Starting phenix.real_space_refine on Thu Mar 5 17:44:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vf9_31948/03_2026/7vf9_31948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vf9_31948/03_2026/7vf9_31948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vf9_31948/03_2026/7vf9_31948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vf9_31948/03_2026/7vf9_31948.map" model { file = "/net/cci-nas-00/data/ceres_data/7vf9_31948/03_2026/7vf9_31948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vf9_31948/03_2026/7vf9_31948.cif" } resolution = 4.04 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 86 5.16 5 C 15244 2.51 5 N 4427 2.21 5 O 4487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24247 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1587 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1508 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 9387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 9387 Classifications: {'peptide': 1324} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 53, 'TRANS': 1270} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 968 Unresolved non-hydrogen angles: 1243 Unresolved non-hydrogen dihedrals: 740 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'ASP:plan': 29, 'GLU:plan': 49, 'GLN:plan1': 12, 'ARG:plan': 19, 'PHE:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 16, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 556 Chain: "D" Number of atoms: 9407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 9407 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 60, 'TRANS': 1278} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1019 Unresolved non-hydrogen angles: 1308 Unresolved non-hydrogen dihedrals: 803 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLU:plan': 49, 'ASN:plan1': 15, 'TYR:plan': 5, 'ARG:plan': 22, 'HIS:plan': 8, 'ASP:plan': 41, 'PHE:plan': 10, 'GLN:plan1': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 631 Chain: "E" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 463 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1892 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 17, 'HIS:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 8, 'ARG:plan': 8, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12896 SG CYS D 70 111.686 49.089 70.575 1.00 63.72 S ATOM 18908 SG CYS D 888 80.197 69.653 125.220 1.00 33.02 S ATOM 18969 SG CYS D 898 76.769 69.429 127.302 1.00 25.74 S Time building chain proxies: 5.52, per 1000 atoms: 0.23 Number of scatterers: 24247 At special positions: 0 Unit cell: (143.77, 162.068, 159.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 86 16.00 Mg 1 11.99 O 4487 8.00 N 4427 7.00 C 15244 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6330 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 46 sheets defined 39.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 removed outlier: 4.319A pdb=" N HIS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 50 removed outlier: 3.581A pdb=" N ARG A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.506A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 211 through 229 removed outlier: 4.155A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.713A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.517A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.743A pdb=" N ALA B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.897A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.138A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.892A pdb=" N ALA C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 58 " --> pdb=" O HIS C 54 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.935A pdb=" N VAL C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.551A pdb=" N ALA C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 removed outlier: 3.757A pdb=" N LEU C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.621A pdb=" N ILE C 298 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 299 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.869A pdb=" N LEU C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.868A pdb=" N ASP C 354 " --> pdb=" O PRO C 350 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.545A pdb=" N ALA C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 395 removed outlier: 3.756A pdb=" N THR C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.583A pdb=" N LYS C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 443 removed outlier: 3.505A pdb=" N ILE C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 433 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 485 removed outlier: 3.507A pdb=" N MET C 464 " --> pdb=" O CYS C 460 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 465 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 472 " --> pdb=" O GLN C 468 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 4.144A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 511 removed outlier: 3.660A pdb=" N ILE C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 511 " --> pdb=" O ILE C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.645A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.999A pdb=" N TYR C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.914A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 655 removed outlier: 3.815A pdb=" N VAL C 655 " --> pdb=" O PRO C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 665 removed outlier: 4.117A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 673 removed outlier: 3.820A pdb=" N LEU C 672 " --> pdb=" O ALA C 669 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE C 673 " --> pdb=" O ALA C 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 669 through 673' Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 691 removed outlier: 3.800A pdb=" N ASN C 689 " --> pdb=" O LEU C 685 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 691 " --> pdb=" O GLY C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 717 removed outlier: 4.023A pdb=" N ARG C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 716 " --> pdb=" O ASN C 712 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 717 " --> pdb=" O VAL C 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 711 through 717' Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 863 through 870 removed outlier: 3.825A pdb=" N LEU C 867 " --> pdb=" O GLY C 863 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN C 868 " --> pdb=" O GLU C 864 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS C 869 " --> pdb=" O ALA C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 912 removed outlier: 3.783A pdb=" N LEU C 907 " --> pdb=" O GLU C 903 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 912 " --> pdb=" O ARG C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 982 removed outlier: 3.742A pdb=" N ILE C 953 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 954 " --> pdb=" O ALA C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.664A pdb=" N ASP C1044 " --> pdb=" O GLN C1040 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 4.732A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1151 removed outlier: 4.178A pdb=" N ILE C1129 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C1137 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C1150 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.708A pdb=" N LYS C1160 " --> pdb=" O ALA C1156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C1165 " --> pdb=" O PHE C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1191 removed outlier: 3.828A pdb=" N ILE C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C1186 " --> pdb=" O ASN C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1194 No H-bonds generated for 'chain 'C' and resid 1192 through 1194' Processing helix chain 'C' and resid 1206 through 1217 removed outlier: 3.509A pdb=" N LEU C1214 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C1216 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1287 through 1296 removed outlier: 3.582A pdb=" N LEU C1293 " --> pdb=" O GLU C1289 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR C1296 " --> pdb=" O ALA C1292 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1308 removed outlier: 3.642A pdb=" N LEU C1306 " --> pdb=" O LEU C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1312 through 1326 Processing helix chain 'C' and resid 1335 through 1347 removed outlier: 3.652A pdb=" N VAL C1340 " --> pdb=" O GLU C1336 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C1341 " --> pdb=" O SER C1337 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C1347 " --> pdb=" O LYS C1343 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.821A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.007A pdb=" N ARG D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 114 through 119 removed outlier: 4.225A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.789A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.621A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.526A pdb=" N PHE D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.830A pdb=" N VAL D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN D 190 " --> pdb=" O HIS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.544A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.500A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.532A pdb=" N MET D 237 " --> pdb=" O PRO D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 281 removed outlier: 4.057A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 removed outlier: 3.769A pdb=" N ARG D 293 " --> pdb=" O ASP D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 308 removed outlier: 3.709A pdb=" N LEU D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.934A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.855A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.542A pdb=" N PHE D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.505A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.520A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.513A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 480 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.516A pdb=" N MET D 513 " --> pdb=" O GLY D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.587A pdb=" N ALA D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 540 " --> pdb=" O ALA D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.666A pdb=" N PHE D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 3.730A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 removed outlier: 4.065A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.542A pdb=" N PHE D 644 " --> pdb=" O VAL D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.514A pdb=" N ASP D 659 " --> pdb=" O ASN D 655 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 662 " --> pdb=" O THR D 658 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 666 " --> pdb=" O LYS D 662 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 668 " --> pdb=" O ILE D 664 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA D 669 " --> pdb=" O GLU D 665 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 670 " --> pdb=" O SER D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.506A pdb=" N TYR D 679 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 687 " --> pdb=" O ILE D 683 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.692A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 741 removed outlier: 3.750A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.651A pdb=" N PHE D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 774 " --> pdb=" O LEU D 770 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 802 removed outlier: 3.654A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.799A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 871 " --> pdb=" O LYS D 867 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET D 875 " --> pdb=" O PHE D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.751A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 4.015A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.772A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1222 removed outlier: 3.882A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1216 through 1222' Processing helix chain 'D' and resid 1226 through 1245 removed outlier: 3.608A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.187A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.897A pdb=" N LEU D1292 " --> pdb=" O GLU D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 4.178A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D1315 " --> pdb=" O LYS D1311 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.718A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.738A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D1336 " --> pdb=" O LEU D1332 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 removed outlier: 3.533A pdb=" N GLU D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D1376 " --> pdb=" O GLN D1372 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 removed outlier: 3.554A pdb=" N LEU E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.579A pdb=" N LYS E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN E 29 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.741A pdb=" N VAL E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 52 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 68 removed outlier: 3.667A pdb=" N ASP E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.956A pdb=" N GLU F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 91 removed outlier: 3.809A pdb=" N VAL F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.623A pdb=" N GLU F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 114 removed outlier: 3.753A pdb=" N ARG F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG F 113 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 137 removed outlier: 3.609A pdb=" N LEU F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU F 132 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 163 removed outlier: 4.299A pdb=" N TRP F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 156 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN F 157 " --> pdb=" O TRP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 195 removed outlier: 3.523A pdb=" N LYS F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU F 179 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 180 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 207 removed outlier: 3.582A pdb=" N ILE F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.756A pdb=" N LYS F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 250 through 271 removed outlier: 3.501A pdb=" N THR F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 281 removed outlier: 3.619A pdb=" N GLU F 277 " --> pdb=" O ASP F 273 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 278 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 324 removed outlier: 3.616A pdb=" N ILE F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 312 " --> pdb=" O ARG F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 334 removed outlier: 3.722A pdb=" N PHE F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 3.639A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP A 198 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 4.098A pdb=" N VAL A 98 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 104 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 4.149A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 removed outlier: 3.553A pdb=" N ALA A 174 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.339A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 204 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 201 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 185 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 3.998A pdb=" N GLY B 53 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS B 144 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 59 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 142 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE B 61 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN B 140 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.272A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.452A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 70 through 79 removed outlier: 6.914A pdb=" N LYS C 103 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR C 77 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG C 101 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 79 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 119 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 70 through 79 removed outlier: 6.914A pdb=" N LYS C 103 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR C 77 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG C 101 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 79 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.780A pdb=" N VAL C 148 " --> pdb=" O GLN C 518 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN C 518 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 456 through 458 removed outlier: 3.592A pdb=" N VAL C 535 " --> pdb=" O ASN C 578 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 164 removed outlier: 6.729A pdb=" N ASP C 164 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 175 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N TYR C 176 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C 192 " --> pdb=" O TYR C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.504A pdb=" N LEU C 243 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS C 235 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU C 244 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 233 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 232 " --> pdb=" O THR C 340 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 340 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 234 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 338 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 254 through 255 removed outlier: 4.205A pdb=" N ALA C 255 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG C 272 " --> pdb=" O ALA C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC2, first strand: chain 'C' and resid 585 through 586 removed outlier: 5.321A pdb=" N GLU C 607 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC4, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC5, first strand: chain 'C' and resid 721 through 722 removed outlier: 3.775A pdb=" N ALA C 789 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 755 through 757 removed outlier: 6.971A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC8, first strand: chain 'C' and resid 1224 through 1225 removed outlier: 3.574A pdb=" N ALA C1084 " --> pdb=" O LEU C1248 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU C 823 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE C1096 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE C1113 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG C 806 " --> pdb=" O ILE C1113 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU C1115 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 808 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C 805 " --> pdb=" O MET C1245 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 837 through 844 removed outlier: 4.466A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 892 through 893 removed outlier: 3.510A pdb=" N THR C 893 " --> pdb=" O LYS C 919 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.571A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.571A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1284 through 1286 Processing sheet with id=AD5, first strand: chain 'C' and resid 1350 through 1352 removed outlier: 3.593A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 8.461A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.640A pdb=" N VAL D 145 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.591A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 550 through 556 removed outlier: 3.617A pdb=" N VAL D 550 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 554 " --> pdb=" O ASN D 566 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 556 " --> pdb=" O THR D 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR D 564 " --> pdb=" O ILE D 556 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.620A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 950 through 951 removed outlier: 6.733A pdb=" N VAL D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.866A pdb=" N HIS D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 981 " --> pdb=" O HIS D 961 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 974 through 975 Processing sheet with id=AE6, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 4.047A pdb=" N ILE D1124 " --> pdb=" O HIS D1025 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1098 through 1099 removed outlier: 3.881A pdb=" N GLY D1033 " --> pdb=" O VAL D1115 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D1115 " --> pdb=" O GLY D1033 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.852A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D1107 " --> pdb=" O ILE D1059 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 3.663A pdb=" N GLU D1202 " --> pdb=" O ILE D1163 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 3.566A pdb=" N ASP D1278 " --> pdb=" O VAL D1264 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2388 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: 5.30 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8436 1.34 - 1.46: 4435 1.46 - 1.58: 11544 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 24565 Sorted by residual: bond pdb=" CA VAL C 925 " pdb=" CB VAL C 925 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.91e-01 bond pdb=" N ILE D1357 " pdb=" CA ILE D1357 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.77e-01 bond pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.27e-02 6.20e+03 5.47e-01 bond pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 1.514 1.504 0.010 1.41e-02 5.03e+03 5.23e-01 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.350 -0.017 2.34e-02 1.83e+03 4.98e-01 ... (remaining 24560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 32746 1.18 - 2.36: 437 2.36 - 3.55: 131 3.55 - 4.73: 15 4.73 - 5.91: 8 Bond angle restraints: 33337 Sorted by residual: angle pdb=" N VAL D 591 " pdb=" CA VAL D 591 " pdb=" C VAL D 591 " ideal model delta sigma weight residual 112.80 109.78 3.02 1.15e+00 7.56e-01 6.90e+00 angle pdb=" N VAL D 611 " pdb=" CA VAL D 611 " pdb=" C VAL D 611 " ideal model delta sigma weight residual 111.62 109.77 1.85 7.90e-01 1.60e+00 5.46e+00 angle pdb=" C ILE D 500 " pdb=" N VAL D 501 " pdb=" CA VAL D 501 " ideal model delta sigma weight residual 119.72 123.86 -4.14 2.01e+00 2.48e-01 4.23e+00 angle pdb=" CA VAL D 592 " pdb=" C VAL D 592 " pdb=" N ASN D 593 " ideal model delta sigma weight residual 116.60 119.23 -2.63 1.45e+00 4.76e-01 3.28e+00 angle pdb=" C GLY D1137 " pdb=" N LEU D1138 " pdb=" CA LEU D1138 " ideal model delta sigma weight residual 120.09 122.28 -2.19 1.25e+00 6.40e-01 3.08e+00 ... (remaining 33332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 14307 17.43 - 34.85: 581 34.85 - 52.28: 70 52.28 - 69.71: 12 69.71 - 87.13: 12 Dihedral angle restraints: 14982 sinusoidal: 5182 harmonic: 9800 Sorted by residual: dihedral pdb=" CB GLU C1168 " pdb=" CG GLU C1168 " pdb=" CD GLU C1168 " pdb=" OE1 GLU C1168 " ideal model delta sinusoidal sigma weight residual 0.00 -87.13 87.13 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU D 225 " pdb=" CG GLU D 225 " pdb=" CD GLU D 225 " pdb=" OE1 GLU D 225 " ideal model delta sinusoidal sigma weight residual 0.00 -84.97 84.97 1 3.00e+01 1.11e-03 9.73e+00 dihedral pdb=" CB GLU F 320 " pdb=" CG GLU F 320 " pdb=" CD GLU F 320 " pdb=" OE1 GLU F 320 " ideal model delta sinusoidal sigma weight residual 0.00 84.68 -84.68 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 14979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2583 0.031 - 0.062: 1007 0.062 - 0.092: 205 0.092 - 0.123: 177 0.123 - 0.154: 4 Chirality restraints: 3976 Sorted by residual: chirality pdb=" CB ILE D 500 " pdb=" CA ILE D 500 " pdb=" CG1 ILE D 500 " pdb=" CG2 ILE D 500 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE C 673 " pdb=" N ILE C 673 " pdb=" C ILE C 673 " pdb=" CB ILE C 673 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 821 " pdb=" N ILE C 821 " pdb=" C ILE C 821 " pdb=" CB ILE C 821 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 3973 not shown) Planarity restraints: 4392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 502 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO D 851 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO D1139 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " -0.015 5.00e-02 4.00e+02 ... (remaining 4389 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 760 2.72 - 3.27: 22809 3.27 - 3.81: 34270 3.81 - 4.36: 41716 4.36 - 4.90: 71338 Nonbonded interactions: 170893 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.176 2.170 nonbonded pdb=" O SER C 667 " pdb=" OG SER C 671 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OD1 ASP C 325 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 10 " pdb=" O GLN B 225 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.284 2.170 ... (remaining 170888 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 'A' and (resid 8 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 57 or (resid 58 through 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 throug \ h 66 and (name N or name CA or name C or name O or name CB )) or resid 67 throug \ h 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or re \ sid 76 through 79 or (resid 80 and (name N or name CA or name C or name O or nam \ e CB )) or resid 81 through 89 or (resid 90 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or resid 91 through 92 or (resid 93 \ and (name N or name CA or name C or name O or name CB )) or resid 94 or (resid 9 \ 5 and (name N or name CA or name C or name O or name CB or name CG )) or resid 9 \ 6 through 104 or (resid 105 and (name N or name CA or name C or name O or name C \ B )) or resid 109 through 113 or (resid 114 and (name N or name CA or name C or \ name O or name CB )) or resid 115 through 118 or (resid 119 and (name N or name \ CA or name C or name O or name CB )) or resid 120 through 134 or resid 139 throu \ gh 141 or (resid 142 and (name N or name CA or name C or name O or name CB )) or \ resid 143 through 157 or (resid 169 and (name N or name CA or name C or name O \ or name CB )) or resid 170 through 182 or (resid 183 and (name N or name CA or n \ ame C or name O or name CB )) or resid 184 through 229 or (resid 230 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or resid 27 through 71 or (resid 72 and (name N or name CA or name C or name \ O or name CB )) or resid 73 through 116 or (resid 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 through 126 or (resid 127 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 128 through \ 139 or (resid 140 and (name N or name CA or name C or name O or name CB or name \ CG )) or resid 141 through 151 or (resid 152 and (name N or name CA or name C or \ name O or name CB )) or resid 153 through 193 or (resid 194 through 196 and (na \ me N or name CA or name C or name O or name CB )) or resid 197 through 212 or (r \ esid 213 through 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 230)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.530 Find NCS groups from input model: 0.220 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 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 : 0.003 0.398 24568 Z= 0.128 Angle : 0.385 5.909 33337 Z= 0.228 Chirality : 0.038 0.154 3976 Planarity : 0.002 0.039 4392 Dihedral : 9.647 87.134 8652 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.11), residues: 3397 helix: -4.56 (0.05), residues: 1095 sheet: -0.99 (0.26), residues: 339 loop : -2.36 (0.11), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 278 TYR 0.004 0.000 TYR C1296 PHE 0.017 0.000 PHE D1325 TRP 0.003 0.000 TRP C 187 HIS 0.001 0.000 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00141 (24565) covalent geometry : angle 0.38463 (33337) hydrogen bonds : bond 0.34680 ( 833) hydrogen bonds : angle 9.49125 ( 2388) metal coordination : bond 0.27773 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 576 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 46 >>> skipping Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 116 GLN cc_start: 0.6438 (mt0) cc_final: 0.6139 (tm-30) REVERT: B 21 GLN cc_start: 0.7209 (mp10) cc_final: 0.6721 (tp40) REVERT: B 35 PHE cc_start: 0.7731 (m-80) cc_final: 0.7148 (m-80) REVERT: B 37 HIS cc_start: 0.8180 (t70) cc_final: 0.7970 (t70) REVERT: B 76 GLU cc_start: 0.8062 (mp0) cc_final: 0.7310 (mt-10) REVERT: B 130 ILE cc_start: 0.8694 (mm) cc_final: 0.8210 (mm) REVERT: B 184 TYR cc_start: 0.8842 (p90) cc_final: 0.8551 (p90) REVERT: C 134 MET cc_start: 0.9117 (ptt) cc_final: 0.8799 (ppp) REVERT: C 522 GLN cc_start: 0.7955 (tt0) cc_final: 0.7708 (tt0) REVERT: C 647 PHE cc_start: 0.7687 (t80) cc_final: 0.7455 (m-80) REVERT: C 709 MET cc_start: 0.8509 (mmm) cc_final: 0.8069 (tpp) REVERT: C 756 TYR cc_start: 0.8552 (m-80) cc_final: 0.8070 (m-80) REVERT: C 951 LEU cc_start: 0.8330 (pp) cc_final: 0.7922 (tp) REVERT: C 956 MET cc_start: 0.6561 (ttt) cc_final: 0.6132 (ttp) REVERT: C 1192 ARG cc_start: 0.8310 (ptm160) cc_final: 0.7172 (ttp80) REVERT: C 1208 ARG cc_start: 0.7823 (ptm-80) cc_final: 0.7217 (ttp-170) REVERT: C 1261 ARG cc_start: 0.7960 (ttt-90) cc_final: 0.7703 (ptt-90) REVERT: C 1320 TYR cc_start: 0.8484 (t80) cc_final: 0.8257 (t80) REVERT: D 66 LYS cc_start: 0.6951 (ptmt) cc_final: 0.6662 (mptt) REVERT: D 265 LEU cc_start: 0.8864 (tp) cc_final: 0.8384 (tp) REVERT: D 418 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6554 (mm-30) REVERT: D 625 MET cc_start: 0.7640 (ttp) cc_final: 0.7228 (ttp) REVERT: D 990 ARG cc_start: 0.5578 (ptt180) cc_final: 0.5033 (ptp-170) REVERT: D 1151 LYS cc_start: 0.7314 (mtmt) cc_final: 0.6979 (pptt) REVERT: E 21 MET cc_start: 0.8498 (mmm) cc_final: 0.7606 (mmm) REVERT: F 96 ARG cc_start: 0.6366 (mtt180) cc_final: 0.5919 (ptm-80) REVERT: F 117 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6569 (mtt180) REVERT: F 274 LYS cc_start: 0.5911 (tptp) cc_final: 0.5455 (ttpt) REVERT: F 277 GLU cc_start: 0.6855 (pp20) cc_final: 0.6095 (pp20) outliers start: 3 outliers final: 3 residues processed: 579 average time/residue: 0.2006 time to fit residues: 168.6221 Evaluate side-chains 359 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 356 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 66 HIS A 225 GLN B 17 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 623 GLN C 682 ASN C 837 HIS C 839 GLN C 957 GLN C1027 GLN C1055 GLN C1133 HIS C1167 ASN C1235 GLN C1322 ASN D 104 HIS D 448 GLN D 458 ASN D 465 GLN D 477 GLN D 929 GLN F 129 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147786 restraints weight = 39637.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147006 restraints weight = 50457.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147437 restraints weight = 46452.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146467 restraints weight = 41576.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147312 restraints weight = 34973.420| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24568 Z= 0.116 Angle : 0.503 6.976 33337 Z= 0.261 Chirality : 0.041 0.155 3976 Planarity : 0.004 0.054 4392 Dihedral : 2.681 12.472 3669 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.12), residues: 3397 helix: -2.35 (0.12), residues: 1171 sheet: -0.68 (0.26), residues: 355 loop : -1.89 (0.12), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1316 TYR 0.016 0.001 TYR D 679 PHE 0.021 0.001 PHE C 228 TRP 0.016 0.001 TRP D 409 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00248 (24565) covalent geometry : angle 0.50307 (33337) hydrogen bonds : bond 0.05580 ( 833) hydrogen bonds : angle 5.19679 ( 2388) metal coordination : bond 0.01999 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: B 21 GLN cc_start: 0.7270 (mp10) cc_final: 0.6907 (tp40) REVERT: B 76 GLU cc_start: 0.7774 (mp0) cc_final: 0.7379 (mt-10) REVERT: B 86 LYS cc_start: 0.6675 (mttm) cc_final: 0.6163 (mttm) REVERT: B 130 ILE cc_start: 0.8723 (mm) cc_final: 0.8508 (mm) REVERT: B 184 TYR cc_start: 0.8938 (p90) cc_final: 0.8725 (p90) REVERT: B 205 GLU cc_start: 0.7941 (mp0) cc_final: 0.7626 (mp0) REVERT: C 37 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7591 (mt-10) REVERT: C 374 MET cc_start: 0.7736 (mmm) cc_final: 0.7274 (mmm) REVERT: C 520 MET cc_start: 0.7608 (ttp) cc_final: 0.7360 (ttp) REVERT: C 522 GLN cc_start: 0.7845 (tt0) cc_final: 0.7602 (tt0) REVERT: C 709 MET cc_start: 0.8675 (mmm) cc_final: 0.8254 (tpp) REVERT: C 756 TYR cc_start: 0.8563 (m-80) cc_final: 0.8169 (m-80) REVERT: C 951 LEU cc_start: 0.8444 (pp) cc_final: 0.8030 (tp) REVERT: C 1192 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7623 (ptm160) REVERT: C 1208 ARG cc_start: 0.7251 (ptm-80) cc_final: 0.6802 (ptt-90) REVERT: C 1261 ARG cc_start: 0.8198 (ttt-90) cc_final: 0.7790 (ptt-90) REVERT: C 1320 TYR cc_start: 0.8331 (t80) cc_final: 0.7920 (t80) REVERT: C 1344 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7381 (mt-10) REVERT: D 66 LYS cc_start: 0.7036 (ptmt) cc_final: 0.6738 (mptt) REVERT: D 418 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6832 (mm-30) REVERT: D 457 TYR cc_start: 0.8779 (m-80) cc_final: 0.8263 (m-80) REVERT: D 500 ILE cc_start: 0.8899 (mt) cc_final: 0.8620 (mt) REVERT: D 541 GLN cc_start: 0.8607 (mp10) cc_final: 0.8283 (mp10) REVERT: D 625 MET cc_start: 0.7713 (ttp) cc_final: 0.7427 (ttp) REVERT: D 990 ARG cc_start: 0.5484 (ptt180) cc_final: 0.5060 (ptp-170) REVERT: D 1151 LYS cc_start: 0.7339 (mtmt) cc_final: 0.7006 (pptt) REVERT: D 1221 LEU cc_start: 0.7683 (pt) cc_final: 0.6472 (tp) REVERT: D 1236 GLU cc_start: 0.7150 (tp30) cc_final: 0.6675 (tp30) REVERT: E 42 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7022 (mm-30) REVERT: F 117 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6738 (mtt90) REVERT: F 155 ILE cc_start: 0.8278 (tt) cc_final: 0.7874 (mt) REVERT: F 217 MET cc_start: 0.7532 (mmm) cc_final: 0.7218 (mmp) REVERT: F 274 LYS cc_start: 0.6169 (tptp) cc_final: 0.5689 (tttm) REVERT: F 277 GLU cc_start: 0.6577 (pp20) cc_final: 0.5876 (pp20) outliers start: 2 outliers final: 2 residues processed: 431 average time/residue: 0.1700 time to fit residues: 112.8675 Evaluate side-chains 316 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 314 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 84 ASN B 116 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 HIS C1224 GLN C1322 ASN D 465 GLN D 777 HIS D 951 GLN F 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.160109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140046 restraints weight = 40352.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138245 restraints weight = 57166.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139363 restraints weight = 52411.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139163 restraints weight = 33784.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139371 restraints weight = 32679.006| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24568 Z= 0.201 Angle : 0.594 6.990 33337 Z= 0.309 Chirality : 0.045 0.170 3976 Planarity : 0.004 0.050 4392 Dihedral : 3.565 14.699 3669 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.14 % Allowed : 5.36 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 3397 helix: -1.30 (0.14), residues: 1182 sheet: -0.55 (0.26), residues: 368 loop : -1.63 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1345 TYR 0.018 0.002 TYR C 583 PHE 0.020 0.002 PHE D 437 TRP 0.029 0.002 TRP D 409 HIS 0.008 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00469 (24565) covalent geometry : angle 0.59450 (33337) hydrogen bonds : bond 0.04923 ( 833) hydrogen bonds : angle 4.90312 ( 2388) metal coordination : bond 0.00623 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 175 SER cc_start: 0.8288 (m) cc_final: 0.7759 (p) REVERT: B 21 GLN cc_start: 0.7505 (mp10) cc_final: 0.7175 (tt0) REVERT: B 37 HIS cc_start: 0.7948 (t-90) cc_final: 0.7665 (t70) REVERT: B 76 GLU cc_start: 0.8052 (mp0) cc_final: 0.7177 (mt-10) REVERT: B 86 LYS cc_start: 0.6838 (mttt) cc_final: 0.6481 (mttt) REVERT: B 97 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 130 ILE cc_start: 0.8864 (mm) cc_final: 0.8595 (mm) REVERT: B 184 TYR cc_start: 0.8911 (p90) cc_final: 0.8242 (p90) REVERT: C 37 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 155 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7558 (mtp180) REVERT: C 520 MET cc_start: 0.7821 (ttp) cc_final: 0.7535 (ttp) REVERT: C 522 GLN cc_start: 0.7844 (tt0) cc_final: 0.7554 (tt0) REVERT: C 564 CYS cc_start: 0.9283 (t) cc_final: 0.8898 (t) REVERT: C 647 PHE cc_start: 0.7760 (t80) cc_final: 0.7459 (m-80) REVERT: C 1097 MET cc_start: 0.6925 (mmt) cc_final: 0.6711 (mmt) REVERT: C 1208 ARG cc_start: 0.7338 (ptm-80) cc_final: 0.6879 (ptt-90) REVERT: C 1308 VAL cc_start: 0.8742 (t) cc_final: 0.8152 (t) REVERT: C 1320 TYR cc_start: 0.8737 (t80) cc_final: 0.8103 (t80) REVERT: C 1344 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7294 (mt-10) REVERT: D 94 LEU cc_start: 0.8183 (mp) cc_final: 0.7490 (tp) REVERT: D 220 ARG cc_start: 0.7183 (mmt90) cc_final: 0.6677 (mtp180) REVERT: D 457 TYR cc_start: 0.9016 (m-80) cc_final: 0.8507 (m-80) REVERT: D 645 VAL cc_start: 0.8647 (p) cc_final: 0.8383 (m) REVERT: D 990 ARG cc_start: 0.6011 (ptt180) cc_final: 0.5532 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7712 (pt) cc_final: 0.6592 (tp) REVERT: D 1236 GLU cc_start: 0.7231 (tp30) cc_final: 0.6870 (tp30) REVERT: D 1342 ASP cc_start: 0.6473 (t70) cc_final: 0.6129 (t70) REVERT: E 42 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7241 (mm-30) REVERT: F 117 ARG cc_start: 0.7295 (mmm160) cc_final: 0.6916 (mtt90) REVERT: F 217 MET cc_start: 0.8032 (mmm) cc_final: 0.7598 (mmp) REVERT: F 274 LYS cc_start: 0.6119 (tptp) cc_final: 0.5764 (tttt) REVERT: F 277 GLU cc_start: 0.6825 (pp20) cc_final: 0.6302 (pp20) REVERT: F 281 ARG cc_start: 0.6243 (mtt180) cc_final: 0.5552 (mmm160) outliers start: 4 outliers final: 2 residues processed: 391 average time/residue: 0.1778 time to fit residues: 107.3591 Evaluate side-chains 298 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 249 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 282 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 116 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS C1128 GLN C1252 HIS D 642 ASN D 951 GLN F 129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145256 restraints weight = 39771.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142541 restraints weight = 54681.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140618 restraints weight = 45933.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140146 restraints weight = 41926.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140717 restraints weight = 38362.877| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24568 Z= 0.096 Angle : 0.480 8.368 33337 Z= 0.242 Chirality : 0.041 0.169 3976 Planarity : 0.003 0.043 4392 Dihedral : 3.181 14.378 3669 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3397 helix: -0.64 (0.15), residues: 1180 sheet: -0.39 (0.27), residues: 350 loop : -1.38 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 53 TYR 0.015 0.001 TYR D 679 PHE 0.016 0.001 PHE C1285 TRP 0.011 0.001 TRP C 187 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00218 (24565) covalent geometry : angle 0.47961 (33337) hydrogen bonds : bond 0.03568 ( 833) hydrogen bonds : angle 4.38169 ( 2388) metal coordination : bond 0.00179 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 384 time to evaluate : 0.839 Fit side-chains Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 175 SER cc_start: 0.8432 (m) cc_final: 0.8126 (t) REVERT: A 184 TYR cc_start: 0.8364 (p90) cc_final: 0.8092 (p90) REVERT: A 199 LYS cc_start: 0.8390 (pttt) cc_final: 0.8177 (pttm) REVERT: B 21 GLN cc_start: 0.7615 (mp10) cc_final: 0.7196 (tt0) REVERT: B 76 GLU cc_start: 0.8042 (mp0) cc_final: 0.7153 (mt-10) REVERT: B 130 ILE cc_start: 0.8875 (mm) cc_final: 0.8582 (mm) REVERT: C 329 LYS cc_start: 0.6663 (mttt) cc_final: 0.6454 (mmtp) REVERT: C 520 MET cc_start: 0.7681 (ttp) cc_final: 0.7422 (ttp) REVERT: C 647 PHE cc_start: 0.7893 (t80) cc_final: 0.7481 (m-80) REVERT: C 690 MET cc_start: 0.7742 (mmp) cc_final: 0.6891 (mmm) REVERT: C 1208 ARG cc_start: 0.7180 (ptm-80) cc_final: 0.6798 (ptt-90) REVERT: C 1320 TYR cc_start: 0.8612 (t80) cc_final: 0.8051 (t80) REVERT: C 1344 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7424 (mt-10) REVERT: D 220 ARG cc_start: 0.7100 (mmt90) cc_final: 0.6462 (mtp180) REVERT: D 457 TYR cc_start: 0.8954 (m-80) cc_final: 0.8411 (m-80) REVERT: D 603 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7997 (ttmt) REVERT: D 645 VAL cc_start: 0.8708 (p) cc_final: 0.8465 (m) REVERT: D 990 ARG cc_start: 0.5918 (ptt180) cc_final: 0.5485 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7717 (pt) cc_final: 0.6603 (tp) REVERT: D 1236 GLU cc_start: 0.7189 (tp30) cc_final: 0.6807 (tp30) REVERT: D 1342 ASP cc_start: 0.6896 (t70) cc_final: 0.6435 (t70) REVERT: E 42 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7234 (mm-30) REVERT: F 117 ARG cc_start: 0.7258 (mmm160) cc_final: 0.6793 (mtt90) REVERT: F 217 MET cc_start: 0.8127 (mmm) cc_final: 0.7628 (mmp) outliers start: 4 outliers final: 3 residues processed: 388 average time/residue: 0.1622 time to fit residues: 97.6558 Evaluate side-chains 309 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 311 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 266 optimal weight: 0.0170 chunk 299 optimal weight: 5.9990 chunk 219 optimal weight: 0.0570 chunk 77 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1328 HIS D 951 GLN F 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143524 restraints weight = 39891.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142821 restraints weight = 54608.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141934 restraints weight = 45389.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141689 restraints weight = 43531.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142291 restraints weight = 35260.230| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24568 Z= 0.102 Angle : 0.474 7.068 33337 Z= 0.241 Chirality : 0.042 0.209 3976 Planarity : 0.003 0.042 4392 Dihedral : 3.158 14.472 3669 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.19 % Allowed : 2.14 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3397 helix: -0.19 (0.15), residues: 1183 sheet: -0.35 (0.26), residues: 376 loop : -1.26 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 86 TYR 0.012 0.001 TYR D 679 PHE 0.015 0.001 PHE C 390 TRP 0.011 0.001 TRP C 187 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00235 (24565) covalent geometry : angle 0.47362 (33337) hydrogen bonds : bond 0.03346 ( 833) hydrogen bonds : angle 4.18864 ( 2388) metal coordination : bond 0.00257 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 372 time to evaluate : 0.966 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 184 TYR cc_start: 0.8405 (p90) cc_final: 0.8140 (p90) REVERT: B 21 GLN cc_start: 0.7668 (mp10) cc_final: 0.7214 (tt0) REVERT: B 130 ILE cc_start: 0.8850 (mm) cc_final: 0.8501 (mm) REVERT: B 222 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8489 (mp) REVERT: C 647 PHE cc_start: 0.7942 (t80) cc_final: 0.7475 (m-80) REVERT: C 691 GLN cc_start: 0.7367 (mt0) cc_final: 0.7162 (mt0) REVERT: C 951 LEU cc_start: 0.8399 (pp) cc_final: 0.8050 (tp) REVERT: C 1208 ARG cc_start: 0.7315 (ptm-80) cc_final: 0.6889 (ptt-90) REVERT: C 1320 TYR cc_start: 0.8668 (t80) cc_final: 0.8066 (t80) REVERT: D 94 LEU cc_start: 0.8443 (mp) cc_final: 0.7478 (tp) REVERT: D 220 ARG cc_start: 0.7089 (mmt90) cc_final: 0.6632 (mtp180) REVERT: D 457 TYR cc_start: 0.8949 (m-80) cc_final: 0.8417 (m-80) REVERT: D 603 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7878 (ttmt) REVERT: D 645 VAL cc_start: 0.8746 (p) cc_final: 0.8478 (m) REVERT: D 990 ARG cc_start: 0.5984 (ptt180) cc_final: 0.5598 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7683 (pt) cc_final: 0.6565 (tp) REVERT: D 1236 GLU cc_start: 0.7077 (tp30) cc_final: 0.6705 (tp30) REVERT: D 1342 ASP cc_start: 0.6794 (t70) cc_final: 0.6540 (t70) REVERT: E 42 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7156 (mm-30) REVERT: F 117 ARG cc_start: 0.7284 (mmm160) cc_final: 0.6873 (mtt90) REVERT: F 217 MET cc_start: 0.8101 (mmm) cc_final: 0.7627 (mmp) outliers start: 6 outliers final: 3 residues processed: 377 average time/residue: 0.1562 time to fit residues: 93.1831 Evaluate side-chains 296 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 313 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 280 optimal weight: 20.0000 chunk 251 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 224 GLN C1252 HIS D 951 GLN F 129 ASN F 311 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145473 restraints weight = 40013.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141843 restraints weight = 53146.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137304 restraints weight = 43356.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137933 restraints weight = 45175.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138744 restraints weight = 36300.684| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24568 Z= 0.096 Angle : 0.466 9.328 33337 Z= 0.235 Chirality : 0.041 0.190 3976 Planarity : 0.003 0.043 4392 Dihedral : 3.132 14.570 3669 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.14 % Allowed : 1.68 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3397 helix: 0.07 (0.16), residues: 1184 sheet: -0.30 (0.27), residues: 377 loop : -1.14 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 86 TYR 0.022 0.001 TYR D 679 PHE 0.014 0.001 PHE D 116 TRP 0.011 0.001 TRP C 187 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00217 (24565) covalent geometry : angle 0.46637 (33337) hydrogen bonds : bond 0.03137 ( 833) hydrogen bonds : angle 4.12266 ( 2388) metal coordination : bond 0.00229 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 361 time to evaluate : 0.817 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 142 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7926 (mptt) REVERT: A 184 TYR cc_start: 0.8396 (p90) cc_final: 0.8023 (p90) REVERT: B 21 GLN cc_start: 0.7682 (mp10) cc_final: 0.7262 (tt0) REVERT: B 130 ILE cc_start: 0.8894 (mm) cc_final: 0.8601 (mm) REVERT: C 546 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6670 (mm-30) REVERT: C 690 MET cc_start: 0.7593 (mmp) cc_final: 0.7031 (mmm) REVERT: C 951 LEU cc_start: 0.8467 (pp) cc_final: 0.8142 (tp) REVERT: C 954 GLU cc_start: 0.6393 (tt0) cc_final: 0.5920 (tp30) REVERT: C 1208 ARG cc_start: 0.7219 (ptm-80) cc_final: 0.6798 (ttp-170) REVERT: C 1320 TYR cc_start: 0.8684 (t80) cc_final: 0.8033 (t80) REVERT: D 114 ILE cc_start: 0.7988 (tp) cc_final: 0.7719 (tp) REVERT: D 220 ARG cc_start: 0.7138 (mmt90) cc_final: 0.6558 (mtp180) REVERT: D 457 TYR cc_start: 0.8960 (m-80) cc_final: 0.8355 (m-80) REVERT: D 603 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7898 (ttmt) REVERT: D 645 VAL cc_start: 0.8758 (p) cc_final: 0.8485 (m) REVERT: D 990 ARG cc_start: 0.6185 (ptt180) cc_final: 0.5716 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7747 (pt) cc_final: 0.6712 (tp) REVERT: D 1236 GLU cc_start: 0.7035 (tp30) cc_final: 0.6699 (tp30) REVERT: D 1342 ASP cc_start: 0.6602 (t70) cc_final: 0.6276 (t70) REVERT: E 42 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7155 (mm-30) REVERT: F 117 ARG cc_start: 0.7197 (mmm160) cc_final: 0.6713 (mtt90) REVERT: F 155 ILE cc_start: 0.8175 (tt) cc_final: 0.7702 (mt) REVERT: F 217 MET cc_start: 0.8282 (mmm) cc_final: 0.7714 (mmp) outliers start: 5 outliers final: 3 residues processed: 365 average time/residue: 0.1628 time to fit residues: 94.4289 Evaluate side-chains 300 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 113 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 309 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 171 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN F 129 ASN F 311 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144361 restraints weight = 39869.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143392 restraints weight = 55541.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143255 restraints weight = 51342.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142698 restraints weight = 43782.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143406 restraints weight = 38325.993| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24568 Z= 0.092 Angle : 0.465 8.952 33337 Z= 0.233 Chirality : 0.041 0.195 3976 Planarity : 0.003 0.042 4392 Dihedral : 3.102 15.107 3669 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.14 % Allowed : 1.63 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3397 helix: 0.29 (0.16), residues: 1183 sheet: -0.23 (0.27), residues: 377 loop : -1.02 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 86 TYR 0.009 0.001 TYR D 679 PHE 0.013 0.001 PHE B 176 TRP 0.010 0.001 TRP C 187 HIS 0.003 0.000 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00211 (24565) covalent geometry : angle 0.46475 (33337) hydrogen bonds : bond 0.03026 ( 833) hydrogen bonds : angle 4.03303 ( 2388) metal coordination : bond 0.00213 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 368 time to evaluate : 0.859 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 142 LYS cc_start: 0.8440 (ttmt) cc_final: 0.7919 (mptt) REVERT: A 184 TYR cc_start: 0.8344 (p90) cc_final: 0.7976 (p90) REVERT: A 188 ASN cc_start: 0.7409 (m-40) cc_final: 0.6765 (m-40) REVERT: B 21 GLN cc_start: 0.7671 (mp10) cc_final: 0.7243 (tt0) REVERT: B 22 THR cc_start: 0.8212 (p) cc_final: 0.7936 (p) REVERT: B 130 ILE cc_start: 0.8888 (mm) cc_final: 0.8500 (mm) REVERT: C 951 LEU cc_start: 0.8382 (pp) cc_final: 0.8066 (tp) REVERT: C 1197 MET cc_start: 0.8118 (mmm) cc_final: 0.7780 (mmm) REVERT: C 1208 ARG cc_start: 0.7216 (ptm-80) cc_final: 0.6826 (ttp-170) REVERT: C 1320 TYR cc_start: 0.8655 (t80) cc_final: 0.8033 (t80) REVERT: D 114 ILE cc_start: 0.7946 (tp) cc_final: 0.7691 (tp) REVERT: D 220 ARG cc_start: 0.7076 (mmt90) cc_final: 0.6665 (mtp180) REVERT: D 457 TYR cc_start: 0.8925 (m-80) cc_final: 0.8360 (m-80) REVERT: D 603 LYS cc_start: 0.8377 (mtmt) cc_final: 0.7913 (ttmt) REVERT: D 645 VAL cc_start: 0.8770 (p) cc_final: 0.8491 (m) REVERT: D 722 MET cc_start: 0.8190 (tpp) cc_final: 0.7880 (tpp) REVERT: D 990 ARG cc_start: 0.6268 (ptt180) cc_final: 0.5877 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7666 (pt) cc_final: 0.6660 (tp) REVERT: D 1236 GLU cc_start: 0.7006 (tp30) cc_final: 0.6680 (tp30) REVERT: D 1342 ASP cc_start: 0.6588 (t70) cc_final: 0.6321 (t70) REVERT: E 42 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7281 (mm-30) REVERT: F 117 ARG cc_start: 0.7211 (mmm160) cc_final: 0.6895 (mtt90) REVERT: F 217 MET cc_start: 0.7955 (mmm) cc_final: 0.7455 (mmp) outliers start: 5 outliers final: 3 residues processed: 372 average time/residue: 0.1499 time to fit residues: 88.5686 Evaluate side-chains 298 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 7 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 304 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 116 GLN C1128 GLN C1252 HIS D 951 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143449 restraints weight = 40077.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140406 restraints weight = 56189.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137552 restraints weight = 40075.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138031 restraints weight = 39413.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138043 restraints weight = 34935.686| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24568 Z= 0.111 Angle : 0.499 8.303 33337 Z= 0.251 Chirality : 0.042 0.207 3976 Planarity : 0.003 0.044 4392 Dihedral : 3.227 15.251 3669 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3397 helix: 0.35 (0.16), residues: 1189 sheet: -0.18 (0.27), residues: 362 loop : -0.99 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 86 TYR 0.026 0.001 TYR D 679 PHE 0.010 0.001 PHE D 116 TRP 0.012 0.001 TRP C 187 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00258 (24565) covalent geometry : angle 0.49909 (33337) hydrogen bonds : bond 0.03175 ( 833) hydrogen bonds : angle 4.07631 ( 2388) metal coordination : bond 0.00270 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 356 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 142 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7851 (mptt) REVERT: A 184 TYR cc_start: 0.8360 (p90) cc_final: 0.7931 (p90) REVERT: B 21 GLN cc_start: 0.7772 (mp10) cc_final: 0.7295 (tt0) REVERT: B 22 THR cc_start: 0.8223 (p) cc_final: 0.7990 (p) REVERT: B 130 ILE cc_start: 0.8935 (mm) cc_final: 0.8616 (mm) REVERT: C 546 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6687 (mm-30) REVERT: C 690 MET cc_start: 0.7762 (mmp) cc_final: 0.7521 (mmm) REVERT: C 951 LEU cc_start: 0.8374 (pp) cc_final: 0.8066 (tp) REVERT: C 1197 MET cc_start: 0.8125 (mmm) cc_final: 0.7769 (mmm) REVERT: C 1320 TYR cc_start: 0.8628 (t80) cc_final: 0.7892 (t80) REVERT: D 114 ILE cc_start: 0.8002 (tp) cc_final: 0.7731 (tp) REVERT: D 220 ARG cc_start: 0.7200 (mmt90) cc_final: 0.6637 (mtp180) REVERT: D 445 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7477 (mttp) REVERT: D 457 TYR cc_start: 0.8895 (m-80) cc_final: 0.8364 (m-80) REVERT: D 603 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7930 (ttmt) REVERT: D 645 VAL cc_start: 0.8762 (p) cc_final: 0.8491 (m) REVERT: D 990 ARG cc_start: 0.6262 (ptt180) cc_final: 0.5875 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7781 (pt) cc_final: 0.6703 (tp) REVERT: D 1236 GLU cc_start: 0.7096 (tp30) cc_final: 0.6762 (tp30) REVERT: E 42 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7286 (mm-30) REVERT: F 117 ARG cc_start: 0.7238 (mmm160) cc_final: 0.6799 (mtt90) REVERT: F 155 ILE cc_start: 0.7926 (tt) cc_final: 0.7515 (mt) REVERT: F 217 MET cc_start: 0.8146 (mmm) cc_final: 0.7568 (mmp) outliers start: 4 outliers final: 3 residues processed: 360 average time/residue: 0.1430 time to fit residues: 82.5634 Evaluate side-chains 293 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 175 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 295 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 1 optimal weight: 0.0870 chunk 146 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 116 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 951 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138474 restraints weight = 40397.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136705 restraints weight = 57671.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138097 restraints weight = 54197.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137997 restraints weight = 35756.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138273 restraints weight = 35372.468| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24568 Z= 0.140 Angle : 0.532 7.968 33337 Z= 0.270 Chirality : 0.043 0.198 3976 Planarity : 0.003 0.044 4392 Dihedral : 3.491 17.611 3669 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.09 % Allowed : 1.35 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3397 helix: 0.34 (0.16), residues: 1189 sheet: -0.21 (0.27), residues: 362 loop : -1.02 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 86 TYR 0.013 0.001 TYR D 512 PHE 0.014 0.001 PHE C 510 TRP 0.015 0.002 TRP C 187 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00328 (24565) covalent geometry : angle 0.53199 (33337) hydrogen bonds : bond 0.03437 ( 833) hydrogen bonds : angle 4.22041 ( 2388) metal coordination : bond 0.00400 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 338 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 142 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7884 (mptt) REVERT: A 184 TYR cc_start: 0.8413 (p90) cc_final: 0.8034 (p90) REVERT: A 188 ASN cc_start: 0.7608 (m-40) cc_final: 0.6751 (m-40) REVERT: B 21 GLN cc_start: 0.7849 (mp10) cc_final: 0.7305 (tt0) REVERT: B 22 THR cc_start: 0.8207 (p) cc_final: 0.7984 (p) REVERT: B 86 LYS cc_start: 0.6817 (mttm) cc_final: 0.5368 (mttm) REVERT: B 130 ILE cc_start: 0.8740 (mm) cc_final: 0.8491 (mm) REVERT: B 205 GLU cc_start: 0.8171 (pm20) cc_final: 0.7938 (pm20) REVERT: C 564 CYS cc_start: 0.9178 (t) cc_final: 0.8955 (t) REVERT: C 690 MET cc_start: 0.7989 (mmp) cc_final: 0.7222 (mmm) REVERT: C 951 LEU cc_start: 0.8359 (pp) cc_final: 0.8046 (tp) REVERT: C 1197 MET cc_start: 0.8256 (mmm) cc_final: 0.8040 (mmm) REVERT: C 1320 TYR cc_start: 0.8583 (t80) cc_final: 0.7825 (t80) REVERT: D 114 ILE cc_start: 0.7976 (tp) cc_final: 0.7701 (tp) REVERT: D 220 ARG cc_start: 0.6975 (mmt90) cc_final: 0.6703 (mtp180) REVERT: D 445 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7629 (ttmt) REVERT: D 457 TYR cc_start: 0.8893 (m-80) cc_final: 0.8400 (m-80) REVERT: D 603 LYS cc_start: 0.8504 (mtmt) cc_final: 0.7914 (ttmt) REVERT: D 645 VAL cc_start: 0.8790 (p) cc_final: 0.8571 (m) REVERT: D 990 ARG cc_start: 0.6408 (ptt180) cc_final: 0.6096 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7814 (pt) cc_final: 0.6704 (tp) REVERT: D 1236 GLU cc_start: 0.7117 (tp30) cc_final: 0.6761 (tp30) REVERT: E 42 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7274 (mm-30) REVERT: F 117 ARG cc_start: 0.7281 (mmm160) cc_final: 0.6934 (mtt90) REVERT: F 217 MET cc_start: 0.7908 (mmm) cc_final: 0.7423 (mmp) outliers start: 4 outliers final: 3 residues processed: 342 average time/residue: 0.1512 time to fit residues: 83.1087 Evaluate side-chains 277 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 321 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 74 optimal weight: 0.0870 chunk 112 optimal weight: 3.9990 chunk 301 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 316 optimal weight: 0.1980 chunk 164 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 116 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 581 GLN D 951 GLN F 311 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142361 restraints weight = 40078.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141490 restraints weight = 54658.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140993 restraints weight = 49846.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140554 restraints weight = 44823.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140872 restraints weight = 39839.439| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24568 Z= 0.106 Angle : 0.505 8.318 33337 Z= 0.254 Chirality : 0.042 0.194 3976 Planarity : 0.003 0.043 4392 Dihedral : 3.357 16.138 3669 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.09 % Allowed : 0.47 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3397 helix: 0.49 (0.16), residues: 1191 sheet: -0.21 (0.27), residues: 362 loop : -0.96 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 86 TYR 0.024 0.001 TYR D 679 PHE 0.017 0.001 PHE C 390 TRP 0.013 0.001 TRP C 187 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00248 (24565) covalent geometry : angle 0.50522 (33337) hydrogen bonds : bond 0.03114 ( 833) hydrogen bonds : angle 4.08814 ( 2388) metal coordination : bond 0.00244 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 339 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 309 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 248 >>> skipping REVERT: A 142 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7902 (mptt) REVERT: A 175 SER cc_start: 0.8323 (t) cc_final: 0.8103 (t) REVERT: A 184 TYR cc_start: 0.8371 (p90) cc_final: 0.7969 (p90) REVERT: B 21 GLN cc_start: 0.7816 (mp10) cc_final: 0.7311 (tt0) REVERT: C 690 MET cc_start: 0.7942 (mmp) cc_final: 0.7706 (mmm) REVERT: C 886 ASP cc_start: 0.8029 (m-30) cc_final: 0.7335 (t0) REVERT: C 951 LEU cc_start: 0.8313 (pp) cc_final: 0.8040 (tp) REVERT: C 1197 MET cc_start: 0.8249 (mmm) cc_final: 0.8041 (mmm) REVERT: C 1320 TYR cc_start: 0.8527 (t80) cc_final: 0.7728 (t80) REVERT: D 114 ILE cc_start: 0.8000 (tp) cc_final: 0.7714 (tp) REVERT: D 445 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7639 (ttpp) REVERT: D 457 TYR cc_start: 0.8926 (m-80) cc_final: 0.8425 (m-80) REVERT: D 466 MET cc_start: 0.7228 (ptp) cc_final: 0.6925 (ptp) REVERT: D 603 LYS cc_start: 0.8454 (mtmt) cc_final: 0.7898 (ttmt) REVERT: D 645 VAL cc_start: 0.8772 (p) cc_final: 0.8521 (m) REVERT: D 722 MET cc_start: 0.8218 (tpp) cc_final: 0.7925 (tpp) REVERT: D 990 ARG cc_start: 0.6449 (ptt180) cc_final: 0.6186 (ptp-170) REVERT: D 1221 LEU cc_start: 0.7735 (pt) cc_final: 0.6667 (tp) REVERT: D 1236 GLU cc_start: 0.7060 (tp30) cc_final: 0.6741 (tp30) REVERT: E 42 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7347 (mm-30) REVERT: F 117 ARG cc_start: 0.7342 (mmm160) cc_final: 0.6985 (mtt90) REVERT: F 155 ILE cc_start: 0.8056 (tt) cc_final: 0.7728 (mt) REVERT: F 217 MET cc_start: 0.7933 (mmm) cc_final: 0.7496 (mmp) outliers start: 4 outliers final: 3 residues processed: 343 average time/residue: 0.1441 time to fit residues: 79.5610 Evaluate side-chains 286 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 203 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 331 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 253 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 329 optimal weight: 0.4980 chunk 287 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 84 ASN B 116 GLN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN D 424 ASN D 951 GLN F 311 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135274 restraints weight = 40717.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133898 restraints weight = 53787.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134992 restraints weight = 50679.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134369 restraints weight = 34385.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134714 restraints weight = 31766.699| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24568 Z= 0.179 Angle : 0.594 8.481 33337 Z= 0.304 Chirality : 0.044 0.201 3976 Planarity : 0.004 0.049 4392 Dihedral : 3.846 18.351 3669 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.14 % Allowed : 0.56 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3397 helix: 0.27 (0.16), residues: 1181 sheet: -0.24 (0.27), residues: 370 loop : -1.11 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1262 TYR 0.020 0.002 TYR D 679 PHE 0.015 0.002 PHE D 116 TRP 0.019 0.002 TRP C 187 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00423 (24565) covalent geometry : angle 0.59446 (33337) hydrogen bonds : bond 0.03834 ( 833) hydrogen bonds : angle 4.44673 ( 2388) metal coordination : bond 0.00513 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.23 seconds wall clock time: 60 minutes 35.82 seconds (3635.82 seconds total)