Starting phenix.real_space_refine on Thu Mar 21 02:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwp_14190/03_2024/7qwp_14190.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwp_14190/03_2024/7qwp_14190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwp_14190/03_2024/7qwp_14190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwp_14190/03_2024/7qwp_14190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwp_14190/03_2024/7qwp_14190.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwp_14190/03_2024/7qwp_14190.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 102 5.16 5 C 17968 2.51 5 N 5130 2.21 5 O 5734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C ARG 1246": "NH1" <-> "NH2" Residue "C ARG 1269": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1372": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 196": "NH1" <-> "NH2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M ARG 237": "NH1" <-> "NH2" Residue "M ARG 240": "NH1" <-> "NH2" Residue "M ARG 296": "NH1" <-> "NH2" Residue "M ARG 383": "NH1" <-> "NH2" Residue "M ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29006 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2316 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1673 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 10135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10135 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 451 Unresolved non-hydrogen angles: 545 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 284 Chain: "D" Number of atoms: 9638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 9638 Classifications: {'peptide': 1333} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 53, 'TRANS': 1279} Chain breaks: 6 Unresolved non-hydrogen bonds: 768 Unresolved non-hydrogen angles: 946 Unresolved non-hydrogen dihedrals: 635 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 22, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 28, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 462 Chain: "E" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 552 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3216 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 15.27, per 1000 atoms: 0.53 Number of scatterers: 29006 At special positions: 0 Unit cell: (148.5, 180.4, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 72 15.00 O 5734 8.00 N 5130 7.00 C 17968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.74 Conformation dependent library (CDL) restraints added in 5.4 seconds 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6846 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 37 sheets defined 38.7% alpha, 10.4% beta 33 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 9.38 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.003A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.796A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.680A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.561A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.639A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.516A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.592A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.562A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.539A pdb=" N LYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 9' Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.192A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.606A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.522A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.241A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.898A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 removed outlier: 3.994A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.921A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 390 removed outlier: 4.558A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 removed outlier: 3.525A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.817A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.866A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.655A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.778A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.925A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.548A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.443A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.798A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 4.083A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.805A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.890A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.411A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.805A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.545A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1174 removed outlier: 3.841A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.908A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C1243 " --> pdb=" O VAL C1239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1238 through 1243' Processing helix chain 'C' and resid 1271 through 1280 removed outlier: 3.726A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C1280 " --> pdb=" O TRP C1276 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.546A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 4.246A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.749A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.710A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.892A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 removed outlier: 4.634A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.713A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.560A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.775A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.633A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 266 through 285 removed outlier: 3.527A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 341 removed outlier: 3.926A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.626A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.972A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.594A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 538 removed outlier: 4.269A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.642A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 removed outlier: 3.903A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.760A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.563A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.589A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 702 removed outlier: 4.534A pdb=" N VAL D 682 " --> pdb=" O ARG D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 738 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.712A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 876 Processing helix chain 'D' and resid 914 through 919 removed outlier: 3.547A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.516A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.874A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.061A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1291 removed outlier: 4.588A pdb=" N ILE D1287 " --> pdb=" O SER D1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.614A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1310 through 1316 Processing helix chain 'D' and resid 1318 through 1322 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.898A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 4.347A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.981A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'M' and resid 16 through 28 removed outlier: 3.604A pdb=" N ARG M 24 " --> pdb=" O GLN M 20 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 121 through 131 removed outlier: 3.722A pdb=" N GLN M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL M 128 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU M 129 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.819A pdb=" N ALA M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 165 removed outlier: 3.720A pdb=" N VAL M 162 " --> pdb=" O ILE M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.908A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG M 181 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN M 183 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 206 removed outlier: 3.944A pdb=" N LEU M 200 " --> pdb=" O ARG M 196 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.769A pdb=" N ASP M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 228 removed outlier: 3.822A pdb=" N LEU M 227 " --> pdb=" O HIS M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 240 removed outlier: 4.529A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 244 through 255 removed outlier: 3.816A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU M 252 " --> pdb=" O GLU M 248 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 264 removed outlier: 3.626A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 306 removed outlier: 3.897A pdb=" N ALA M 305 " --> pdb=" O GLN M 301 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET M 306 " --> pdb=" O GLN M 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 301 through 306' Processing helix chain 'M' and resid 313 through 351 removed outlier: 3.901A pdb=" N ILE M 347 " --> pdb=" O VAL M 343 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL M 348 " --> pdb=" O SER M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 357 removed outlier: 3.577A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 362 Processing helix chain 'M' and resid 366 through 372 Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.661A pdb=" N ARG M 383 " --> pdb=" O SER M 379 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 403 removed outlier: 4.135A pdb=" N PHE M 403 " --> pdb=" O LEU M 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 399 through 403' Processing helix chain 'M' and resid 410 through 412 No H-bonds generated for 'chain 'M' and resid 410 through 412' Processing helix chain 'M' and resid 417 through 431 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 465 removed outlier: 3.578A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 6.134A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.620A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.973A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 28 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.655A pdb=" N GLY B 149 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 57 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.269A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 3.842A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 114 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75 removed outlier: 3.842A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.143A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.246A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.613A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 7.076A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 755 through 758 removed outlier: 6.452A pdb=" N ILE C 765 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.868A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.928A pdb=" N VAL C1225 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1210 " --> pdb=" O VAL C1225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 839 removed outlier: 4.086A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1335 through 1336 Processing sheet with id=AC9, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.582A pdb=" N PHE D 35 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 244 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 145 through 148 removed outlier: 3.518A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 353 through 357 Processing sheet with id=AD3, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.594A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.015A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 825 through 826 removed outlier: 3.731A pdb=" N VAL D 825 " --> pdb=" O GLU D 833 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AD7, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AD8, first strand: chain 'D' and resid 1265 through 1266 Processing sheet with id=AD9, first strand: chain 'M' and resid 286 through 289 removed outlier: 3.628A pdb=" N THR M 286 " --> pdb=" O ARG M 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG M 279 " --> pdb=" O THR M 286 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 406 through 408 975 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 13.17 Time building geometry restraints manager: 12.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4907 1.28 - 1.41: 6680 1.41 - 1.55: 17487 1.55 - 1.68: 316 1.68 - 1.81: 181 Bond restraints: 29571 Sorted by residual: bond pdb=" O3' DG T 13 " pdb=" P DC T 14 " ideal model delta sigma weight residual 1.607 1.474 0.133 1.50e-02 4.44e+03 7.86e+01 bond pdb=" CA ARG M 196 " pdb=" C ARG M 196 " ideal model delta sigma weight residual 1.523 1.415 0.108 1.34e-02 5.57e+03 6.49e+01 bond pdb=" O3' DT T 9 " pdb=" P DC T 10 " ideal model delta sigma weight residual 1.607 1.489 0.118 1.50e-02 4.44e+03 6.14e+01 bond pdb=" CA THR M 142 " pdb=" C THR M 142 " ideal model delta sigma weight residual 1.522 1.415 0.107 1.39e-02 5.18e+03 5.98e+01 bond pdb=" CA ILE M 165 " pdb=" CB ILE M 165 " ideal model delta sigma weight residual 1.540 1.457 0.084 1.15e-02 7.56e+03 5.27e+01 ... (remaining 29566 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.82: 253 102.82 - 111.12: 12113 111.12 - 119.42: 13116 119.42 - 127.71: 14687 127.71 - 136.01: 267 Bond angle restraints: 40436 Sorted by residual: angle pdb=" C5' DG T 13 " pdb=" C4' DG T 13 " pdb=" O4' DG T 13 " ideal model delta sigma weight residual 109.40 130.32 -20.92 1.50e+00 4.44e-01 1.95e+02 angle pdb=" O3' DG T 13 " pdb=" P DC T 14 " pdb=" O5' DC T 14 " ideal model delta sigma weight residual 104.00 120.05 -16.05 1.50e+00 4.44e-01 1.14e+02 angle pdb=" C5' DC N -11 " pdb=" C4' DC N -11 " pdb=" O4' DC N -11 " ideal model delta sigma weight residual 109.40 122.31 -12.91 1.50e+00 4.44e-01 7.41e+01 angle pdb=" CA ILE M 264 " pdb=" C ILE M 264 " pdb=" N GLN M 265 " ideal model delta sigma weight residual 115.28 105.57 9.71 1.14e+00 7.69e-01 7.25e+01 angle pdb=" N ILE M 158 " pdb=" CA ILE M 158 " pdb=" C ILE M 158 " ideal model delta sigma weight residual 111.45 103.64 7.81 9.30e-01 1.16e+00 7.05e+01 ... (remaining 40431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 17257 32.42 - 64.83: 610 64.83 - 97.25: 8 97.25 - 129.67: 0 129.67 - 162.08: 1 Dihedral angle restraints: 17876 sinusoidal: 7272 harmonic: 10604 Sorted by residual: dihedral pdb=" C LEU M 31 " pdb=" N LEU M 31 " pdb=" CA LEU M 31 " pdb=" CB LEU M 31 " ideal model delta harmonic sigma weight residual -122.60 -139.61 17.01 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" C GLN M 183 " pdb=" N GLN M 183 " pdb=" CA GLN M 183 " pdb=" CB GLN M 183 " ideal model delta harmonic sigma weight residual -122.60 -106.43 -16.17 0 2.50e+00 1.60e-01 4.18e+01 dihedral pdb=" N ASP M 275 " pdb=" C ASP M 275 " pdb=" CA ASP M 275 " pdb=" CB ASP M 275 " ideal model delta harmonic sigma weight residual 122.80 137.95 -15.15 0 2.50e+00 1.60e-01 3.67e+01 ... (remaining 17873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 4692 0.200 - 0.400: 70 0.400 - 0.601: 3 0.601 - 0.801: 1 0.801 - 1.001: 1 Chirality restraints: 4767 Sorted by residual: chirality pdb=" C4' DG T 13 " pdb=" C5' DG T 13 " pdb=" O4' DG T 13 " pdb=" C3' DG T 13 " both_signs ideal model delta sigma weight residual False -2.53 -1.52 -1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA LEU M 31 " pdb=" N LEU M 31 " pdb=" C LEU M 31 " pdb=" CB LEU M 31 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA ARG M 311 " pdb=" N ARG M 311 " pdb=" C ARG M 311 " pdb=" CB ARG M 311 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.32e+00 ... (remaining 4764 not shown) Planarity restraints: 5059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 285 " 0.090 2.00e-02 2.50e+03 5.47e-02 7.48e+01 pdb=" CG TRP M 285 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP M 285 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP M 285 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP M 285 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TRP M 285 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP M 285 " -0.079 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 285 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 285 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP M 285 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 206 " -0.085 2.00e-02 2.50e+03 5.46e-02 5.22e+01 pdb=" CG PHE M 206 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE M 206 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE M 206 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE M 206 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE M 206 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE M 206 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N -11 " 0.066 2.00e-02 2.50e+03 3.96e-02 3.53e+01 pdb=" N1 DC N -11 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DC N -11 " -0.041 2.00e-02 2.50e+03 pdb=" O2 DC N -11 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DC N -11 " 0.041 2.00e-02 2.50e+03 pdb=" C4 DC N -11 " 0.015 2.00e-02 2.50e+03 pdb=" N4 DC N -11 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC N -11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC N -11 " -0.000 2.00e-02 2.50e+03 ... (remaining 5056 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1231 2.71 - 3.26: 28842 3.26 - 3.81: 44487 3.81 - 4.35: 54253 4.35 - 4.90: 90300 Nonbonded interactions: 219113 Sorted by model distance: nonbonded pdb=" N GLN A 194 " pdb=" OE1 GLN A 194 " model vdw 2.165 2.520 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.197 2.440 nonbonded pdb=" O SER C 166 " pdb=" OG SER C 166 " model vdw 2.201 2.440 nonbonded pdb=" O THR D1310 " pdb=" OG SER D1313 " model vdw 2.212 2.440 nonbonded pdb=" CB GLU A 29 " pdb=" CD PRO A 30 " model vdw 2.228 3.840 ... (remaining 219108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.260 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 83.280 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 29571 Z= 0.433 Angle : 0.985 20.921 40436 Z= 0.627 Chirality : 0.061 1.001 4767 Planarity : 0.004 0.056 5059 Dihedral : 13.757 162.083 11030 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.51 % Favored : 93.16 % Rotamer: Outliers : 7.21 % Allowed : 7.63 % Favored : 85.16 % Cbeta Deviations : 0.23 % 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: -3.22 (0.12), residues: 3655 helix: -1.28 (0.14), residues: 1227 sheet: -1.89 (0.28), residues: 285 loop : -2.83 (0.11), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.004 TRP M 285 HIS 0.021 0.001 HIS M 391 PHE 0.103 0.003 PHE M 206 TYR 0.050 0.001 TYR M 153 ARG 0.032 0.000 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 865 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7296 (mmm160) REVERT: A 79 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 166 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8103 (ptt-90) REVERT: B 17 GLU cc_start: 0.7480 (pt0) cc_final: 0.7273 (mp0) REVERT: C 160 ASP cc_start: 0.7744 (m-30) cc_final: 0.7295 (t70) REVERT: C 169 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5776 (mtmt) REVERT: C 187 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7472 (tt0) REVERT: C 396 ASP cc_start: 0.6406 (t70) cc_final: 0.6201 (t70) REVERT: C 488 MET cc_start: 0.8743 (mmm) cc_final: 0.8446 (mmp) REVERT: C 565 GLU cc_start: 0.6150 (tp30) cc_final: 0.5918 (mt-10) REVERT: C 639 LYS cc_start: 0.7412 (mttp) cc_final: 0.6499 (mtmm) REVERT: C 905 ILE cc_start: 0.8230 (mt) cc_final: 0.7921 (mm) REVERT: C 1230 MET cc_start: 0.8031 (ttt) cc_final: 0.7821 (ttm) REVERT: D 20 ILE cc_start: 0.6843 (tp) cc_final: 0.6217 (mt) REVERT: D 44 ILE cc_start: 0.7798 (tt) cc_final: 0.7095 (pt) REVERT: D 123 ARG cc_start: 0.7234 (mmt90) cc_final: 0.6447 (mmt180) REVERT: D 142 GLU cc_start: 0.8478 (pt0) cc_final: 0.8205 (pm20) REVERT: D 264 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6586 (t0) REVERT: D 326 SER cc_start: 0.8561 (p) cc_final: 0.7922 (p) REVERT: D 340 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.5817 (mm-40) REVERT: D 695 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8150 (tppt) REVERT: D 1040 MET cc_start: 0.3071 (mtp) cc_final: 0.2443 (mmt) REVERT: D 1260 MET cc_start: 0.9099 (ptt) cc_final: 0.8834 (ptp) REVERT: D 1266 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8215 (pt) REVERT: D 1278 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7077 (mt-10) REVERT: M 21 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8880 (mt0) REVERT: M 27 GLN cc_start: 0.8897 (pt0) cc_final: 0.8382 (tp40) REVERT: M 28 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8464 (pt) REVERT: M 115 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8809 (mm-30) REVERT: M 157 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7930 (tm-30) REVERT: M 185 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: M 212 TRP cc_start: 0.8639 (m-90) cc_final: 0.8404 (m-90) REVERT: M 223 HIS cc_start: 0.8806 (m-70) cc_final: 0.8039 (m90) REVERT: M 306 MET cc_start: 0.7977 (mtp) cc_final: 0.7325 (mtm) REVERT: M 337 ASN cc_start: 0.8566 (m-40) cc_final: 0.8246 (m110) REVERT: M 401 TYR cc_start: 0.8725 (t80) cc_final: 0.8483 (t80) REVERT: M 403 PHE cc_start: 0.9263 (m-80) cc_final: 0.8993 (m-80) REVERT: M 441 LYS cc_start: 0.9472 (tptt) cc_final: 0.8173 (mtpt) outliers start: 202 outliers final: 65 residues processed: 1011 average time/residue: 0.4420 time to fit residues: 678.6914 Evaluate side-chains 546 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 469 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 112 TYR Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 237 ARG Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 336 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 291 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 chunk 177 optimal weight: 0.0470 chunk 217 optimal weight: 10.0000 chunk 337 optimal weight: 0.9980 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 283 GLN B 132 HIS C 327 GLN C 343 HIS C 462 ASN C 628 HIS C 684 ASN C 832 HIS C1244 HIS ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 560 ASN D 651 HIS D 667 GLN D 680 ASN D 702 GLN E 29 GLN E 31 GLN M 113 GLN M 262 GLN M 352 GLN M 406 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29571 Z= 0.291 Angle : 0.693 11.503 40436 Z= 0.351 Chirality : 0.046 0.215 4767 Planarity : 0.005 0.057 5059 Dihedral : 14.942 169.372 4925 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 5.78 % Allowed : 15.55 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -2.23 (0.13), residues: 3655 helix: -0.20 (0.14), residues: 1280 sheet: -1.24 (0.31), residues: 284 loop : -2.46 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1276 HIS 0.011 0.002 HIS D 651 PHE 0.029 0.002 PHE C 38 TYR 0.030 0.002 TYR B 177 ARG 0.011 0.001 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 459 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8503 (mtmm) cc_final: 0.7987 (mtpt) REVERT: A 79 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8502 (mt) REVERT: A 148 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.6916 (ptp90) REVERT: A 199 ASP cc_start: 0.6517 (m-30) cc_final: 0.6256 (m-30) REVERT: B 80 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 132 HIS cc_start: 0.5931 (OUTLIER) cc_final: 0.5496 (t-170) REVERT: C 169 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6370 (mtmt) REVERT: C 170 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8985 (m) REVERT: C 187 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7282 (tt0) REVERT: C 369 MET cc_start: 0.8230 (tmm) cc_final: 0.8029 (tmm) REVERT: C 488 MET cc_start: 0.8803 (mmm) cc_final: 0.8511 (mmp) REVERT: C 696 ASP cc_start: 0.7646 (t70) cc_final: 0.7162 (t0) REVERT: C 870 ILE cc_start: 0.7930 (pt) cc_final: 0.7616 (pt) REVERT: C 962 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8091 (mm-30) REVERT: C 1017 GLN cc_start: 0.8704 (mt0) cc_final: 0.8314 (mt0) REVERT: D 326 SER cc_start: 0.9065 (p) cc_final: 0.8778 (p) REVERT: D 339 ARG cc_start: 0.6788 (mmp80) cc_final: 0.6506 (tmm160) REVERT: D 695 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8256 (tppt) REVERT: D 811 GLU cc_start: 0.6957 (tp30) cc_final: 0.6737 (tp30) REVERT: D 817 HIS cc_start: 0.7838 (m-70) cc_final: 0.7574 (m-70) REVERT: D 821 MET cc_start: 0.8426 (tpp) cc_final: 0.8140 (tpt) REVERT: D 832 LYS cc_start: 0.7868 (mmtm) cc_final: 0.7649 (mmtm) REVERT: D 1040 MET cc_start: 0.3252 (mtp) cc_final: 0.2799 (mmt) REVERT: D 1247 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7388 (ptmt) REVERT: D 1260 MET cc_start: 0.8952 (ptt) cc_final: 0.8723 (ptp) REVERT: D 1266 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8385 (pt) REVERT: D 1278 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7112 (mt-10) REVERT: E 3 ARG cc_start: 0.6712 (tpp-160) cc_final: 0.6488 (tpt170) REVERT: M 27 GLN cc_start: 0.9037 (pt0) cc_final: 0.8711 (tp40) REVERT: M 42 GLU cc_start: 0.8766 (pt0) cc_final: 0.8122 (mp0) REVERT: M 115 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8800 (mp0) REVERT: M 157 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7795 (tm-30) REVERT: M 181 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7523 (tpt90) REVERT: M 185 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7315 (m-10) REVERT: M 271 TYR cc_start: 0.6049 (m-10) cc_final: 0.5545 (m-10) REVERT: M 376 MET cc_start: 0.8630 (mmm) cc_final: 0.8331 (mmm) outliers start: 162 outliers final: 78 residues processed: 588 average time/residue: 0.4414 time to fit residues: 415.9841 Evaluate side-chains 453 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 363 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 315 ASP Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 230 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 338 optimal weight: 5.9990 chunk 365 optimal weight: 8.9990 chunk 301 optimal weight: 0.0870 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 271 optimal weight: 20.0000 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN C 808 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN D 560 ASN D 651 HIS D 667 GLN D 702 GLN E 29 GLN E 62 GLN M 183 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29571 Z= 0.153 Angle : 0.585 12.696 40436 Z= 0.291 Chirality : 0.042 0.164 4767 Planarity : 0.004 0.066 5059 Dihedral : 14.386 168.052 4820 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 4.03 % Allowed : 18.62 % 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: -1.65 (0.13), residues: 3655 helix: 0.50 (0.15), residues: 1262 sheet: -0.82 (0.32), residues: 273 loop : -2.27 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 285 HIS 0.015 0.001 HIS M 406 PHE 0.018 0.001 PHE C 38 TYR 0.025 0.001 TYR C1018 ARG 0.007 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 389 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 148 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.6922 (ptp90) REVERT: A 199 ASP cc_start: 0.6271 (m-30) cc_final: 0.6032 (m-30) REVERT: B 80 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7951 (mt-10) REVERT: C 160 ASP cc_start: 0.7430 (t70) cc_final: 0.7115 (t70) REVERT: C 169 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6461 (mtmt) REVERT: C 488 MET cc_start: 0.8800 (mmm) cc_final: 0.8584 (mmp) REVERT: C 696 ASP cc_start: 0.7745 (t70) cc_final: 0.7323 (t0) REVERT: C 725 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: C 766 ASN cc_start: 0.8244 (t0) cc_final: 0.7913 (t0) REVERT: C 960 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8517 (tm) REVERT: C 1243 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7685 (ttt) REVERT: D 229 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8580 (tp-100) REVERT: D 339 ARG cc_start: 0.6792 (mmp80) cc_final: 0.6572 (tmm-80) REVERT: D 423 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8488 (pp) REVERT: D 626 TYR cc_start: 0.8141 (m-10) cc_final: 0.7750 (m-10) REVERT: D 695 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8204 (tppt) REVERT: D 811 GLU cc_start: 0.6901 (tp30) cc_final: 0.6686 (tp30) REVERT: D 817 HIS cc_start: 0.7472 (m-70) cc_final: 0.7227 (m-70) REVERT: D 818 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6525 (tm-30) REVERT: D 821 MET cc_start: 0.8436 (tpp) cc_final: 0.8156 (tpt) REVERT: D 1040 MET cc_start: 0.3102 (mtp) cc_final: 0.2642 (mmt) REVERT: D 1247 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7330 (ptmt) REVERT: D 1266 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8408 (pt) REVERT: D 1278 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7167 (mt-10) REVERT: E 35 LYS cc_start: 0.6607 (mmmm) cc_final: 0.6402 (mmmm) REVERT: E 62 GLN cc_start: 0.8048 (tp40) cc_final: 0.7759 (tp-100) REVERT: M 27 GLN cc_start: 0.9048 (pt0) cc_final: 0.8719 (tp40) REVERT: M 185 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: M 194 ASP cc_start: 0.8995 (m-30) cc_final: 0.8550 (t0) REVERT: M 202 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8695 (mt0) REVERT: M 232 PHE cc_start: 0.8292 (m-10) cc_final: 0.7954 (m-10) REVERT: M 374 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.7914 (m) REVERT: M 376 MET cc_start: 0.8718 (mmm) cc_final: 0.8315 (mmm) REVERT: M 397 PHE cc_start: 0.8465 (m-80) cc_final: 0.7988 (m-80) REVERT: M 402 PHE cc_start: 0.9082 (m-10) cc_final: 0.8840 (m-10) outliers start: 113 outliers final: 61 residues processed: 477 average time/residue: 0.4255 time to fit residues: 327.9088 Evaluate side-chains 426 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 352 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 177 optimal weight: 0.0050 chunk 321 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 HIS D 651 HIS D 702 GLN E 29 GLN M 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29571 Z= 0.169 Angle : 0.570 11.871 40436 Z= 0.283 Chirality : 0.041 0.203 4767 Planarity : 0.004 0.058 5059 Dihedral : 14.263 167.961 4802 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.17 % Favored : 92.75 % Rotamer: Outliers : 4.50 % Allowed : 19.16 % Favored : 76.35 % 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: -1.35 (0.14), residues: 3655 helix: 0.79 (0.15), residues: 1262 sheet: -0.72 (0.32), residues: 278 loop : -2.10 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 285 HIS 0.004 0.001 HIS D 651 PHE 0.015 0.001 PHE C 38 TYR 0.018 0.001 TYR C1018 ARG 0.006 0.000 ARG M 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 370 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8501 (mt) REVERT: A 148 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7015 (ptp90) REVERT: B 80 GLU cc_start: 0.8557 (mt-10) cc_final: 0.7800 (mt-10) REVERT: B 99 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.8986 (mt) REVERT: C 39 ILE cc_start: 0.8035 (tp) cc_final: 0.7834 (tp) REVERT: C 160 ASP cc_start: 0.7564 (t70) cc_final: 0.7276 (t70) REVERT: C 169 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6521 (mtmt) REVERT: C 187 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7319 (mt-10) REVERT: C 488 MET cc_start: 0.8806 (mmm) cc_final: 0.8605 (mmp) REVERT: C 696 ASP cc_start: 0.7769 (t70) cc_final: 0.7320 (t0) REVERT: C 725 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: C 766 ASN cc_start: 0.8251 (t0) cc_final: 0.7967 (t0) REVERT: C 944 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7266 (ptt180) REVERT: C 960 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8663 (tm) REVERT: C 1038 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: D 339 ARG cc_start: 0.6766 (mmp80) cc_final: 0.6477 (tmm-80) REVERT: D 423 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8487 (pp) REVERT: D 695 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8106 (tmmm) REVERT: D 817 HIS cc_start: 0.7570 (m-70) cc_final: 0.7310 (m-70) REVERT: D 821 MET cc_start: 0.8473 (tpp) cc_final: 0.8262 (tpt) REVERT: D 866 GLU cc_start: 0.7053 (tp30) cc_final: 0.6841 (tp30) REVERT: D 1040 MET cc_start: 0.3089 (mtp) cc_final: 0.2635 (mmt) REVERT: D 1247 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7451 (ptmt) REVERT: D 1266 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8457 (pt) REVERT: D 1278 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7212 (mt-10) REVERT: E 3 ARG cc_start: 0.6614 (tpt170) cc_final: 0.6188 (tpt170) REVERT: M 27 GLN cc_start: 0.9016 (pt0) cc_final: 0.8719 (tp40) REVERT: M 185 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: M 194 ASP cc_start: 0.9026 (m-30) cc_final: 0.8599 (t0) REVERT: M 374 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8166 (m) REVERT: M 376 MET cc_start: 0.8739 (mmm) cc_final: 0.8405 (mmm) REVERT: M 402 PHE cc_start: 0.9130 (m-10) cc_final: 0.8812 (m-10) outliers start: 126 outliers final: 79 residues processed: 468 average time/residue: 0.4047 time to fit residues: 301.8320 Evaluate side-chains 431 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 338 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 239 THR Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 30.0000 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN C 343 HIS C 808 ASN D 560 ASN D 651 HIS D 702 GLN E 29 GLN M 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 29571 Z= 0.485 Angle : 0.765 12.196 40436 Z= 0.388 Chirality : 0.048 0.275 4767 Planarity : 0.005 0.057 5059 Dihedral : 14.587 166.861 4798 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.26 % Favored : 91.60 % Rotamer: Outliers : 5.85 % Allowed : 18.80 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3655 helix: 0.37 (0.15), residues: 1275 sheet: -0.97 (0.31), residues: 302 loop : -2.22 (0.12), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 285 HIS 0.021 0.002 HIS M 406 PHE 0.027 0.002 PHE C 828 TYR 0.020 0.002 TYR C 92 ARG 0.008 0.001 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 343 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.7267 (ptp90) REVERT: A 199 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7054 (t0) REVERT: C 169 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6053 (mtmt) REVERT: C 195 PHE cc_start: 0.7755 (m-10) cc_final: 0.7542 (m-10) REVERT: C 451 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8477 (ptm160) REVERT: C 488 MET cc_start: 0.8929 (mmm) cc_final: 0.8668 (mmp) REVERT: C 696 ASP cc_start: 0.7931 (t70) cc_final: 0.7394 (t0) REVERT: C 960 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8707 (tm) REVERT: C 1038 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: C 1253 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8582 (mm) REVERT: D 4 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8480 (tp) REVERT: D 196 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8797 (tm-30) REVERT: D 314 ARG cc_start: 0.7218 (ptt90) cc_final: 0.6848 (ptt90) REVERT: D 324 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8204 (pp) REVERT: D 334 LYS cc_start: 0.7101 (tppt) cc_final: 0.6450 (mmtm) REVERT: D 339 ARG cc_start: 0.6710 (mmp80) cc_final: 0.6388 (tmm160) REVERT: D 660 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: D 695 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8331 (tmmm) REVERT: D 698 MET cc_start: 0.8305 (mmt) cc_final: 0.7841 (mmt) REVERT: D 714 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: D 817 HIS cc_start: 0.7749 (m-70) cc_final: 0.7469 (m-70) REVERT: D 818 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6833 (tm-30) REVERT: D 1263 LYS cc_start: 0.7620 (mmmt) cc_final: 0.6890 (tmtt) REVERT: D 1266 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8432 (pt) REVERT: D 1278 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7320 (mt-10) REVERT: M 27 GLN cc_start: 0.9046 (pt0) cc_final: 0.8748 (tp40) REVERT: M 125 MET cc_start: 0.8982 (tpp) cc_final: 0.8734 (tpp) REVERT: M 185 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7240 (m-10) REVERT: M 194 ASP cc_start: 0.9066 (m-30) cc_final: 0.8641 (t0) REVERT: M 374 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.7768 (m) REVERT: M 376 MET cc_start: 0.8819 (mmm) cc_final: 0.8425 (mmm) REVERT: M 397 PHE cc_start: 0.8203 (m-10) cc_final: 0.7982 (m-80) outliers start: 164 outliers final: 100 residues processed: 471 average time/residue: 0.4134 time to fit residues: 305.9871 Evaluate side-chains 430 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 315 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 112 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 239 THR Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.6980 chunk 323 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN C 437 ASN C 808 ASN E 62 GLN M 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29571 Z= 0.171 Angle : 0.601 12.159 40436 Z= 0.301 Chirality : 0.042 0.221 4767 Planarity : 0.004 0.055 5059 Dihedral : 14.281 166.097 4790 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 4.10 % Allowed : 20.87 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3655 helix: 0.74 (0.15), residues: 1285 sheet: -0.79 (0.31), residues: 285 loop : -2.06 (0.12), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 285 HIS 0.004 0.001 HIS A 128 PHE 0.012 0.001 PHE C1323 TYR 0.028 0.001 TYR D 626 ARG 0.006 0.000 ARG C1269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 349 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7115 (ptp90) REVERT: B 125 LYS cc_start: 0.7872 (ptmm) cc_final: 0.7527 (ptmm) REVERT: C 39 ILE cc_start: 0.8345 (tp) cc_final: 0.7930 (tp) REVERT: C 188 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: C 488 MET cc_start: 0.8925 (mmm) cc_final: 0.8694 (mmp) REVERT: C 545 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6605 (t80) REVERT: C 696 ASP cc_start: 0.7996 (t70) cc_final: 0.7541 (t0) REVERT: C 960 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8686 (tm) REVERT: C 1170 MET cc_start: 0.8709 (mmm) cc_final: 0.8411 (tpp) REVERT: D 196 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8830 (tm-30) REVERT: D 314 ARG cc_start: 0.7121 (ptt90) cc_final: 0.6773 (ptt90) REVERT: D 324 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8165 (pp) REVERT: D 334 LYS cc_start: 0.7198 (tppt) cc_final: 0.6706 (mmtt) REVERT: D 339 ARG cc_start: 0.6657 (mmp80) cc_final: 0.6411 (tmm160) REVERT: D 423 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8425 (pp) REVERT: D 660 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: D 695 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8212 (tmmm) REVERT: D 817 HIS cc_start: 0.7642 (m-70) cc_final: 0.7402 (m-70) REVERT: D 818 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6801 (tm-30) REVERT: D 1040 MET cc_start: 0.3992 (mmm) cc_final: 0.2711 (mmm) REVERT: D 1263 LYS cc_start: 0.7329 (mmmt) cc_final: 0.6645 (tmtt) REVERT: D 1266 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8422 (pt) REVERT: D 1278 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7359 (mt-10) REVERT: M 27 GLN cc_start: 0.9057 (pt0) cc_final: 0.8806 (tp40) REVERT: M 115 GLU cc_start: 0.8947 (mp0) cc_final: 0.8530 (mp0) REVERT: M 180 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8605 (tttm) REVERT: M 185 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: M 194 ASP cc_start: 0.9090 (m-30) cc_final: 0.8668 (t0) REVERT: M 223 HIS cc_start: 0.8630 (m90) cc_final: 0.8411 (m90) REVERT: M 256 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7874 (mt) REVERT: M 271 TYR cc_start: 0.6087 (m-10) cc_final: 0.5729 (m-10) REVERT: M 374 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.7914 (m) REVERT: M 376 MET cc_start: 0.8788 (mmm) cc_final: 0.8414 (mmm) outliers start: 115 outliers final: 75 residues processed: 438 average time/residue: 0.4116 time to fit residues: 285.0861 Evaluate side-chains 405 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 317 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 358 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 218 optimal weight: 0.0170 chunk 165 optimal weight: 9.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN D 702 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN M 406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29571 Z= 0.334 Angle : 0.660 12.702 40436 Z= 0.333 Chirality : 0.045 0.227 4767 Planarity : 0.005 0.053 5059 Dihedral : 14.265 165.637 4784 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.56 % Favored : 91.38 % Rotamer: Outliers : 4.96 % Allowed : 20.59 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3655 helix: 0.65 (0.15), residues: 1299 sheet: -0.83 (0.31), residues: 296 loop : -2.13 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 285 HIS 0.008 0.001 HIS M 223 PHE 0.018 0.002 PHE C1221 TYR 0.032 0.002 TYR D 995 ARG 0.008 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 328 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7187 (ptp90) REVERT: B 125 LYS cc_start: 0.8135 (ptmm) cc_final: 0.7615 (ptmm) REVERT: C 39 ILE cc_start: 0.8484 (tp) cc_final: 0.8022 (tp) REVERT: C 169 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.5773 (pttt) REVERT: C 188 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: C 488 MET cc_start: 0.8937 (mmm) cc_final: 0.8695 (mmp) REVERT: C 545 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6700 (t80) REVERT: C 696 ASP cc_start: 0.8037 (t70) cc_final: 0.7568 (t0) REVERT: C 960 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8721 (tm) REVERT: C 1038 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8259 (tm-30) REVERT: C 1170 MET cc_start: 0.8728 (mmm) cc_final: 0.8447 (tpp) REVERT: D 196 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8818 (tm-30) REVERT: D 314 ARG cc_start: 0.7250 (ptt90) cc_final: 0.6815 (ptt90) REVERT: D 324 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8125 (pp) REVERT: D 334 LYS cc_start: 0.7209 (tppt) cc_final: 0.6338 (mmtm) REVERT: D 339 ARG cc_start: 0.6802 (mmp80) cc_final: 0.6524 (tmm160) REVERT: D 466 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8705 (tpp) REVERT: D 660 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: D 695 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8239 (tmmm) REVERT: D 817 HIS cc_start: 0.7692 (m-70) cc_final: 0.7449 (m-70) REVERT: D 818 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6839 (tm-30) REVERT: D 1040 MET cc_start: 0.3752 (mmm) cc_final: 0.2577 (mmm) REVERT: D 1263 LYS cc_start: 0.7540 (mmmt) cc_final: 0.6905 (tmtt) REVERT: D 1266 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8436 (pt) REVERT: D 1278 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7394 (mt-10) REVERT: M 27 GLN cc_start: 0.9056 (pt0) cc_final: 0.8830 (tp40) REVERT: M 185 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: M 194 ASP cc_start: 0.9088 (m-30) cc_final: 0.8671 (t0) REVERT: M 256 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8018 (mt) REVERT: M 374 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.7756 (m) REVERT: M 376 MET cc_start: 0.8817 (mmm) cc_final: 0.8415 (mmm) outliers start: 139 outliers final: 97 residues processed: 435 average time/residue: 0.4257 time to fit residues: 293.1522 Evaluate side-chains 422 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 312 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 950 GLU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 406 HIS Chi-restraints excluded: chain M residue 409 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 702 GLN M 357 GLN ** M 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29571 Z= 0.204 Angle : 0.615 11.977 40436 Z= 0.308 Chirality : 0.042 0.219 4767 Planarity : 0.004 0.054 5059 Dihedral : 14.165 165.484 4781 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.72 % Favored : 92.20 % Rotamer: Outliers : 4.35 % Allowed : 21.30 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3655 helix: 0.85 (0.15), residues: 1298 sheet: -0.78 (0.31), residues: 295 loop : -2.06 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 285 HIS 0.008 0.001 HIS M 406 PHE 0.024 0.001 PHE M 318 TYR 0.027 0.001 TYR D 995 ARG 0.008 0.000 ARG C1269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 326 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7154 (ptp90) REVERT: B 125 LYS cc_start: 0.8066 (ptmm) cc_final: 0.7554 (ptmm) REVERT: B 176 CYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8100 (p) REVERT: C 39 ILE cc_start: 0.8394 (tp) cc_final: 0.7952 (tp) REVERT: C 169 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.5783 (pttt) REVERT: C 188 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: C 429 MET cc_start: 0.9222 (tpp) cc_final: 0.8832 (tpp) REVERT: C 488 MET cc_start: 0.8928 (mmm) cc_final: 0.8683 (mmp) REVERT: C 545 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6695 (t80) REVERT: C 696 ASP cc_start: 0.8004 (t70) cc_final: 0.7532 (t0) REVERT: C 1013 GLN cc_start: 0.8846 (mt0) cc_final: 0.8630 (mp10) REVERT: C 1038 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 1170 MET cc_start: 0.8687 (mmm) cc_final: 0.8415 (tpp) REVERT: C 1232 MET cc_start: 0.8360 (mmm) cc_final: 0.8095 (mtt) REVERT: D 196 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8838 (tm-30) REVERT: D 324 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8039 (pp) REVERT: D 334 LYS cc_start: 0.7169 (tppt) cc_final: 0.6634 (mmtt) REVERT: D 339 ARG cc_start: 0.6779 (mmp80) cc_final: 0.6556 (tmm160) REVERT: D 660 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: D 695 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8225 (tmmm) REVERT: D 817 HIS cc_start: 0.7681 (m-70) cc_final: 0.7463 (m-70) REVERT: D 821 MET cc_start: 0.8140 (tpp) cc_final: 0.7693 (tpt) REVERT: D 827 GLU cc_start: 0.7660 (tp30) cc_final: 0.7436 (tp30) REVERT: D 1040 MET cc_start: 0.3788 (mmm) cc_final: 0.2532 (mmm) REVERT: D 1263 LYS cc_start: 0.7500 (mmmt) cc_final: 0.6840 (tmtt) REVERT: D 1266 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8440 (pt) REVERT: M 27 GLN cc_start: 0.9059 (pt0) cc_final: 0.8822 (tp40) REVERT: M 185 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: M 194 ASP cc_start: 0.9146 (m-30) cc_final: 0.8723 (t0) REVERT: M 256 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7956 (mt) REVERT: M 374 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.7843 (m) REVERT: M 376 MET cc_start: 0.8804 (mmm) cc_final: 0.8391 (mmm) outliers start: 122 outliers final: 94 residues processed: 420 average time/residue: 0.4131 time to fit residues: 273.1308 Evaluate side-chains 421 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 315 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 950 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 409 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 313 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 301 optimal weight: 50.0000 chunk 316 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 283 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 808 ASN C1017 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN D1238 GLN M 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 29571 Z= 0.572 Angle : 0.809 12.668 40436 Z= 0.412 Chirality : 0.050 0.251 4767 Planarity : 0.006 0.081 5059 Dihedral : 14.445 165.062 4781 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.47 % Favored : 90.40 % Rotamer: Outliers : 4.82 % Allowed : 20.76 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3655 helix: 0.32 (0.14), residues: 1310 sheet: -0.94 (0.31), residues: 300 loop : -2.28 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP M 285 HIS 0.009 0.002 HIS C1244 PHE 0.026 0.003 PHE C 828 TYR 0.023 0.002 TYR C 92 ARG 0.013 0.001 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 324 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.7333 (ptp90) REVERT: B 125 LYS cc_start: 0.8235 (ptmm) cc_final: 0.7718 (ptmm) REVERT: B 176 CYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8207 (p) REVERT: C 188 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: C 369 MET cc_start: 0.8441 (ppp) cc_final: 0.8203 (ppp) REVERT: C 429 MET cc_start: 0.9249 (tpp) cc_final: 0.8875 (tpp) REVERT: C 451 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8405 (ptm160) REVERT: C 488 MET cc_start: 0.8966 (mmm) cc_final: 0.8620 (mmp) REVERT: C 545 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6665 (t80) REVERT: C 696 ASP cc_start: 0.8055 (t70) cc_final: 0.7617 (t0) REVERT: C 741 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6423 (ptp) REVERT: C 1232 MET cc_start: 0.8502 (mmm) cc_final: 0.8245 (mtt) REVERT: C 1253 LEU cc_start: 0.8936 (mm) cc_final: 0.8525 (mm) REVERT: D 94 GLN cc_start: 0.7848 (mt0) cc_final: 0.7625 (mp10) REVERT: D 196 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8835 (tm-30) REVERT: D 314 ARG cc_start: 0.7521 (ptt90) cc_final: 0.7294 (ptt90) REVERT: D 324 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8154 (pp) REVERT: D 334 LYS cc_start: 0.7114 (tppt) cc_final: 0.6438 (mmtt) REVERT: D 660 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: D 695 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8290 (tmmm) REVERT: D 817 HIS cc_start: 0.7814 (m-70) cc_final: 0.7582 (m-70) REVERT: D 827 GLU cc_start: 0.7895 (tp30) cc_final: 0.7632 (tp30) REVERT: D 1040 MET cc_start: 0.4060 (mmm) cc_final: 0.3146 (mmt) REVERT: D 1244 GLN cc_start: 0.8079 (tp40) cc_final: 0.7750 (mm-40) REVERT: D 1263 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7235 (tmtt) REVERT: D 1266 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8438 (pt) REVERT: M 27 GLN cc_start: 0.9085 (pt0) cc_final: 0.8843 (tp40) REVERT: M 115 GLU cc_start: 0.9085 (mp0) cc_final: 0.8756 (mp0) REVERT: M 185 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7281 (m-10) REVERT: M 194 ASP cc_start: 0.9133 (m-30) cc_final: 0.8718 (t0) REVERT: M 256 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8327 (mt) REVERT: M 374 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.7794 (m) REVERT: M 376 MET cc_start: 0.8825 (mmm) cc_final: 0.8417 (mmm) outliers start: 135 outliers final: 101 residues processed: 435 average time/residue: 0.4357 time to fit residues: 296.7823 Evaluate side-chains 415 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 301 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 950 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.3980 chunk 353 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 370 optimal weight: 20.0000 chunk 341 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 227 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN D1238 GLN M 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29571 Z= 0.166 Angle : 0.637 12.431 40436 Z= 0.317 Chirality : 0.042 0.214 4767 Planarity : 0.004 0.054 5059 Dihedral : 14.152 164.550 4781 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.61 % Favored : 92.37 % Rotamer: Outliers : 3.07 % Allowed : 22.69 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3655 helix: 0.75 (0.15), residues: 1315 sheet: -0.82 (0.31), residues: 298 loop : -2.09 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 285 HIS 0.032 0.001 HIS M 406 PHE 0.012 0.001 PHE D 17 TYR 0.021 0.001 TYR D 626 ARG 0.009 0.001 ARG D1148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 338 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7128 (ptp90) REVERT: A 283 GLN cc_start: 0.8379 (mt0) cc_final: 0.8139 (mt0) REVERT: B 125 LYS cc_start: 0.8241 (ptmm) cc_final: 0.7730 (ptmm) REVERT: C 39 ILE cc_start: 0.8313 (tp) cc_final: 0.7908 (tp) REVERT: C 188 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: C 369 MET cc_start: 0.8464 (ppp) cc_final: 0.8218 (ppp) REVERT: C 488 MET cc_start: 0.8964 (mmm) cc_final: 0.8639 (mmp) REVERT: C 545 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6718 (t80) REVERT: C 696 ASP cc_start: 0.8093 (t70) cc_final: 0.7800 (t0) REVERT: C 766 ASN cc_start: 0.8478 (t0) cc_final: 0.8259 (t0) REVERT: C 1084 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (m-30) REVERT: C 1170 MET cc_start: 0.8657 (mmm) cc_final: 0.8446 (tpp) REVERT: D 196 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8870 (tm-30) REVERT: D 324 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8065 (pp) REVERT: D 339 ARG cc_start: 0.6565 (tmm160) cc_final: 0.5584 (mmp80) REVERT: D 416 ILE cc_start: 0.8986 (tt) cc_final: 0.8758 (tt) REVERT: D 660 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: D 695 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8173 (tmmm) REVERT: D 817 HIS cc_start: 0.7614 (m-70) cc_final: 0.7355 (m-70) REVERT: D 827 GLU cc_start: 0.7545 (tp30) cc_final: 0.7218 (tp30) REVERT: D 1040 MET cc_start: 0.3964 (mmm) cc_final: 0.2977 (mmt) REVERT: D 1244 GLN cc_start: 0.7841 (tp40) cc_final: 0.7534 (mm-40) REVERT: D 1263 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7000 (tmtt) REVERT: D 1266 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8392 (pt) REVERT: M 27 GLN cc_start: 0.9057 (pt0) cc_final: 0.8832 (tp40) REVERT: M 185 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6346 (m-10) REVERT: M 194 ASP cc_start: 0.9157 (m-30) cc_final: 0.8723 (t0) REVERT: M 271 TYR cc_start: 0.6382 (m-10) cc_final: 0.6060 (m-10) REVERT: M 374 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.7852 (m) REVERT: M 376 MET cc_start: 0.8805 (mmm) cc_final: 0.8401 (mmm) REVERT: M 446 LEU cc_start: 0.8370 (tp) cc_final: 0.8146 (tp) outliers start: 86 outliers final: 65 residues processed: 406 average time/residue: 0.4155 time to fit residues: 266.5193 Evaluate side-chains 397 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 322 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 944 ARG Chi-restraints excluded: chain C residue 950 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 311 ARG Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.6980 chunk 314 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 43 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 303 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN D 702 GLN D1238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.163899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104127 restraints weight = 47936.601| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.91 r_work: 0.3142 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29571 Z= 0.304 Angle : 0.672 11.693 40436 Z= 0.336 Chirality : 0.044 0.222 4767 Planarity : 0.005 0.053 5059 Dihedral : 14.159 164.029 4779 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.34 % Favored : 91.60 % Rotamer: Outliers : 3.25 % Allowed : 22.58 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3655 helix: 0.72 (0.15), residues: 1311 sheet: -0.81 (0.31), residues: 301 loop : -2.12 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 285 HIS 0.023 0.001 HIS M 406 PHE 0.017 0.002 PHE A 8 TYR 0.023 0.002 TYR D 626 ARG 0.009 0.001 ARG C1269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7622.85 seconds wall clock time: 136 minutes 55.81 seconds (8215.81 seconds total)