Starting phenix.real_space_refine on Wed Apr 10 22:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u24_26307/04_2024/7u24_26307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u24_26307/04_2024/7u24_26307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u24_26307/04_2024/7u24_26307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u24_26307/04_2024/7u24_26307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u24_26307/04_2024/7u24_26307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u24_26307/04_2024/7u24_26307_updated.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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 P 33 5.49 5 S 101 5.16 5 Cl 1 4.86 5 C 13356 2.51 5 N 3504 2.21 5 O 3656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20651 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2672 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 16, 'TRANS': 342} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 9, 'ARG:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2537 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2508 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 9429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 9429 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 577} Link IDs: {'PTRANS': 48, 'TRANS': 1378} Chain breaks: 5 Unresolved non-hydrogen bonds: 1877 Unresolved non-hydrogen angles: 2372 Unresolved non-hydrogen dihedrals: 1461 Unresolved non-hydrogen chiralities: 237 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 45, 'TYR:plan': 2, 'ASN:plan1': 22, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 17, 'GLU:plan': 48, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 897 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 207 Unusual residues: {'ATP': 1, 'POV': 1, 'PTY': 1} Classifications: {'peptide': 2, 'undetermined': 3} Link IDs: {'TRANS': 1, None: 3} Not linked: pdbres="ATP A 401 " pdbres="PTY A 402 " Not linked: pdbres="PTY A 402 " pdbres="POV A 403 " Not linked: pdbres="POV A 403 " pdbres="P5S A 404 " Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 175 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="ATP B 401 " pdbres="POV B 402 " Not linked: pdbres="POV B 402 " pdbres="P5S B 403 " Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 3, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 3} Not linked: pdbres="P5S D 401 " pdbres="ATP D 402 " Not linked: pdbres="ATP D 402 " pdbres="POV D 403 " Not linked: pdbres="POV D 403 " pdbres="P5S D 404 " Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 260 Unusual residues: {'ATP': 1, 'GBM': 1, 'NAG': 1, 'PTY': 4} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.68, per 1000 atoms: 0.61 Number of scatterers: 20651 At special positions: 0 Unit cell: (166.481, 109.122, 141.299, 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) Cl 1 17.00 S 101 16.00 P 33 15.00 O 3656 8.00 N 3504 7.00 C 13356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E2003 " - " ASN E 10 " Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 3.8 seconds 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 21 sheets defined 48.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 68 through 97 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.472A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 68 through 97 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.688A pdb=" N GLU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 180' Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 347 through 357 removed outlier: 3.526A pdb=" N GLU B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 through 97 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 175 through 180 removed outlier: 4.069A pdb=" N THR C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 357 Processing helix chain 'D' and resid 54 through 57 No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 68 through 97 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 170 Processing helix chain 'D' and resid 177 through 180 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 25 through 56 removed outlier: 4.146A pdb=" N ASP E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 72 through 98 removed outlier: 3.949A pdb=" N GLY E 97 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 129 removed outlier: 3.531A pdb=" N TYR E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 159 removed outlier: 3.603A pdb=" N ALA E 138 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 144 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.908A pdb=" N VAL E 185 " --> pdb=" O MET E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.963A pdb=" N ALA E 235 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 259 through 276 Processing helix chain 'E' and resid 284 through 315 removed outlier: 5.471A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 326 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 348 through 351 No H-bonds generated for 'chain 'E' and resid 348 through 351' Processing helix chain 'E' and resid 355 through 399 removed outlier: 3.655A pdb=" N THR E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 433 Processing helix chain 'E' and resid 435 through 455 removed outlier: 4.046A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'E' and resid 471 through 504 removed outlier: 4.238A pdb=" N GLU E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 516 through 563 removed outlier: 4.073A pdb=" N THR E 525 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER E 543 " --> pdb=" O TYR E 539 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 573 through 614 removed outlier: 3.677A pdb=" N LEU E 580 " --> pdb=" O ALA E 576 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 3.948A pdb=" N LEU E 592 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 727 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 805 Processing helix chain 'E' and resid 809 through 814 Processing helix chain 'E' and resid 832 through 844 Processing helix chain 'E' and resid 856 through 859 No H-bonds generated for 'chain 'E' and resid 856 through 859' Processing helix chain 'E' and resid 863 through 880 Processing helix chain 'E' and resid 891 through 897 Proline residue: E 895 - end of helix No H-bonds generated for 'chain 'E' and resid 891 through 897' Processing helix chain 'E' and resid 916 through 918 No H-bonds generated for 'chain 'E' and resid 916 through 918' Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 1001 through 1008 Processing helix chain 'E' and resid 1010 through 1042 removed outlier: 4.061A pdb=" N LEU E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) Processing helix chain 'E' and resid 1061 through 1106 removed outlier: 3.792A pdb=" N LEU E1074 " --> pdb=" O LEU E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1134 removed outlier: 4.263A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 Processing helix chain 'E' and resid 1164 through 1209 removed outlier: 3.523A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.030A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1211 through 1216 Processing helix chain 'E' and resid 1220 through 1273 removed outlier: 3.588A pdb=" N ALA E1237 " --> pdb=" O SER E1233 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1320 removed outlier: 4.079A pdb=" N TYR E1287 " --> pdb=" O LEU E1283 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E1294 " --> pdb=" O MET E1290 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E1315 " --> pdb=" O ALA E1311 " (cutoff:3.500A) Processing helix chain 'E' and resid 1386 through 1393 removed outlier: 4.341A pdb=" N PHE E1393 " --> pdb=" O SER E1389 " (cutoff:3.500A) Processing helix chain 'E' and resid 1410 through 1412 No H-bonds generated for 'chain 'E' and resid 1410 through 1412' Processing helix chain 'E' and resid 1415 through 1418 No H-bonds generated for 'chain 'E' and resid 1415 through 1418' Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1451 through 1458 Processing helix chain 'E' and resid 1461 through 1466 Processing helix chain 'E' and resid 1476 through 1478 No H-bonds generated for 'chain 'E' and resid 1476 through 1478' Processing helix chain 'E' and resid 1485 through 1497 Processing helix chain 'E' and resid 1513 through 1530 Processing helix chain 'E' and resid 1540 through 1542 No H-bonds generated for 'chain 'E' and resid 1540 through 1542' Processing helix chain 'E' and resid 1564 through 1569 Processing helix chain 'E' and resid 1572 through 1577 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.714A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 215 through 220 Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.165A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.842A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 236 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= I, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.606A pdb=" N SER B 327 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= K, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.624A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.616A pdb=" N GLY C 289 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= N, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= O, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= P, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.719A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 234 through 237 Processing sheet with id= R, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= S, first strand: chain 'E' and resid 708 through 711 removed outlier: 6.416A pdb=" N VAL E 884 " --> pdb=" O THR E 709 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE E 711 " --> pdb=" O VAL E 884 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU E 886 " --> pdb=" O ILE E 711 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 901 through 904 removed outlier: 3.695A pdb=" N ARG E 910 " --> pdb=" O ALA E 902 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS E 904 " --> pdb=" O ILE E 908 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE E 908 " --> pdb=" O LYS E 904 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 1549 through 1552 removed outlier: 3.984A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2889 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: 7.22 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3164 1.31 - 1.44: 5618 1.44 - 1.56: 12080 1.56 - 1.69: 61 1.69 - 1.82: 160 Bond restraints: 21083 Sorted by residual: bond pdb=" C17 GBM E2001 " pdb=" N8 GBM E2001 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C26 GBM E2001 " pdb=" N10 GBM E2001 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C28 GBM E2001 " pdb=" O7 GBM E2001 " ideal model delta sigma weight residual 1.339 1.400 -0.061 2.00e-02 2.50e+03 9.16e+00 bond pdb=" C1 NAG E2003 " pdb=" O5 NAG E2003 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C17 GBM E2001 " pdb=" N9 GBM E2001 " ideal model delta sigma weight residual 1.394 1.453 -0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 21078 not shown) Histogram of bond angle deviations from ideal: 92.91 - 102.31: 87 102.31 - 111.72: 10678 111.72 - 121.12: 12291 121.12 - 130.53: 5536 130.53 - 139.93: 134 Bond angle restraints: 28726 Sorted by residual: angle pdb=" C LEU E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta sigma weight residual 122.65 115.70 6.95 1.60e+00 3.91e-01 1.88e+01 angle pdb=" N VAL D 244 " pdb=" CA VAL D 244 " pdb=" C VAL D 244 " ideal model delta sigma weight residual 113.20 109.52 3.68 9.60e-01 1.09e+00 1.47e+01 angle pdb=" C VAL E 33 " pdb=" N VAL E 34 " pdb=" CA VAL E 34 " ideal model delta sigma weight residual 120.33 122.96 -2.63 8.00e-01 1.56e+00 1.08e+01 angle pdb=" C ASN E 223 " pdb=" N LEU E 224 " pdb=" CA LEU E 224 " ideal model delta sigma weight residual 120.38 124.15 -3.77 1.37e+00 5.33e-01 7.57e+00 angle pdb=" CA LEU A 275 " pdb=" CB LEU A 275 " pdb=" CG LEU A 275 " ideal model delta sigma weight residual 116.30 125.59 -9.29 3.50e+00 8.16e-02 7.05e+00 ... (remaining 28721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 12232 35.79 - 71.59: 309 71.59 - 107.38: 49 107.38 - 143.17: 31 143.17 - 178.97: 16 Dihedral angle restraints: 12637 sinusoidal: 4584 harmonic: 8053 Sorted by residual: dihedral pdb=" CA ALA E 251 " pdb=" C ALA E 251 " pdb=" N LYS E 252 " pdb=" CA LYS E 252 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C21 P5S D 401 " pdb=" C17 P5S D 401 " pdb=" C20 P5S D 401 " pdb=" O18 P5S D 401 " ideal model delta sinusoidal sigma weight residual 9.80 -169.17 178.97 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 P5S B 404 " pdb=" C17 P5S B 404 " pdb=" C20 P5S B 404 " pdb=" O18 P5S B 404 " ideal model delta sinusoidal sigma weight residual 9.80 -173.32 -176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2389 0.037 - 0.074: 684 0.074 - 0.111: 272 0.111 - 0.149: 40 0.149 - 0.186: 1 Chirality restraints: 3386 Sorted by residual: chirality pdb=" CG LEU E 218 " pdb=" CB LEU E 218 " pdb=" CD1 LEU E 218 " pdb=" CD2 LEU E 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 3383 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 219 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO E 220 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 220 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 220 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C17 P5S B 403 " -0.032 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C20 P5S B 403 " 0.009 2.00e-02 2.50e+03 pdb=" O18 P5S B 403 " 0.012 2.00e-02 2.50e+03 pdb=" O19 P5S B 403 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 253 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 254 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 254 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 254 " 0.023 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4339 2.78 - 3.31: 19671 3.31 - 3.84: 33141 3.84 - 4.37: 36482 4.37 - 4.90: 64551 Nonbonded interactions: 158184 Sorted by model distance: nonbonded pdb=" OH TYR B 268 " pdb=" OD2 ASP B 350 " model vdw 2.254 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" OG SER A 208 " model vdw 2.277 2.520 nonbonded pdb=" O GLN E 992 " pdb=" NH1 ARG E1187 " model vdw 2.305 2.520 nonbonded pdb=" O TRP E 75 " pdb=" OG1 THR E 78 " model vdw 2.305 2.440 nonbonded pdb=" NH1 ARG D 32 " pdb=" O GLN D 279 " model vdw 2.307 2.520 ... (remaining 158179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 178 or (resid 179 and (name N or n \ ame CA or name C or name O or name CB )) or resid 180 through 272 or (resid 273 \ through 274 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 5 through 306 or (resid 307 through 308 and (name N or name CA or name C or name \ O or name CB )) or resid 309 through 320 or (resid 321 through 323 and (name N \ or name CA or name C or name O or name CB )) or resid 324 through 350 or (resid \ 351 through 358 and (name N or name CA or name C or name O or name CB )) or resi \ d 405)) selection = (chain 'B' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 64 or (resid 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 272 or (resid 273 th \ rough 274 and (name N or name CA or name C or name O or name CB )) or resid 275 \ through 306 or (resid 307 through 308 and (name N or name CA or name C or name O \ or name CB )) or resid 309 through 320 or (resid 321 through 323 and (name N or \ name CA or name C or name O or name CB )) or resid 324 through 353 or (resid 35 \ 4 through 358 and (name N or name CA or name C or name O or name CB )) or resid \ 404)) selection = (chain 'C' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 41 or (resid 42 and (name N or na \ me CA or name C or name O or name CB )) or resid 43 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 206 or \ (resid 207 and (name N or name CA or name C or name O or name CB )) or resid 208 \ through 272 or (resid 273 through 274 and (name N or name CA or name C or name \ O or name CB )) or resid 275 through 306 or (resid 307 through 308 and (name N o \ r name CA or name C or name O or name CB )) or resid 309 through 320 or (resid 3 \ 21 through 323 and (name N or name CA or name C or name O or name CB )) or resid \ 324 through 350 or (resid 351 through 358 and (name N or name CA or name C or n \ ame O or name CB )) or resid 403)) selection = (chain 'D' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 41 or (resid 42 and (name N or na \ me CA or name C or name O or name CB )) or resid 43 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 273 or \ (resid 274 and (name N or name CA or name C or name O or name CB )) or resid 275 \ through 322 or (resid 323 and (name N or name CA or name C or name O or name CB \ )) or resid 324 through 358 or resid 405)) } 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: 1.300 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: 0.000 Extract box with map and model: 1.800 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 56.100 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.002 0.111 21083 Z= 0.156 Angle : 0.496 9.292 28726 Z= 0.236 Chirality : 0.041 0.186 3386 Planarity : 0.004 0.049 3559 Dihedral : 18.813 178.967 7384 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2750 helix: 0.90 (0.14), residues: 1343 sheet: -2.52 (0.30), residues: 262 loop : -1.80 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E1037 HIS 0.004 0.000 HIS E 125 PHE 0.010 0.001 PHE A 333 TYR 0.012 0.001 TYR E1219 ARG 0.003 0.000 ARG E1187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 574 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 SER cc_start: 0.8956 (t) cc_final: 0.8737 (t) REVERT: A 158 MET cc_start: 0.7921 (mmm) cc_final: 0.7716 (tpp) REVERT: A 210 ILE cc_start: 0.9159 (mt) cc_final: 0.8905 (tt) REVERT: A 223 THR cc_start: 0.9388 (m) cc_final: 0.9170 (p) REVERT: A 269 ASP cc_start: 0.8237 (m-30) cc_final: 0.8003 (m-30) REVERT: A 276 HIS cc_start: 0.8601 (p-80) cc_final: 0.8315 (p-80) REVERT: A 302 THR cc_start: 0.9347 (t) cc_final: 0.9069 (m) REVERT: B 47 LYS cc_start: 0.8527 (mttt) cc_final: 0.8149 (mttm) REVERT: B 113 SER cc_start: 0.9294 (m) cc_final: 0.8676 (t) REVERT: B 114 ILE cc_start: 0.8818 (mm) cc_final: 0.8387 (mt) REVERT: B 125 ILE cc_start: 0.8766 (mm) cc_final: 0.8419 (mt) REVERT: C 58 ASP cc_start: 0.7948 (p0) cc_final: 0.7666 (p0) REVERT: C 113 SER cc_start: 0.8998 (m) cc_final: 0.8686 (t) REVERT: C 158 MET cc_start: 0.7654 (mmm) cc_final: 0.7440 (mmm) REVERT: C 171 THR cc_start: 0.9269 (p) cc_final: 0.9032 (p) REVERT: C 210 ILE cc_start: 0.9222 (mt) cc_final: 0.8771 (tt) REVERT: C 248 SER cc_start: 0.9288 (p) cc_final: 0.9059 (m) REVERT: C 290 VAL cc_start: 0.9582 (p) cc_final: 0.9315 (m) REVERT: C 335 ASN cc_start: 0.8472 (m110) cc_final: 0.8216 (m-40) REVERT: D 43 ASN cc_start: 0.8199 (t0) cc_final: 0.7793 (t0) REVERT: D 47 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8326 (mttm) REVERT: D 107 ASN cc_start: 0.8158 (t0) cc_final: 0.7863 (t0) REVERT: D 158 MET cc_start: 0.7632 (mmm) cc_final: 0.7401 (mmm) REVERT: D 212 SER cc_start: 0.8769 (m) cc_final: 0.8283 (p) REVERT: D 261 ILE cc_start: 0.9091 (mt) cc_final: 0.8854 (mt) REVERT: D 290 VAL cc_start: 0.9678 (p) cc_final: 0.9329 (m) REVERT: E 40 LEU cc_start: 0.8936 (mp) cc_final: 0.8300 (mt) REVERT: E 51 TRP cc_start: 0.7725 (t60) cc_final: 0.7413 (t60) REVERT: E 158 TYR cc_start: 0.6684 (t80) cc_final: 0.6217 (t80) REVERT: E 224 LEU cc_start: 0.9359 (tp) cc_final: 0.9147 (tp) REVERT: E 326 HIS cc_start: 0.8381 (t-90) cc_final: 0.8060 (t70) REVERT: E 361 LEU cc_start: 0.8653 (tp) cc_final: 0.8386 (mp) REVERT: E 483 GLN cc_start: 0.7786 (tt0) cc_final: 0.7236 (tm-30) REVERT: E 530 MET cc_start: 0.7524 (tpp) cc_final: 0.7173 (tpp) REVERT: E 817 HIS cc_start: 0.7516 (m-70) cc_final: 0.7143 (m-70) REVERT: E 1103 ASN cc_start: 0.8210 (m-40) cc_final: 0.7963 (m110) REVERT: E 1171 LEU cc_start: 0.8053 (tp) cc_final: 0.7682 (tt) REVERT: E 1189 LEU cc_start: 0.9166 (mt) cc_final: 0.8963 (mt) REVERT: E 1197 GLN cc_start: 0.8562 (pp30) cc_final: 0.8095 (pp30) REVERT: E 1219 TYR cc_start: 0.6299 (t80) cc_final: 0.5985 (t80) outliers start: 2 outliers final: 2 residues processed: 575 average time/residue: 0.3256 time to fit residues: 291.0434 Evaluate side-chains 480 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 478 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 1283 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 10.0000 chunk 206 optimal weight: 50.0000 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 213 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 313 GLN C 43 ASN D 48 ASN E 105 HIS E 491 HIS E 498 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21083 Z= 0.238 Angle : 0.551 8.993 28726 Z= 0.279 Chirality : 0.044 0.163 3386 Planarity : 0.004 0.050 3559 Dihedral : 20.093 175.858 3792 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.20 % Allowed : 12.19 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2750 helix: 1.46 (0.15), residues: 1318 sheet: -2.02 (0.29), residues: 290 loop : -1.60 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 91 HIS 0.006 0.001 HIS E 125 PHE 0.027 0.002 PHE A 75 TYR 0.018 0.002 TYR E 772 ARG 0.005 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 481 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 SER cc_start: 0.8981 (t) cc_final: 0.8764 (t) REVERT: A 158 MET cc_start: 0.7978 (mmm) cc_final: 0.7764 (tpp) REVERT: A 223 THR cc_start: 0.9449 (m) cc_final: 0.9217 (p) REVERT: A 269 ASP cc_start: 0.8229 (m-30) cc_final: 0.7959 (m-30) REVERT: A 276 HIS cc_start: 0.8633 (p-80) cc_final: 0.8419 (p-80) REVERT: B 88 MET cc_start: 0.7977 (tpp) cc_final: 0.7653 (tpp) REVERT: B 114 ILE cc_start: 0.8935 (mm) cc_final: 0.8505 (mt) REVERT: B 125 ILE cc_start: 0.8895 (mm) cc_final: 0.8550 (mt) REVERT: B 137 MET cc_start: 0.7622 (mtm) cc_final: 0.6837 (mtm) REVERT: B 348 GLN cc_start: 0.8071 (mt0) cc_final: 0.7867 (mt0) REVERT: C 58 ASP cc_start: 0.8182 (p0) cc_final: 0.7910 (p0) REVERT: C 113 SER cc_start: 0.9046 (m) cc_final: 0.8680 (t) REVERT: C 212 SER cc_start: 0.9062 (m) cc_final: 0.8360 (t) REVERT: C 290 VAL cc_start: 0.9590 (OUTLIER) cc_final: 0.9328 (m) REVERT: C 314 ARG cc_start: 0.8210 (ptp-170) cc_final: 0.8005 (ptp-170) REVERT: C 335 ASN cc_start: 0.8367 (m110) cc_final: 0.8130 (m-40) REVERT: D 47 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8360 (mttm) REVERT: D 107 ASN cc_start: 0.7604 (t0) cc_final: 0.7341 (t0) REVERT: D 158 MET cc_start: 0.7596 (mmm) cc_final: 0.7189 (mmm) REVERT: D 170 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8555 (tptp) REVERT: D 176 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8058 (mmt90) REVERT: D 206 ARG cc_start: 0.8580 (mmt90) cc_final: 0.8309 (mmt90) REVERT: D 212 SER cc_start: 0.8827 (m) cc_final: 0.8370 (p) REVERT: D 261 ILE cc_start: 0.9164 (mt) cc_final: 0.8946 (mt) REVERT: D 290 VAL cc_start: 0.9676 (OUTLIER) cc_final: 0.9245 (m) REVERT: E 39 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8634 (tt) REVERT: E 84 VAL cc_start: 0.9338 (m) cc_final: 0.9011 (t) REVERT: E 158 TYR cc_start: 0.7031 (t80) cc_final: 0.6601 (t80) REVERT: E 218 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8164 (pp) REVERT: E 299 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8407 (mp) REVERT: E 326 HIS cc_start: 0.8544 (t-90) cc_final: 0.8180 (t70) REVERT: E 361 LEU cc_start: 0.8507 (tp) cc_final: 0.8252 (mp) REVERT: E 370 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7487 (mmt180) REVERT: E 397 ASN cc_start: 0.8847 (t0) cc_final: 0.8591 (t0) REVERT: E 483 GLN cc_start: 0.7820 (tt0) cc_final: 0.7355 (tm-30) REVERT: E 491 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6383 (m170) REVERT: E 530 MET cc_start: 0.7474 (tpp) cc_final: 0.7145 (tpp) REVERT: E 817 HIS cc_start: 0.7327 (m-70) cc_final: 0.7033 (m-70) REVERT: E 1103 ASN cc_start: 0.8396 (m-40) cc_final: 0.8079 (m-40) REVERT: E 1218 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8311 (tpp80) REVERT: E 1219 TYR cc_start: 0.6120 (t80) cc_final: 0.5658 (t80) outliers start: 56 outliers final: 36 residues processed: 506 average time/residue: 0.3179 time to fit residues: 251.8834 Evaluate side-chains 493 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 451 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 206 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 0.0000 chunk 248 optimal weight: 50.0000 chunk 268 optimal weight: 40.0000 chunk 221 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 313 GLN D 48 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21083 Z= 0.258 Angle : 0.543 13.091 28726 Z= 0.273 Chirality : 0.044 0.159 3386 Planarity : 0.004 0.048 3559 Dihedral : 19.020 177.769 3792 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.29 % Allowed : 14.76 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2750 helix: 1.66 (0.15), residues: 1326 sheet: -1.84 (0.29), residues: 303 loop : -1.54 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 430 HIS 0.009 0.001 HIS E 491 PHE 0.026 0.002 PHE A 75 TYR 0.016 0.002 TYR E 230 ARG 0.006 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 443 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8440 (ttm170) cc_final: 0.7804 (mtm110) REVERT: A 158 MET cc_start: 0.7957 (mmm) cc_final: 0.7656 (mmm) REVERT: A 199 MET cc_start: 0.8231 (mmm) cc_final: 0.7976 (mmp) REVERT: A 223 THR cc_start: 0.9435 (m) cc_final: 0.9203 (p) REVERT: A 269 ASP cc_start: 0.8220 (m-30) cc_final: 0.7958 (m-30) REVERT: B 114 ILE cc_start: 0.8988 (mm) cc_final: 0.8533 (mt) REVERT: B 125 ILE cc_start: 0.8950 (mm) cc_final: 0.8588 (mt) REVERT: B 137 MET cc_start: 0.7667 (mtm) cc_final: 0.6919 (mtm) REVERT: B 314 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7564 (mtm180) REVERT: C 58 ASP cc_start: 0.8141 (p0) cc_final: 0.7850 (p0) REVERT: C 76 THR cc_start: 0.9112 (m) cc_final: 0.8881 (m) REVERT: C 113 SER cc_start: 0.9028 (m) cc_final: 0.8672 (t) REVERT: C 160 ASN cc_start: 0.8602 (m-40) cc_final: 0.8387 (t0) REVERT: C 290 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9345 (m) REVERT: C 314 ARG cc_start: 0.8255 (ptp-170) cc_final: 0.7977 (mtp180) REVERT: D 41 ASN cc_start: 0.8707 (t0) cc_final: 0.8350 (t0) REVERT: D 47 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8473 (mttm) REVERT: D 107 ASN cc_start: 0.7893 (t0) cc_final: 0.7587 (t0) REVERT: D 212 SER cc_start: 0.8880 (m) cc_final: 0.8389 (p) REVERT: D 261 ILE cc_start: 0.9183 (mt) cc_final: 0.8972 (mt) REVERT: D 290 VAL cc_start: 0.9682 (OUTLIER) cc_final: 0.9267 (m) REVERT: E 84 VAL cc_start: 0.9334 (m) cc_final: 0.9044 (t) REVERT: E 158 TYR cc_start: 0.7091 (t80) cc_final: 0.6716 (t80) REVERT: E 164 PHE cc_start: 0.7723 (m-80) cc_final: 0.7297 (m-80) REVERT: E 218 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8340 (pp) REVERT: E 299 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8456 (mp) REVERT: E 361 LEU cc_start: 0.8513 (tp) cc_final: 0.8242 (mp) REVERT: E 817 HIS cc_start: 0.7356 (m-70) cc_final: 0.7039 (m-70) REVERT: E 1103 ASN cc_start: 0.8475 (m-40) cc_final: 0.8147 (m-40) REVERT: E 1219 TYR cc_start: 0.6079 (t80) cc_final: 0.5685 (t80) outliers start: 75 outliers final: 56 residues processed: 479 average time/residue: 0.2977 time to fit residues: 227.8218 Evaluate side-chains 496 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 435 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1156 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 263 optimal weight: 50.0000 chunk 130 optimal weight: 0.4980 chunk 236 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 128 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21083 Z= 0.186 Angle : 0.511 10.644 28726 Z= 0.256 Chirality : 0.043 0.163 3386 Planarity : 0.004 0.049 3559 Dihedral : 17.885 172.143 3792 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.18 % Allowed : 16.70 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2750 helix: 1.91 (0.15), residues: 1325 sheet: -1.65 (0.31), residues: 288 loop : -1.41 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E1037 HIS 0.006 0.001 HIS E 125 PHE 0.025 0.001 PHE A 75 TYR 0.025 0.001 TYR E 772 ARG 0.006 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 445 time to evaluate : 2.348 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8429 (ttm170) cc_final: 0.7808 (mtm110) REVERT: A 92 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8574 (tp) REVERT: A 199 MET cc_start: 0.8267 (mmm) cc_final: 0.7894 (mmp) REVERT: A 262 ASP cc_start: 0.6996 (t0) cc_final: 0.6632 (t0) REVERT: A 269 ASP cc_start: 0.8201 (m-30) cc_final: 0.7932 (m-30) REVERT: A 325 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7150 (mtp85) REVERT: B 114 ILE cc_start: 0.8966 (mm) cc_final: 0.8518 (mt) REVERT: B 125 ILE cc_start: 0.8927 (mm) cc_final: 0.8557 (mt) REVERT: B 137 MET cc_start: 0.7617 (mtm) cc_final: 0.6913 (mtm) REVERT: C 58 ASP cc_start: 0.8137 (p0) cc_final: 0.7835 (p0) REVERT: C 113 SER cc_start: 0.9008 (m) cc_final: 0.8678 (t) REVERT: C 290 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9339 (m) REVERT: D 41 ASN cc_start: 0.8714 (t0) cc_final: 0.8416 (t0) REVERT: D 47 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8462 (mttm) REVERT: D 107 ASN cc_start: 0.7844 (t0) cc_final: 0.7507 (t0) REVERT: D 170 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8730 (tptp) REVERT: D 212 SER cc_start: 0.8885 (m) cc_final: 0.8387 (p) REVERT: D 261 ILE cc_start: 0.9103 (mt) cc_final: 0.8863 (mt) REVERT: D 290 VAL cc_start: 0.9669 (OUTLIER) cc_final: 0.9255 (m) REVERT: E 84 VAL cc_start: 0.9315 (m) cc_final: 0.9022 (t) REVERT: E 139 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8734 (mp) REVERT: E 158 TYR cc_start: 0.6822 (t80) cc_final: 0.6563 (t80) REVERT: E 164 PHE cc_start: 0.7625 (m-80) cc_final: 0.7213 (m-80) REVERT: E 218 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8347 (pp) REVERT: E 299 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8414 (mp) REVERT: E 327 LEU cc_start: 0.8077 (tp) cc_final: 0.7823 (tp) REVERT: E 361 LEU cc_start: 0.8508 (tp) cc_final: 0.8238 (mp) REVERT: E 590 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (mm) REVERT: E 817 HIS cc_start: 0.7369 (m-70) cc_final: 0.7030 (m-70) REVERT: E 1103 ASN cc_start: 0.8529 (m-40) cc_final: 0.8222 (m-40) REVERT: E 1212 THR cc_start: 0.8763 (p) cc_final: 0.8307 (t) REVERT: E 1272 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7226 (mp) outliers start: 73 outliers final: 46 residues processed: 480 average time/residue: 0.3057 time to fit residues: 234.9355 Evaluate side-chains 486 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 432 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1156 VAL Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 40.0000 chunk 149 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 40.0000 chunk 108 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 182 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 134 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 279 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21083 Z= 0.429 Angle : 0.654 10.412 28726 Z= 0.329 Chirality : 0.048 0.231 3386 Planarity : 0.005 0.055 3559 Dihedral : 17.714 167.606 3788 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.12 % Allowed : 16.53 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2750 helix: 1.53 (0.14), residues: 1324 sheet: -1.78 (0.29), residues: 303 loop : -1.56 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 83 HIS 0.009 0.001 HIS E 125 PHE 0.024 0.002 PHE A 75 TYR 0.032 0.002 TYR E 772 ARG 0.018 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 434 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8239 (ttp-170) REVERT: A 93 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8584 (mt) REVERT: A 108 VAL cc_start: 0.9356 (t) cc_final: 0.8928 (m) REVERT: A 196 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7891 (tp) REVERT: A 262 ASP cc_start: 0.7202 (t0) cc_final: 0.6829 (t0) REVERT: B 114 ILE cc_start: 0.9141 (mm) cc_final: 0.8765 (mt) REVERT: B 137 MET cc_start: 0.7795 (mtm) cc_final: 0.7045 (mtm) REVERT: B 281 LEU cc_start: 0.8912 (tp) cc_final: 0.8619 (tp) REVERT: C 58 ASP cc_start: 0.8268 (p0) cc_final: 0.7890 (p0) REVERT: C 76 THR cc_start: 0.9129 (m) cc_final: 0.8795 (m) REVERT: C 113 SER cc_start: 0.9080 (m) cc_final: 0.8739 (t) REVERT: C 259 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8509 (t-170) REVERT: C 290 VAL cc_start: 0.9559 (OUTLIER) cc_final: 0.9353 (m) REVERT: D 41 ASN cc_start: 0.8641 (t0) cc_final: 0.8293 (t0) REVERT: D 47 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8487 (mttm) REVERT: D 107 ASN cc_start: 0.7941 (t0) cc_final: 0.7668 (t0) REVERT: D 108 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8753 (p) REVERT: D 173 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8278 (mm-40) REVERT: D 212 SER cc_start: 0.8999 (m) cc_final: 0.8607 (p) REVERT: D 290 VAL cc_start: 0.9636 (OUTLIER) cc_final: 0.9224 (m) REVERT: D 336 THR cc_start: 0.8911 (p) cc_final: 0.8503 (p) REVERT: E 139 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8844 (mp) REVERT: E 164 PHE cc_start: 0.7735 (m-80) cc_final: 0.7382 (m-80) REVERT: E 218 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8788 (pp) REVERT: E 299 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8536 (mp) REVERT: E 361 LEU cc_start: 0.8560 (tp) cc_final: 0.8278 (mp) REVERT: E 397 ASN cc_start: 0.9093 (t0) cc_final: 0.8824 (t0) REVERT: E 445 ILE cc_start: 0.9074 (mm) cc_final: 0.8604 (mp) REVERT: E 530 MET cc_start: 0.7246 (tpp) cc_final: 0.6923 (tpp) REVERT: E 590 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8141 (mm) REVERT: E 602 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7655 (mtmt) REVERT: E 1103 ASN cc_start: 0.8512 (m-40) cc_final: 0.8223 (m-40) REVERT: E 1272 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7264 (mp) outliers start: 107 outliers final: 75 residues processed: 487 average time/residue: 0.3187 time to fit residues: 255.1713 Evaluate side-chains 507 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 421 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1307 ILE Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 264 optimal weight: 50.0000 chunk 219 optimal weight: 40.0000 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 128 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21083 Z= 0.251 Angle : 0.557 9.962 28726 Z= 0.278 Chirality : 0.045 0.214 3386 Planarity : 0.004 0.050 3559 Dihedral : 17.236 168.144 3788 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.86 % Allowed : 18.31 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2750 helix: 1.80 (0.15), residues: 1315 sheet: -1.70 (0.30), residues: 288 loop : -1.50 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E1033 HIS 0.007 0.001 HIS E 125 PHE 0.023 0.002 PHE A 75 TYR 0.025 0.001 TYR E 772 ARG 0.006 0.000 ARG E 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 430 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.9299 (t) cc_final: 0.8870 (m) REVERT: A 196 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7880 (tp) REVERT: A 262 ASP cc_start: 0.7073 (t0) cc_final: 0.6751 (t0) REVERT: B 114 ILE cc_start: 0.9143 (mm) cc_final: 0.8760 (mt) REVERT: B 125 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8823 (mt) REVERT: B 137 MET cc_start: 0.7644 (mtm) cc_final: 0.6959 (mtm) REVERT: B 281 LEU cc_start: 0.8770 (tp) cc_final: 0.8510 (tp) REVERT: C 58 ASP cc_start: 0.8242 (p0) cc_final: 0.7934 (p0) REVERT: C 76 THR cc_start: 0.9122 (m) cc_final: 0.8786 (m) REVERT: C 113 SER cc_start: 0.9061 (m) cc_final: 0.8762 (t) REVERT: D 41 ASN cc_start: 0.8651 (t0) cc_final: 0.8314 (t0) REVERT: D 47 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8405 (mttm) REVERT: D 107 ASN cc_start: 0.7904 (t0) cc_final: 0.7632 (t0) REVERT: D 108 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8673 (p) REVERT: D 212 SER cc_start: 0.9005 (m) cc_final: 0.8531 (p) REVERT: D 290 VAL cc_start: 0.9632 (OUTLIER) cc_final: 0.9241 (m) REVERT: D 332 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8118 (mtmm) REVERT: E 139 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8816 (mp) REVERT: E 158 TYR cc_start: 0.7257 (t80) cc_final: 0.7020 (t80) REVERT: E 164 PHE cc_start: 0.7693 (m-80) cc_final: 0.7350 (m-80) REVERT: E 227 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8644 (mttp) REVERT: E 299 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8435 (mp) REVERT: E 327 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7598 (mp) REVERT: E 361 LEU cc_start: 0.8529 (tp) cc_final: 0.8273 (mp) REVERT: E 397 ASN cc_start: 0.9058 (t0) cc_final: 0.8751 (t0) REVERT: E 530 MET cc_start: 0.7184 (tpp) cc_final: 0.6908 (tpp) REVERT: E 590 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8082 (mm) REVERT: E 602 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7633 (mtmt) REVERT: E 1103 ASN cc_start: 0.8501 (m-40) cc_final: 0.8215 (m-40) REVERT: E 1272 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7165 (mp) outliers start: 85 outliers final: 63 residues processed: 470 average time/residue: 0.3095 time to fit residues: 235.1974 Evaluate side-chains 486 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 413 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 50.0000 chunk 29 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 263 optimal weight: 0.5980 chunk 164 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 128 GLN D 128 GLN E 71 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21083 Z= 0.236 Angle : 0.553 9.992 28726 Z= 0.274 Chirality : 0.044 0.194 3386 Planarity : 0.004 0.046 3559 Dihedral : 16.921 167.310 3788 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.09 % Allowed : 18.82 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2750 helix: 1.91 (0.15), residues: 1316 sheet: -1.69 (0.30), residues: 303 loop : -1.48 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E1033 HIS 0.006 0.001 HIS E 125 PHE 0.021 0.002 PHE B 75 TYR 0.017 0.001 TYR E 772 ARG 0.007 0.000 ARG E 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 420 time to evaluate : 2.216 Fit side-chains revert: symmetry clash REVERT: A 108 VAL cc_start: 0.9298 (t) cc_final: 0.8863 (m) REVERT: A 196 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 262 ASP cc_start: 0.7074 (t0) cc_final: 0.6732 (t0) REVERT: B 58 ASP cc_start: 0.8137 (p0) cc_final: 0.7777 (p0) REVERT: B 114 ILE cc_start: 0.9116 (mm) cc_final: 0.8720 (mt) REVERT: B 125 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8819 (mt) REVERT: B 137 MET cc_start: 0.7640 (mtm) cc_final: 0.6948 (mtm) REVERT: C 58 ASP cc_start: 0.8242 (p0) cc_final: 0.7929 (p0) REVERT: C 76 THR cc_start: 0.9123 (m) cc_final: 0.8773 (m) REVERT: C 113 SER cc_start: 0.9045 (m) cc_final: 0.8753 (t) REVERT: D 41 ASN cc_start: 0.8637 (t0) cc_final: 0.8319 (t0) REVERT: D 47 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8329 (mttm) REVERT: D 107 ASN cc_start: 0.7882 (t0) cc_final: 0.7592 (t0) REVERT: D 108 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8679 (p) REVERT: D 128 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: D 212 SER cc_start: 0.9006 (m) cc_final: 0.8500 (p) REVERT: D 290 VAL cc_start: 0.9651 (OUTLIER) cc_final: 0.9252 (m) REVERT: D 332 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8148 (mtmm) REVERT: E 139 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8825 (mp) REVERT: E 140 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8447 (tt) REVERT: E 158 TYR cc_start: 0.7267 (t80) cc_final: 0.7046 (t80) REVERT: E 164 PHE cc_start: 0.7587 (m-80) cc_final: 0.7246 (m-80) REVERT: E 178 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8814 (mm) REVERT: E 227 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8756 (mttp) REVERT: E 299 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8443 (mp) REVERT: E 361 LEU cc_start: 0.8524 (tp) cc_final: 0.8273 (mp) REVERT: E 397 ASN cc_start: 0.9068 (t0) cc_final: 0.8758 (t0) REVERT: E 530 MET cc_start: 0.7166 (tpp) cc_final: 0.6929 (tpp) REVERT: E 590 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8065 (mm) REVERT: E 1088 TRP cc_start: 0.7953 (t60) cc_final: 0.7001 (t60) REVERT: E 1103 ASN cc_start: 0.8378 (m-40) cc_final: 0.8112 (m-40) REVERT: E 1272 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7160 (mp) REVERT: E 1316 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7080 (t-90) outliers start: 89 outliers final: 68 residues processed: 465 average time/residue: 0.3045 time to fit residues: 228.7368 Evaluate side-chains 496 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 415 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 206 optimal weight: 40.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 128 GLN B 57 GLN D 128 GLN E 126 ASN E 707 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21083 Z= 0.202 Angle : 0.541 9.488 28726 Z= 0.267 Chirality : 0.044 0.179 3386 Planarity : 0.004 0.047 3559 Dihedral : 16.668 166.625 3788 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.21 % Allowed : 18.94 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2750 helix: 2.03 (0.15), residues: 1316 sheet: -1.63 (0.30), residues: 293 loop : -1.42 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.006 0.001 HIS E 125 PHE 0.021 0.001 PHE A 75 TYR 0.012 0.001 TYR E 107 ARG 0.008 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 417 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: A 108 VAL cc_start: 0.9289 (t) cc_final: 0.8847 (m) REVERT: A 196 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 199 MET cc_start: 0.8077 (mmm) cc_final: 0.7693 (mmp) REVERT: A 262 ASP cc_start: 0.7020 (t0) cc_final: 0.6711 (t0) REVERT: B 58 ASP cc_start: 0.8073 (p0) cc_final: 0.7775 (p0) REVERT: B 84 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8197 (tt) REVERT: B 114 ILE cc_start: 0.9097 (mm) cc_final: 0.8711 (mt) REVERT: B 125 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8808 (mt) REVERT: B 137 MET cc_start: 0.7599 (mtm) cc_final: 0.6998 (mtm) REVERT: C 58 ASP cc_start: 0.8246 (p0) cc_final: 0.7936 (p0) REVERT: C 76 THR cc_start: 0.9118 (m) cc_final: 0.8766 (m) REVERT: C 113 SER cc_start: 0.9015 (m) cc_final: 0.8747 (t) REVERT: C 158 MET cc_start: 0.7862 (mmm) cc_final: 0.7531 (tpp) REVERT: D 41 ASN cc_start: 0.8624 (t0) cc_final: 0.8334 (t0) REVERT: D 47 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8323 (mttm) REVERT: D 107 ASN cc_start: 0.7773 (t0) cc_final: 0.7460 (t0) REVERT: D 108 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8679 (p) REVERT: D 212 SER cc_start: 0.8974 (m) cc_final: 0.8439 (p) REVERT: D 290 VAL cc_start: 0.9639 (OUTLIER) cc_final: 0.9251 (m) REVERT: D 332 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8146 (mtmm) REVERT: E 139 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8740 (mp) REVERT: E 140 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8427 (tt) REVERT: E 158 TYR cc_start: 0.7226 (t80) cc_final: 0.7023 (t80) REVERT: E 164 PHE cc_start: 0.7583 (m-80) cc_final: 0.7237 (m-80) REVERT: E 178 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8783 (mm) REVERT: E 227 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8769 (mttp) REVERT: E 361 LEU cc_start: 0.8527 (tp) cc_final: 0.8259 (mp) REVERT: E 397 ASN cc_start: 0.9064 (t0) cc_final: 0.8791 (t0) REVERT: E 590 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8005 (mm) REVERT: E 1088 TRP cc_start: 0.7938 (t60) cc_final: 0.6992 (t60) REVERT: E 1103 ASN cc_start: 0.8355 (m-40) cc_final: 0.8094 (m-40) REVERT: E 1272 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7145 (mp) outliers start: 91 outliers final: 71 residues processed: 466 average time/residue: 0.2960 time to fit residues: 224.0919 Evaluate side-chains 494 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 412 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 221 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 128 GLN B 128 GLN B 152 GLN D 128 GLN E 707 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21083 Z= 0.388 Angle : 0.626 9.776 28726 Z= 0.311 Chirality : 0.047 0.180 3386 Planarity : 0.005 0.048 3559 Dihedral : 16.824 165.685 3788 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.66 % Allowed : 18.65 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2750 helix: 1.72 (0.15), residues: 1322 sheet: -1.79 (0.29), residues: 308 loop : -1.52 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 90 HIS 0.008 0.001 HIS E 125 PHE 0.028 0.002 PHE E1164 TYR 0.014 0.002 TYR E 772 ARG 0.007 0.001 ARG E 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 421 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8616 (ttm170) cc_final: 0.7982 (mtm110) REVERT: A 108 VAL cc_start: 0.9326 (t) cc_final: 0.8889 (m) REVERT: A 196 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7908 (tp) REVERT: A 262 ASP cc_start: 0.7081 (t0) cc_final: 0.6744 (t0) REVERT: B 58 ASP cc_start: 0.8183 (p0) cc_final: 0.7819 (p0) REVERT: B 84 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8266 (tt) REVERT: B 114 ILE cc_start: 0.9136 (mm) cc_final: 0.8776 (mt) REVERT: B 125 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8873 (mt) REVERT: C 58 ASP cc_start: 0.8353 (p0) cc_final: 0.7958 (p0) REVERT: C 76 THR cc_start: 0.9162 (m) cc_final: 0.8793 (m) REVERT: C 113 SER cc_start: 0.9064 (m) cc_final: 0.8786 (t) REVERT: C 259 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.8494 (t-170) REVERT: C 268 TYR cc_start: 0.8711 (t80) cc_final: 0.8222 (t80) REVERT: D 41 ASN cc_start: 0.8619 (t0) cc_final: 0.8340 (t0) REVERT: D 47 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8198 (mttm) REVERT: D 107 ASN cc_start: 0.7883 (t0) cc_final: 0.7582 (t0) REVERT: D 108 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8762 (p) REVERT: D 173 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8267 (mm-40) REVERT: D 212 SER cc_start: 0.9046 (m) cc_final: 0.8586 (p) REVERT: D 290 VAL cc_start: 0.9602 (OUTLIER) cc_final: 0.9239 (m) REVERT: D 332 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8140 (mtmm) REVERT: E 139 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8751 (mp) REVERT: E 158 TYR cc_start: 0.7416 (t80) cc_final: 0.7184 (t80) REVERT: E 164 PHE cc_start: 0.7733 (m-80) cc_final: 0.7434 (m-80) REVERT: E 190 ILE cc_start: 0.8682 (mm) cc_final: 0.8470 (mm) REVERT: E 227 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8722 (mttp) REVERT: E 299 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8501 (mp) REVERT: E 361 LEU cc_start: 0.8568 (tp) cc_final: 0.8280 (mp) REVERT: E 397 ASN cc_start: 0.9119 (t0) cc_final: 0.8827 (t0) REVERT: E 445 ILE cc_start: 0.9136 (mm) cc_final: 0.8733 (mp) REVERT: E 530 MET cc_start: 0.7217 (tpp) cc_final: 0.6966 (tpp) REVERT: E 590 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8107 (mm) REVERT: E 1272 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7274 (mp) outliers start: 99 outliers final: 79 residues processed: 472 average time/residue: 0.2967 time to fit residues: 225.1021 Evaluate side-chains 505 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 415 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 3.9990 chunk 259 optimal weight: 40.0000 chunk 158 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 250 optimal weight: 50.0000 chunk 216 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 128 GLN E 707 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21083 Z= 0.337 Angle : 0.608 9.684 28726 Z= 0.302 Chirality : 0.046 0.203 3386 Planarity : 0.004 0.046 3559 Dihedral : 16.758 165.475 3788 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.21 % Allowed : 19.05 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2750 helix: 1.76 (0.15), residues: 1315 sheet: -1.89 (0.29), residues: 302 loop : -1.51 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 90 HIS 0.008 0.001 HIS E 125 PHE 0.023 0.002 PHE A 75 TYR 0.014 0.002 TYR E 107 ARG 0.008 0.001 ARG D 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 419 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: A 108 VAL cc_start: 0.9326 (t) cc_final: 0.8887 (m) REVERT: A 196 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 262 ASP cc_start: 0.7024 (t0) cc_final: 0.6678 (t0) REVERT: B 58 ASP cc_start: 0.8186 (p0) cc_final: 0.7833 (p0) REVERT: B 84 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8272 (tt) REVERT: B 114 ILE cc_start: 0.9130 (mm) cc_final: 0.8767 (mt) REVERT: B 125 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8857 (mt) REVERT: B 314 ARG cc_start: 0.8305 (mtm110) cc_final: 0.8048 (mtp-110) REVERT: C 76 THR cc_start: 0.9161 (m) cc_final: 0.8779 (m) REVERT: C 113 SER cc_start: 0.9075 (m) cc_final: 0.8809 (t) REVERT: C 259 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8461 (t-170) REVERT: D 41 ASN cc_start: 0.8616 (t0) cc_final: 0.8308 (t0) REVERT: D 47 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8189 (mttm) REVERT: D 107 ASN cc_start: 0.7861 (t0) cc_final: 0.7548 (t0) REVERT: D 108 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8769 (p) REVERT: D 173 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8259 (mm-40) REVERT: D 200 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7631 (tt) REVERT: D 212 SER cc_start: 0.9054 (m) cc_final: 0.8571 (p) REVERT: D 249 ILE cc_start: 0.8376 (tp) cc_final: 0.8112 (tp) REVERT: D 290 VAL cc_start: 0.9607 (OUTLIER) cc_final: 0.9226 (m) REVERT: D 332 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8132 (mtmm) REVERT: E 139 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8681 (mp) REVERT: E 158 TYR cc_start: 0.7414 (t80) cc_final: 0.7166 (t80) REVERT: E 164 PHE cc_start: 0.7505 (m-80) cc_final: 0.7236 (m-80) REVERT: E 190 ILE cc_start: 0.8669 (mm) cc_final: 0.8457 (mm) REVERT: E 227 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8742 (mttp) REVERT: E 299 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8482 (mp) REVERT: E 361 LEU cc_start: 0.8744 (tp) cc_final: 0.8472 (mp) REVERT: E 397 ASN cc_start: 0.9117 (t0) cc_final: 0.8831 (t0) REVERT: E 445 ILE cc_start: 0.9137 (mm) cc_final: 0.8722 (mp) REVERT: E 590 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8047 (mm) REVERT: E 602 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7746 (mtmt) REVERT: E 1272 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7255 (mp) outliers start: 91 outliers final: 77 residues processed: 468 average time/residue: 0.2872 time to fit residues: 217.2889 Evaluate side-chains 505 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 416 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 27 optimal weight: 0.0570 chunk 39 optimal weight: 5.9990 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 128 GLN B 128 GLN B 313 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.158539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.129417 restraints weight = 24397.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.129817 restraints weight = 18579.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.132050 restraints weight = 14287.931| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21083 Z= 0.319 Angle : 0.602 9.803 28726 Z= 0.299 Chirality : 0.046 0.199 3386 Planarity : 0.004 0.046 3559 Dihedral : 16.668 164.956 3788 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.38 % Allowed : 18.88 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2750 helix: 1.82 (0.15), residues: 1305 sheet: -1.89 (0.29), residues: 292 loop : -1.52 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 90 HIS 0.008 0.001 HIS E 125 PHE 0.023 0.002 PHE A 75 TYR 0.014 0.002 TYR E 107 ARG 0.008 0.001 ARG D 192 =============================================================================== Job complete usr+sys time: 4545.52 seconds wall clock time: 83 minutes 45.94 seconds (5025.94 seconds total)