.8920 (mtt) cc_final: 0.8571 (mtm) REVERT: L 988 ASP cc_start: 0.7788 (t0) cc_final: 0.7267 (p0) REVERT: L 1019 ARG cc_start: 0.7573 (ttp80) cc_final: 0.6700 (tpp80) REVERT: L 1031 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7017 (mmmm) REVERT: L 1041 GLU cc_start: 0.7138 (tt0) cc_final: 0.6308 (mm-30) REVERT: L 1073 GLU cc_start: 0.7560 (pp20) cc_final: 0.6999 (tm-30) REVERT: L 1128 ASP cc_start: 0.7964 (p0) cc_final: 0.7548 (t70) REVERT: L 1129 LYS cc_start: 0.7398 (pttt) cc_final: 0.6952 (pttp) REVERT: L 1334 GLN cc_start: 0.8137 (tt0) cc_final: 0.7295 (tp-100) REVERT: L 1388 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7482 (mm) REVERT: L 1443 SER cc_start: 0.7653 (t) cc_final: 0.7438 (m) REVERT: L 1586 GLU cc_start: 0.7706 (tt0) cc_final: 0.7140 (tp30) REVERT: L 1676 ARG cc_start: 0.6572 (mtm-85) cc_final: 0.6238 (mtm-85) REVERT: L 1776 ARG cc_start: 0.7233 (ptp-110) cc_final: 0.7015 (tmm160) REVERT: L 1783 ASP cc_start: 0.8082 (m-30) cc_final: 0.7860 (m-30) REVERT: L 1881 ASP cc_start: 0.8037 (t70) cc_final: 0.7824 (t70) REVERT: L 1939 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7218 (mm-30) REVERT: L 2011 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7280 (mtm180) REVERT: L 2157 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6995 (mmm-85) REVERT: L 2170 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7367 (mt-10) outliers start: 41 outliers final: 21 residues processed: 302 average time/residue: 0.5735 time to fit residues: 193.9161 Evaluate side-chains 312 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 354 ARG Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 666 LYS Chi-restraints excluded: chain L residue 769 LEU Chi-restraints excluded: chain L residue 873 THR Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1101 THR Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1472 ILE Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1772 THR Chi-restraints excluded: chain L residue 1796 ILE Chi-restraints excluded: chain L residue 1873 SER Chi-restraints excluded: chain L residue 1968 MET Chi-restraints excluded: chain L residue 2054 ASP Chi-restraints excluded: chain L residue 2113 ASN Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2157 ARG Chi-restraints excluded: chain L residue 2170 GLU Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 53 SER Chi-restraints excluded: chain Y residue 76 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 177 optimal weight: 0.0980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1315 ASN L1976 GLN L2113 ASN L2122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.181137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131441 restraints weight = 24162.599| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.22 r_work: 0.3366 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19840 Z= 0.149 Angle : 0.572 10.046 26822 Z= 0.290 Chirality : 0.040 0.159 3074 Planarity : 0.005 0.066 3368 Dihedral : 4.250 28.215 2646 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.03 % Allowed : 12.85 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.17), residues: 2399 helix: 2.21 (0.14), residues: 1398 sheet: 1.33 (0.45), residues: 151 loop : -0.75 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 78 TYR 0.014 0.001 TYR L 382 PHE 0.023 0.002 PHE L 546 TRP 0.018 0.002 TRP L1427 HIS 0.007 0.001 HIS L1643 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (19831) covalent geometry : angle 0.57149 / 0.29 (26821) hydrogen bonds : bond 0.05087 / 3.37 ( 1119) hydrogen bonds : angle 3.80197 / 2.71 ( 3219) metal coordination : bond 0.01624 / 0.71 ( 9) metal coordination : angle 4.20256 / 2.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.695 Fit side-chains REVERT: D 379 LYS cc_start: 0.6513 (tttm) cc_final: 0.6169 (ttmt) REVERT: L 50 LYS cc_start: 0.8325 (tttt) cc_final: 0.7495 (tppt) REVERT: L 77 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7427 (mtp180) REVERT: L 108 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7724 (pt0) REVERT: L 123 LYS cc_start: 0.8436 (mttt) cc_final: 0.8124 (mmtt) REVERT: L 174 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8106 (mm-30) REVERT: L 332 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8078 (mm-30) REVERT: L 350 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: L 354 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7753 (mmt180) REVERT: L 368 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: L 402 ASP cc_start: 0.7037 (t70) cc_final: 0.6768 (m-30) REVERT: L 491 LYS cc_start: 0.8432 (mppt) cc_final: 0.8202 (tppt) REVERT: L 496 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7388 (mmm-85) REVERT: L 570 LYS cc_start: 0.8004 (mttt) cc_final: 0.7740 (mmtm) REVERT: L 911 THR cc_start: 0.8700 (t) cc_final: 0.8281 (p) REVERT: L 967 MET cc_start: 0.8953 (mtt) cc_final: 0.8612 (mtm) REVERT: L 988 ASP cc_start: 0.7831 (t0) cc_final: 0.7314 (p0) REVERT: L 1014 LYS cc_start: 0.7246 (mtpp) cc_final: 0.7011 (mmtt) REVERT: L 1019 ARG cc_start: 0.7521 (ttp80) cc_final: 0.6750 (tpp80) REVERT: L 1031 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7030 (mmmm) REVERT: L 1041 GLU cc_start: 0.7193 (tt0) cc_final: 0.6369 (mm-30) REVERT: L 1073 GLU cc_start: 0.7645 (pp20) cc_final: 0.7084 (tm-30) REVERT: L 1128 ASP cc_start: 0.7984 (p0) cc_final: 0.7584 (t70) REVERT: L 1129 LYS cc_start: 0.7422 (pttt) cc_final: 0.6985 (pttp) REVERT: L 1334 GLN cc_start: 0.8261 (tt0) cc_final: 0.7439 (tp-100) REVERT: L 1388 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7510 (mm) REVERT: L 1586 GLU cc_start: 0.7680 (tt0) cc_final: 0.7189 (tp30) REVERT: L 1676 ARG cc_start: 0.6647 (mtm-85) cc_final: 0.6317 (mtm-85) REVERT: L 1764 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7135 (p) REVERT: L 1783 ASP cc_start: 0.8100 (m-30) cc_final: 0.7893 (m-30) REVERT: L 1881 ASP cc_start: 0.8086 (t70) cc_final: 0.7863 (t70) REVERT: L 1939 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7338 (mm-30) REVERT: L 2011 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7270 (mtm180) REVERT: L 2113 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.8032 (t160) REVERT: L 2157 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.7040 (mmm-85) REVERT: L 2170 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7440 (mt-10) outliers start: 44 outliers final: 21 residues processed: 302 average time/residue: 0.5931 time to fit residues: 201.6681 Evaluate side-chains 314 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 354 ARG Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 568 ILE Chi-restraints excluded: chain L residue 769 LEU Chi-restraints excluded: chain L residue 873 THR Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1101 THR Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1472 ILE Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1764 CYS Chi-restraints excluded: chain L residue 1772 THR Chi-restraints excluded: chain L residue 1796 ILE Chi-restraints excluded: chain L residue 1873 SER Chi-restraints excluded: chain L residue 2054 ASP Chi-restraints excluded: chain L residue 2113 ASN Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2157 ARG Chi-restraints excluded: chain L residue 2170 GLU Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 53 SER Chi-restraints excluded: chain Y residue 76 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 79 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 375 ASN L1315 ASN L1976 GLN L2113 ASN L2122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.181258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130167 restraints weight = 35260.034| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.55 r_work: 0.3342 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19840 Z= 0.146 Angle : 0.576 10.134 26822 Z= 0.291 Chirality : 0.040 0.155 3074 Planarity : 0.005 0.074 3368 Dihedral : 4.238 28.391 2646 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.98 % Allowed : 13.22 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.17), residues: 2399 helix: 2.23 (0.14), residues: 1398 sheet: 1.33 (0.45), residues: 151 loop : -0.75 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG X 78 TYR 0.014 0.001 TYR L 382 PHE 0.015 0.001 PHE L 659 TRP 0.019 0.001 TRP L1427 HIS 0.007 0.001 HIS L1643 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (19831) covalent geometry : angle 0.57589 / 0.29 (26821) hydrogen bonds : bond 0.05011 / 3.31 ( 1119) hydrogen bonds : angle 3.78808 / 2.70 ( 3219) metal coordination : bond 0.01620 / 0.71 ( 9) metal coordination : angle 4.21730 / 2.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.714 Fit side-chains REVERT: A 371 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6406 (mtp) REVERT: D 379 LYS cc_start: 0.6476 (tttm) cc_final: 0.6119 (ttmt) REVERT: L 50 LYS cc_start: 0.8311 (tttt) cc_final: 0.7454 (tppt) REVERT: L 77 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7448 (mtp180) REVERT: L 108 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7673 (pt0) REVERT: L 123 LYS cc_start: 0.8422 (mttt) cc_final: 0.8095 (mmtt) REVERT: L 174 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8129 (mm-30) REVERT: L 332 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8110 (mm-30) REVERT: L 350 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: L 354 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7786 (mmt180) REVERT: L 368 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: L 402 ASP cc_start: 0.7039 (t70) cc_final: 0.6768 (m-30) REVERT: L 491 LYS cc_start: 0.8444 (mppt) cc_final: 0.8183 (tppt) REVERT: L 496 ARG cc_start: 0.7764 (mmm-85) cc_final: 0.7403 (mmm-85) REVERT: L 570 LYS cc_start: 0.7990 (mttt) cc_final: 0.7706 (mmtm) REVERT: L 911 THR cc_start: 0.8684 (t) cc_final: 0.8261 (p) REVERT: L 967 MET cc_start: 0.8944 (mtt) cc_final: 0.8597 (mtm) REVERT: L 988 ASP cc_start: 0.7890 (t0) cc_final: 0.7321 (p0) REVERT: L 1014 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6961 (mmtt) REVERT: L 1019 ARG cc_start: 0.7509 (ttp80) cc_final: 0.6734 (tpp80) REVERT: L 1031 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7009 (mmmm) REVERT: L 1041 GLU cc_start: 0.7216 (tt0) cc_final: 0.6362 (mm-30) REVERT: L 1073 GLU cc_start: 0.7657 (pp20) cc_final: 0.7089 (tm-30) REVERT: L 1128 ASP cc_start: 0.8016 (p0) cc_final: 0.7583 (t70) REVERT: L 1129 LYS cc_start: 0.7386 (pttt) cc_final: 0.6930 (pttp) REVERT: L 1334 GLN cc_start: 0.8265 (tt0) cc_final: 0.7434 (tp-100) REVERT: L 1388 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7489 (mm) REVERT: L 1443 SER cc_start: 0.7712 (t) cc_final: 0.7460 (m) REVERT: L 1498 ASP cc_start: 0.6722 (m-30) cc_final: 0.6417 (m-30) REVERT: L 1586 GLU cc_start: 0.7718 (tt0) cc_final: 0.7192 (tp30) REVERT: L 1676 ARG cc_start: 0.6629 (mtm-85) cc_final: 0.6301 (mtm-85) REVERT: L 1764 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7174 (p) REVERT: L 1776 ARG cc_start: 0.7529 (tmm160) cc_final: 0.7229 (pmt-80) REVERT: L 1783 ASP cc_start: 0.8146 (m-30) cc_final: 0.7929 (m-30) REVERT: L 1881 ASP cc_start: 0.8131 (t70) cc_final: 0.7912 (t70) REVERT: L 1939 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7358 (mm-30) REVERT: L 2011 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7287 (mtm180) REVERT: L 2113 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7826 (t160) REVERT: L 2115 LYS cc_start: 0.6550 (mtpm) cc_final: 0.5964 (mmtm) REVERT: L 2157 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.7024 (mmm-85) REVERT: L 2170 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: Y 80 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7523 (mtt) REVERT: Y 129 MET cc_start: 0.7150 (mmp) cc_final: 0.6924 (mmm) outliers start: 43 outliers final: 23 residues processed: 308 average time/residue: 0.5711 time to fit residues: 197.1482 Evaluate side-chains 317 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 354 ARG Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 568 ILE Chi-restraints excluded: chain L residue 769 LEU Chi-restraints excluded: chain L residue 873 THR Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1101 THR Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1472 ILE Chi-restraints excluded: chain L residue 1599 VAL Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1764 CYS Chi-restraints excluded: chain L residue 1772 THR Chi-restraints excluded: chain L residue 1796 ILE Chi-restraints excluded: chain L residue 1873 SER Chi-restraints excluded: chain L residue 2005 VAL Chi-restraints excluded: chain L residue 2054 ASP Chi-restraints excluded: chain L residue 2113 ASN Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2157 ARG Chi-restraints excluded: chain L residue 2170 GLU Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 53 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 172 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 375 ASN L 771 GLN L1315 ASN L1976 GLN L2113 ASN L2122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.180247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136164 restraints weight = 30151.571| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.47 r_work: 0.3346 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19840 Z= 0.169 Angle : 0.607 11.086 26822 Z= 0.306 Chirality : 0.041 0.156 3074 Planarity : 0.005 0.082 3368 Dihedral : 4.330 28.765 2646 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.93 % Allowed : 13.68 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.17), residues: 2399 helix: 2.14 (0.14), residues: 1395 sheet: 1.33 (0.45), residues: 151 loop : -0.79 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG X 78 TYR 0.014 0.002 TYR L 382 PHE 0.022 0.002 PHE L 546 TRP 0.022 0.002 TRP L1427 HIS 0.007 0.001 HIS L1643 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (19831) covalent geometry : angle 0.60698 / 0.31 (26821) hydrogen bonds : bond 0.05388 / 3.57 ( 1119) hydrogen bonds : angle 3.84025 / 2.74 ( 3219) metal coordination : bond 0.01579 / 0.70 ( 9) metal coordination : angle 4.05936 / 2.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: D 379 LYS cc_start: 0.6475 (tttm) cc_final: 0.6120 (ttmt) REVERT: L 50 LYS cc_start: 0.8350 (tttt) cc_final: 0.7545 (tppt) REVERT: L 77 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7444 (mtp180) REVERT: L 108 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7661 (pt0) REVERT: L 123 LYS cc_start: 0.8445 (mttt) cc_final: 0.8084 (mmtt) REVERT: L 174 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8109 (mm-30) REVERT: L 332 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8131 (mm-30) REVERT: L 350 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.6438 (m-80) REVERT: L 354 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7788 (mmt180) REVERT: L 368 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: L 402 ASP cc_start: 0.7017 (t70) cc_final: 0.6763 (m-30) REVERT: L 491 LYS cc_start: 0.8370 (mppt) cc_final: 0.8105 (tppt) REVERT: L 496 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7402 (mmm-85) REVERT: L 570 LYS cc_start: 0.7986 (mttt) cc_final: 0.7691 (mmtm) REVERT: L 911 THR cc_start: 0.8689 (t) cc_final: 0.8261 (p) REVERT: L 967 MET cc_start: 0.8943 (mtt) cc_final: 0.8589 (mtm) REVERT: L 988 ASP cc_start: 0.7879 (t0) cc_final: 0.7319 (p0) REVERT: L 1014 LYS cc_start: 0.7185 (mtpp) cc_final: 0.6947 (mmtt) REVERT: L 1019 ARG cc_start: 0.7447 (ttp80) cc_final: 0.6759 (tpp80) REVERT: L 1031 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.7007 (mmmm) REVERT: L 1041 GLU cc_start: 0.7240 (tt0) cc_final: 0.6411 (mm-30) REVERT: L 1128 ASP cc_start: 0.7996 (p0) cc_final: 0.7588 (t70) REVERT: L 1129 LYS cc_start: 0.7407 (pttt) cc_final: 0.6954 (pttp) REVERT: L 1334 GLN cc_start: 0.8242 (tt0) cc_final: 0.7418 (tp-100) REVERT: L 1388 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7445 (mm) REVERT: L 1443 SER cc_start: 0.7739 (t) cc_final: 0.7434 (m) REVERT: L 1498 ASP cc_start: 0.6718 (m-30) cc_final: 0.6406 (m-30) REVERT: L 1586 GLU cc_start: 0.7704 (tt0) cc_final: 0.7179 (tp30) REVERT: L 1676 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.6298 (mtm-85) REVERT: L 1764 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7139 (p) REVERT: L 1783 ASP cc_start: 0.8194 (m-30) cc_final: 0.7941 (m-30) REVERT: L 1881 ASP cc_start: 0.8133 (t70) cc_final: 0.7911 (t70) REVERT: L 1939 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7373 (mm-30) REVERT: L 1961 ASP cc_start: 0.8169 (t0) cc_final: 0.7892 (t0) REVERT: L 1972 LYS cc_start: 0.7835 (tttp) cc_final: 0.7213 (ttmt) REVERT: L 2011 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7300 (mtm180) REVERT: L 2113 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7793 (t160) REVERT: L 2115 LYS cc_start: 0.6601 (mtpm) cc_final: 0.6034 (mmtm) REVERT: L 2157 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.7023 (mmm-85) REVERT: L 2170 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: Y 80 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7504 (mtt) REVERT: Y 129 MET cc_start: 0.7126 (mmp) cc_final: 0.6909 (mmm) outliers start: 42 outliers final: 24 residues processed: 305 average time/residue: 0.5412 time to fit residues: 184.4885 Evaluate side-chains 315 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 354 ARG Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 370 VAL Chi-restraints excluded: chain L residue 568 ILE Chi-restraints excluded: chain L residue 769 LEU Chi-restraints excluded: chain L residue 873 THR Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1101 THR Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1472 ILE Chi-restraints excluded: chain L residue 1599 VAL Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1725 VAL Chi-restraints excluded: chain L residue 1764 CYS Chi-restraints excluded: chain L residue 1772 THR Chi-restraints excluded: chain L residue 1796 ILE Chi-restraints excluded: chain L residue 1873 SER Chi-restraints excluded: chain L residue 2005 VAL Chi-restraints excluded: chain L residue 2113 ASN Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2157 ARG Chi-restraints excluded: chain L residue 2170 GLU Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 53 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 144 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 chunk 236 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 176 optimal weight: 0.0570 chunk 132 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 GLN L1315 ASN L1748 ASN L1976 GLN L2113 ASN L2122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.183598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139328 restraints weight = 31763.534| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.45 r_work: 0.3398 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19840 Z= 0.109 Angle : 0.538 10.076 26822 Z= 0.270 Chirality : 0.039 0.160 3074 Planarity : 0.004 0.081 3368 Dihedral : 4.056 27.899 2646 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.43 % Allowed : 14.28 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.17), residues: 2399 helix: 2.43 (0.14), residues: 1395 sheet: 1.42 (0.45), residues: 151 loop : -0.61 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG X 78 TYR 0.011 0.001 TYR L 382 PHE 0.013 0.001 PHE L 392 TRP 0.020 0.001 TRP L1427 HIS 0.010 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (19831) covalent geometry : angle 0.53726 / 0.27 (26821) hydrogen bonds : bond 0.04153 / 2.73 ( 1119) hydrogen bonds : angle 3.70380 / 2.64 ( 3219) metal coordination : bond 0.01636 / 0.69 ( 9) metal coordination : angle 4.39820 / 2.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: D 363 LEU cc_start: 0.6561 (tt) cc_final: 0.6351 (tp) REVERT: D 379 LYS cc_start: 0.6401 (tttm) cc_final: 0.6051 (ttmt) REVERT: L 50 LYS cc_start: 0.8318 (tttt) cc_final: 0.7544 (tppt) REVERT: L 77 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7334 (mtp180) REVERT: L 108 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7712 (pt0) REVERT: L 123 LYS cc_start: 0.8360 (mttt) cc_final: 0.8041 (mmtt) REVERT: L 174 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8108 (mm-30) REVERT: L 329 GLU cc_start: 0.7752 (mp0) cc_final: 0.7069 (mm-30) REVERT: L 332 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8051 (mm-30) REVERT: L 350 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: L 354 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7726 (mmt180) REVERT: L 368 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: L 402 ASP cc_start: 0.6968 (t70) cc_final: 0.6719 (m-30) REVERT: L 491 LYS cc_start: 0.8419 (mppt) cc_final: 0.8175 (tppt) REVERT: L 496 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: L 570 LYS cc_start: 0.8012 (mttt) cc_final: 0.7730 (mmtm) REVERT: L 744 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7866 (tm-30) REVERT: L 794 ARG cc_start: 0.6640 (ttm110) cc_final: 0.5941 (mtt-85) REVERT: L 911 THR cc_start: 0.8692 (t) cc_final: 0.8292 (p) REVERT: L 967 MET cc_start: 0.8938 (mtt) cc_final: 0.8604 (mtm) REVERT: L 988 ASP cc_start: 0.7828 (t0) cc_final: 0.7282 (p0) REVERT: L 1014 LYS cc_start: 0.7291 (mtpp) cc_final: 0.7017 (mmtt) REVERT: L 1019 ARG cc_start: 0.7499 (ttp80) cc_final: 0.6752 (tpp80) REVERT: L 1031 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6919 (mmmm) REVERT: L 1037 ASP cc_start: 0.7405 (p0) cc_final: 0.7078 (p0) REVERT: L 1041 GLU cc_start: 0.7199 (tt0) cc_final: 0.6364 (mm-30) REVERT: L 1073 GLU cc_start: 0.7668 (pp20) cc_final: 0.7087 (tm-30) REVERT: L 1128 ASP cc_start: 0.7985 (p0) cc_final: 0.7560 (t70) REVERT: L 1129 LYS cc_start: 0.7337 (pttt) cc_final: 0.6753 (pttm) REVERT: L 1334 GLN cc_start: 0.8200 (tt0) cc_final: 0.7359 (tp-100) REVERT: L 1388 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7473 (mm) REVERT: L 1443 SER cc_start: 0.7764 (t) cc_final: 0.7489 (m) REVERT: L 1484 THR cc_start: 0.7760 (m) cc_final: 0.7387 (p) REVERT: L 1498 ASP cc_start: 0.6698 (m-30) cc_final: 0.6404 (m-30) REVERT: L 1584 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7389 (mt-10) REVERT: L 1586 GLU cc_start: 0.7634 (tt0) cc_final: 0.7125 (tp30) REVERT: L 1676 ARG cc_start: 0.6519 (mtm-85) cc_final: 0.6217 (mtm-85) REVERT: L 1783 ASP cc_start: 0.8109 (m-30) cc_final: 0.7872 (m-30) REVERT: L 1881 ASP cc_start: 0.7990 (t70) cc_final: 0.7787 (t70) REVERT: L 1939 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7311 (mm-30) REVERT: L 1972 LYS cc_start: 0.7878 (tttp) cc_final: 0.7295 (ttmt) REVERT: L 2011 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7319 (mtm180) REVERT: L 2113 ASN cc_start: 0.8184 (t0) cc_final: 0.7795 (t160) REVERT: L 2115 LYS cc_start: 0.6335 (mtpm) cc_final: 0.5840 (mmtm) REVERT: L 2170 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: Y 80 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7517 (mtt) REVERT: Y 129 MET cc_start: 0.7189 (mmp) cc_final: 0.6916 (mmm) outliers start: 31 outliers final: 14 residues processed: 311 average time/residue: 0.5343 time to fit residues: 186.4803 Evaluate side-chains 303 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 354 ARG Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1873 SER Chi-restraints excluded: chain L residue 2054 ASP Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2170 GLU Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 53 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 62 optimal weight: 0.6980 chunk 169 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 222 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 128 optimal weight: 0.0070 chunk 175 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 375 ASN L1315 ASN L2122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.184630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134420 restraints weight = 22331.499| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.90 r_work: 0.3442 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19840 Z= 0.105 Angle : 0.543 12.669 26822 Z= 0.270 Chirality : 0.039 0.166 3074 Planarity : 0.004 0.086 3368 Dihedral : 3.932 26.944 2646 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.97 % Allowed : 15.15 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.18), residues: 2399 helix: 2.51 (0.14), residues: 1400 sheet: 1.45 (0.45), residues: 156 loop : -0.56 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG X 78 TYR 0.010 0.001 TYR L 382 PHE 0.025 0.001 PHE L 546 TRP 0.017 0.001 TRP L1427 HIS 0.007 0.001 HIS L1643 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (19831) covalent geometry : angle 0.54205 / 0.27 (26821) hydrogen bonds : bond 0.03889 / 2.56 ( 1119) hydrogen bonds : angle 3.65373 / 2.60 ( 3219) metal coordination : bond 0.01511 / 0.64 ( 9) metal coordination : angle 4.31249 / 2.27 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4798 Ramachandran restraints generated. 2399 Oldfield, 0 Emsley, 2399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 0.753 Fit side-chains REVERT: D 363 LEU cc_start: 0.6500 (tt) cc_final: 0.6291 (tp) REVERT: D 379 LYS cc_start: 0.6357 (tttm) cc_final: 0.6018 (ttmt) REVERT: L 50 LYS cc_start: 0.8332 (tttt) cc_final: 0.7628 (tppt) REVERT: L 108 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7721 (pt0) REVERT: L 123 LYS cc_start: 0.8311 (mttt) cc_final: 0.8015 (mmtt) REVERT: L 329 GLU cc_start: 0.7640 (mp0) cc_final: 0.6966 (mm-30) REVERT: L 332 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8029 (mm-30) REVERT: L 350 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.6242 (m-80) REVERT: L 354 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7696 (mmt180) REVERT: L 368 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: L 402 ASP cc_start: 0.6910 (t70) cc_final: 0.6688 (m-30) REVERT: L 496 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7383 (mmm-85) REVERT: L 570 LYS cc_start: 0.8009 (mttt) cc_final: 0.7743 (mmtm) REVERT: L 794 ARG cc_start: 0.6601 (ttm110) cc_final: 0.5972 (mtt-85) REVERT: L 911 THR cc_start: 0.8698 (t) cc_final: 0.8317 (p) REVERT: L 967 MET cc_start: 0.8968 (mtt) cc_final: 0.8635 (mtm) REVERT: L 988 ASP cc_start: 0.7744 (t0) cc_final: 0.7267 (p0) REVERT: L 1014 LYS cc_start: 0.7353 (mtpp) cc_final: 0.7036 (mmtt) REVERT: L 1019 ARG cc_start: 0.7485 (ttp80) cc_final: 0.6746 (tpp80) REVERT: L 1031 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6879 (mmmm) REVERT: L 1037 ASP cc_start: 0.7411 (p0) cc_final: 0.7099 (p0) REVERT: L 1041 GLU cc_start: 0.7193 (tt0) cc_final: 0.6386 (mm-30) REVERT: L 1073 GLU cc_start: 0.7580 (pp20) cc_final: 0.7058 (tm-30) REVERT: L 1128 ASP cc_start: 0.7925 (p0) cc_final: 0.7544 (t70) REVERT: L 1129 LYS cc_start: 0.7332 (pttt) cc_final: 0.6789 (pttm) REVERT: L 1334 GLN cc_start: 0.8212 (tt0) cc_final: 0.7382 (tp-100) REVERT: L 1366 GLU cc_start: 0.7851 (mp0) cc_final: 0.7546 (pm20) REVERT: L 1388 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7409 (mm) REVERT: L 1484 THR cc_start: 0.7640 (m) cc_final: 0.7316 (p) REVERT: L 1584 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7332 (mt-10) REVERT: L 1586 GLU cc_start: 0.7572 (tt0) cc_final: 0.7085 (tp30) REVERT: L 1676 ARG cc_start: 0.6472 (mtm-85) cc_final: 0.6157 (mtm-85) REVERT: L 1776 ARG cc_start: 0.7585 (tmm160) cc_final: 0.7364 (pmt-80) REVERT: L 1783 ASP cc_start: 0.8008 (m-30) cc_final: 0.7805 (m-30) REVERT: L 1881 ASP cc_start: 0.7933 (t70) cc_final: 0.7730 (t70) REVERT: L 1939 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7336 (mm-30) REVERT: L 2011 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7327 (mtm180) REVERT: L 2113 ASN cc_start: 0.8098 (t0) cc_final: 0.7789 (t0) REVERT: L 2115 LYS cc_start: 0.6531 (mtpm) cc_final: 0.6030 (mmtm) REVERT: Y 129 MET cc_start: 0.7116 (mmp) cc_final: 0.6867 (mtt) REVERT: Y 145 MET cc_start: 0.6962 (mmp) cc_final: 0.6535 (mmp) outliers start: 21 outliers final: 11 residues processed: 288 average time/residue: 0.5742 time to fit residues: 185.8027 Evaluate side-chains 287 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 354 ARG Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 1031 LYS Chi-restraints excluded: chain L residue 1074 SER Chi-restraints excluded: chain L residue 1235 LEU Chi-restraints excluded: chain L residue 1388 LEU Chi-restraints excluded: chain L residue 1612 LEU Chi-restraints excluded: chain L residue 1933 VAL Chi-restraints excluded: chain L residue 2054 ASP Chi-restraints excluded: chain L residue 2137 ILE Chi-restraints excluded: chain L residue 2174 LEU Chi-restraints excluded: chain Y residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 163 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 771 GLN L2122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137165 restraints weight = 24985.338| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.94 r_work: 0.3428 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19840 Z= 0.118 Angle : 0.555 12.188 26822 Z= 0.276 Chirality : 0.039 0.175 3074 Planarity : 0.004 0.087 3368 Dihedral : 3.982 26.853 2646 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.97 % Allowed : 15.48 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.17), residues: 2399 helix: 2.47 (0.14), residues: 1400 sheet: 1.39 (0.45), residues: 151 loop : -0.59 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG X 78 TYR 0.013 0.001 TYR L 382 PHE 0.013 0.001 PHE L 392 TRP 0.019 0.001 TRP L1427 HIS 0.007 0.001 HIS L1643 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19831) covalent geometry : angle 0.55406 / 0.28 (26821) hydrogen bonds : bond 0.04246 / 2.79 ( 1119) hydrogen bonds : angle 3.66338 / 2.61 ( 3219) metal coordination : bond 0.01592 / 0.69 ( 9) metal coordination : angle 4.37669 / 2.30 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7580.81 seconds wall clock time: 129 minutes 18.87 seconds (7758.87 seconds total)