Starting phenix.real_space_refine on Wed Feb 21 16:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xll_22247/02_2024/6xll_22247_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xll_22247/02_2024/6xll_22247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xll_22247/02_2024/6xll_22247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xll_22247/02_2024/6xll_22247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xll_22247/02_2024/6xll_22247_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xll_22247/02_2024/6xll_22247_updated.pdb" } resolution = 2.7 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= 0.003 sd= 0.157 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 129 5.16 5 C 19191 2.51 5 N 5516 2.21 5 O 6192 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 91": "NH1" <-> "NH2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C GLU 859": "OE1" <-> "OE2" Residue "C ASP 881": "OD1" <-> "OD2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C GLU 1192": "OE1" <-> "OE2" Residue "C ASP 1310": "OD1" <-> "OD2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D GLU 660": "OE1" <-> "OE2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D ASP 812": "OD1" <-> "OD2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D ASP 870": "OD1" <-> "OD2" Residue "D ASP 1007": "OD1" <-> "OD2" Residue "D GLU 1030": "OE1" <-> "OE2" Residue "D ASP 1051": "OD1" <-> "OD2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D ASP 1087": "OD1" <-> "OD2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "D ASP 1119": "OD1" <-> "OD2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D ASP 1212": "OD1" <-> "OD2" Residue "D ASP 1250": "OD1" <-> "OD2" Residue "D ASP 1273": "OD1" <-> "OD2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ASP 149": "OD1" <-> "OD2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F ASP 332": "OD1" <-> "OD2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F ASP 360": "OD1" <-> "OD2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "F ARG 436": "NH1" <-> "NH2" Residue "F ARG 441": "NH1" <-> "NH2" Residue "F GLU 485": "OE1" <-> "OE2" Residue "F ASP 492": "OD1" <-> "OD2" Residue "F ASP 513": "OD1" <-> "OD2" Residue "F ASP 516": "OD1" <-> "OD2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 524": "OE1" <-> "OE2" Residue "F ASP 525": "OD1" <-> "OD2" Residue "F ASP 546": "OD1" <-> "OD2" Residue "F GLU 585": "OE1" <-> "OE2" Residue "F GLU 591": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31134 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1711 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10387 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3878 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 461} Chain breaks: 2 Chain: "N" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "T" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 979 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "R" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP R 1 " pdbres=" C R 2 " Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14513 SG CYS D 70 47.871 44.912 102.226 1.00 99.55 S ATOM 14527 SG CYS D 72 49.530 43.233 104.731 1.00103.46 S ATOM 14635 SG CYS D 85 46.279 44.246 105.601 1.00103.36 S ATOM 14659 SG CYS D 88 49.742 46.469 105.764 1.00101.49 S ATOM 20347 SG CYS D 814 34.065 108.338 86.644 1.00 84.51 S ATOM 20912 SG CYS D 888 37.011 106.549 86.954 1.00 81.65 S ATOM 20963 SG CYS D 895 35.589 106.670 84.135 1.00 76.46 S ATOM 20984 SG CYS D 898 37.204 109.440 84.941 1.00 78.50 S Time building chain proxies: 16.83, per 1000 atoms: 0.54 Number of scatterers: 31134 At special positions: 0 Unit cell: (150.629, 173.29, 182.621, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 129 16.00 P 103 15.00 Mg 1 11.99 O 6192 8.00 N 5516 7.00 C 19191 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.99 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 12 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 40 sheets defined 36.6% alpha, 12.2% beta 43 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 16.65 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.672A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 213 through 233 removed outlier: 3.976A pdb=" N GLU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 213 through 230 removed outlier: 5.174A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.673A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 292 removed outlier: 3.751A pdb=" N ILE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 319 through 328 removed outlier: 3.856A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.862A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 456 through 478 removed outlier: 3.734A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 4.262A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 861 through 863 No H-bonds generated for 'chain 'C' and resid 861 through 863' Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 981 Processing helix chain 'C' and resid 986 through 989 No H-bonds generated for 'chain 'C' and resid 986 through 989' Processing helix chain 'C' and resid 994 through 996 No H-bonds generated for 'chain 'C' and resid 994 through 996' Processing helix chain 'C' and resid 1007 through 1036 removed outlier: 3.565A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C1031 " --> pdb=" O LYS C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1104 Proline residue: C1104 - end of helix Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 4.421A pdb=" N GLU C1114 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C1117 " --> pdb=" O GLU C1114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C1119 " --> pdb=" O HIS C1116 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C1121 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS C1122 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C1126 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN C1129 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1166 through 1175 Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1298 through 1309 removed outlier: 3.851A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1330 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.867A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 376 removed outlier: 4.046A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 415 removed outlier: 3.811A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 4.364A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 504 through 513 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.851A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 614 through 633 removed outlier: 3.743A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 669 Processing helix chain 'D' and resid 675 through 702 removed outlier: 3.865A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 734 through 741 removed outlier: 4.053A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 804 removed outlier: 4.082A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 839 No H-bonds generated for 'chain 'D' and resid 836 through 839' Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 885 through 887 No H-bonds generated for 'chain 'D' and resid 885 through 887' Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 924 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1138 through 1145 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1243 removed outlier: 3.801A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.623A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.749A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1313 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1348 through 1352 Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 3.507A pdb=" N TYR D1363 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR D1365 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D1372 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.669A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'F' and resid 97 through 106 Processing helix chain 'F' and resid 113 through 135 removed outlier: 3.709A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 152 Processing helix chain 'F' and resid 215 through 232 removed outlier: 3.937A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 Processing helix chain 'F' and resid 263 through 291 removed outlier: 4.297A pdb=" N CYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 325 through 333 removed outlier: 4.245A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 350 removed outlier: 3.782A pdb=" N GLN F 342 " --> pdb=" O HIS F 338 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN F 345 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 394 removed outlier: 3.520A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 427 through 446 removed outlier: 3.920A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 Processing helix chain 'F' and resid 480 through 486 removed outlier: 4.572A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 511 through 513 No H-bonds generated for 'chain 'F' and resid 511 through 513' Processing helix chain 'F' and resid 531 through 549 Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 584 through 598 Processing helix chain 'F' and resid 605 through 610 removed outlier: 4.009A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F 610 " --> pdb=" O VAL F 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 605 through 610' Processing sheet with id= A, first strand: chain 'A' and resid 12 through 17 removed outlier: 6.625A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.660A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.457A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= G, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.548A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.908A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= J, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 160 removed outlier: 4.811A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 227 through 231 Processing sheet with id= N, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= O, first strand: chain 'C' and resid 529 through 531 Processing sheet with id= P, first strand: chain 'C' and resid 603 through 607 Processing sheet with id= Q, first strand: chain 'C' and resid 633 through 637 Processing sheet with id= R, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.016A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1226 through 1232 removed outlier: 4.288A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.901A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.036A pdb=" N ASP C 303 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU C 309 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 815 through 819 removed outlier: 6.383A pdb=" N VAL C1075 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL C 818 " --> pdb=" O VAL C1075 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N SER C1077 " --> pdb=" O VAL C 818 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.673A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= Z, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= AA, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= AB, first strand: chain 'D' and resid 547 through 557 Processing sheet with id= AC, first strand: chain 'D' and resid 706 through 709 Processing sheet with id= AD, first strand: chain 'D' and resid 820 through 823 Processing sheet with id= AE, first strand: chain 'D' and resid 957 through 961 Processing sheet with id= AF, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AG, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id= AH, first strand: chain 'D' and resid 1046 through 1049 Processing sheet with id= AI, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AJ, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.590A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.773A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 825 through 827 removed outlier: 3.576A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.911A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 3.680A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 14.43 Time building geometry restraints manager: 13.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9034 1.33 - 1.45: 5308 1.45 - 1.57: 17040 1.57 - 1.69: 202 1.69 - 1.81: 227 Bond restraints: 31811 Sorted by residual: bond pdb=" C ILE C1079 " pdb=" N ASN C1080 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.07e-02 2.33e+03 5.84e+00 bond pdb=" CG1 ILE C1076 " pdb=" CD1 ILE C1076 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 5.00e+00 bond pdb=" CB VAL C1186 " pdb=" CG1 VAL C1186 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.11e+00 bond pdb=" CB ILE C 530 " pdb=" CG2 ILE C 530 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.04e+00 bond pdb=" CA TYR D 75 " pdb=" C TYR D 75 " ideal model delta sigma weight residual 1.521 1.544 -0.023 1.17e-02 7.31e+03 3.87e+00 ... (remaining 31806 not shown) Histogram of bond angle deviations from ideal: 95.89 - 103.54: 618 103.54 - 111.19: 13027 111.19 - 118.84: 13045 118.84 - 126.49: 16143 126.49 - 134.15: 568 Bond angle restraints: 43401 Sorted by residual: angle pdb=" N VAL C 615 " pdb=" CA VAL C 615 " pdb=" C VAL C 615 " ideal model delta sigma weight residual 108.17 99.78 8.39 1.40e+00 5.10e-01 3.59e+01 angle pdb=" N GLN D 504 " pdb=" CA GLN D 504 " pdb=" C GLN D 504 " ideal model delta sigma weight residual 111.37 117.84 -6.47 1.64e+00 3.72e-01 1.56e+01 angle pdb=" N ARG C 540 " pdb=" CA ARG C 540 " pdb=" C ARG C 540 " ideal model delta sigma weight residual 112.34 117.42 -5.08 1.30e+00 5.92e-01 1.53e+01 angle pdb=" C GLU F 219 " pdb=" N LYS F 220 " pdb=" CA LYS F 220 " ideal model delta sigma weight residual 121.66 115.01 6.65 1.76e+00 3.23e-01 1.43e+01 angle pdb=" C PRO C 855 " pdb=" N ASN C 856 " pdb=" CA ASN C 856 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 ... (remaining 43396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 18081 27.72 - 55.45: 1195 55.45 - 83.17: 129 83.17 - 110.89: 11 110.89 - 138.61: 6 Dihedral angle restraints: 19422 sinusoidal: 8818 harmonic: 10604 Sorted by residual: dihedral pdb=" CA PHE C1265 " pdb=" C PHE C1265 " pdb=" N GLY C1266 " pdb=" CA GLY C1266 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual 180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" O3A GTP R 1 " pdb=" O3B GTP R 1 " pdb=" PB GTP R 1 " pdb=" PG GTP R 1 " ideal model delta sinusoidal sigma weight residual -56.21 -164.38 108.18 1 2.00e+01 2.50e-03 3.15e+01 ... (remaining 19419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4112 0.070 - 0.141: 791 0.141 - 0.211: 50 0.211 - 0.282: 3 0.282 - 0.352: 2 Chirality restraints: 4958 Sorted by residual: chirality pdb=" CA VAL C 615 " pdb=" N VAL C 615 " pdb=" C VAL C 615 " pdb=" CB VAL C 615 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ARG C 540 " pdb=" N ARG C 540 " pdb=" C ARG C 540 " pdb=" CB ARG C 540 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ASN C 258 " pdb=" N ASN C 258 " pdb=" C ASN C 258 " pdb=" CB ASN C 258 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4955 not shown) Planarity restraints: 5300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 212 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO B 213 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 75 " 0.027 2.00e-02 2.50e+03 1.58e-02 4.98e+00 pdb=" CG TYR D 75 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 75 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 75 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 75 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 75 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR D 75 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 75 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C1257 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C1258 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C1258 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1258 " -0.030 5.00e-02 4.00e+02 ... (remaining 5297 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 132 2.45 - 3.06: 19539 3.06 - 3.68: 48038 3.68 - 4.29: 73889 4.29 - 4.90: 121617 Nonbonded interactions: 263215 Sorted by model distance: nonbonded pdb=" O3' U R 5 " pdb="MG MG D1501 " model vdw 1.839 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.019 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.068 2.170 nonbonded pdb=" O LEU D 510 " pdb=" OG1 THR D 514 " model vdw 2.212 2.440 ... (remaining 263210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 159 or resid 169 through 234)) selection = (chain 'B' and resid 5 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 5.360 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 99.870 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.009 0.089 31811 Z= 0.581 Angle : 0.816 10.030 43401 Z= 0.457 Chirality : 0.053 0.352 4958 Planarity : 0.006 0.061 5300 Dihedral : 17.254 138.613 12586 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -3.11 (0.11), residues: 3661 helix: -2.16 (0.11), residues: 1446 sheet: -1.91 (0.24), residues: 373 loop : -1.95 (0.12), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 33 HIS 0.009 0.002 HIS D 777 PHE 0.017 0.002 PHE D 338 TYR 0.027 0.003 TYR D 75 ARG 0.006 0.001 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 402 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7870 (ttmm) REVERT: A 103 ASN cc_start: 0.8703 (m-40) cc_final: 0.8413 (m-40) REVERT: A 125 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8028 (tttt) REVERT: A 181 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7391 (mt-10) REVERT: A 205 MET cc_start: 0.8677 (ttt) cc_final: 0.8244 (ttp) REVERT: B 7 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7476 (pp20) REVERT: B 10 LYS cc_start: 0.9121 (mttp) cc_final: 0.8838 (mttp) REVERT: B 145 LYS cc_start: 0.8326 (tttt) cc_final: 0.7955 (ttmm) REVERT: B 152 TYR cc_start: 0.8791 (t80) cc_final: 0.8541 (t80) REVERT: B 156 SER cc_start: 0.8696 (m) cc_final: 0.8362 (p) REVERT: B 170 ARG cc_start: 0.6846 (mtm-85) cc_final: 0.6072 (mpp-170) REVERT: C 46 GLN cc_start: 0.8537 (mt0) cc_final: 0.8304 (mt0) REVERT: C 74 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7561 (ttp-110) REVERT: C 119 GLU cc_start: 0.8490 (pp20) cc_final: 0.8013 (pp20) REVERT: C 200 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7850 (mmm-85) REVERT: C 229 ILE cc_start: 0.8104 (mt) cc_final: 0.7849 (mp) REVERT: C 299 LYS cc_start: 0.7466 (tttp) cc_final: 0.7141 (mtpt) REVERT: C 314 ASN cc_start: 0.8681 (t0) cc_final: 0.8339 (t0) REVERT: C 343 HIS cc_start: 0.6896 (m90) cc_final: 0.6440 (m90) REVERT: C 377 THR cc_start: 0.8038 (p) cc_final: 0.7794 (t) REVERT: C 407 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7081 (ttp-170) REVERT: C 470 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.7144 (mtm-85) REVERT: C 479 LEU cc_start: 0.7700 (mt) cc_final: 0.7353 (mt) REVERT: C 492 MET cc_start: 0.8366 (mtp) cc_final: 0.7942 (mtp) REVERT: C 503 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7819 (mtpm) REVERT: C 515 MET cc_start: 0.8593 (ttp) cc_final: 0.8081 (ttm) REVERT: C 704 MET cc_start: 0.8315 (mmm) cc_final: 0.8115 (mtp) REVERT: C 719 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7513 (mmtt) REVERT: C 805 MET cc_start: 0.8814 (ptm) cc_final: 0.8260 (ptm) REVERT: C 954 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7971 (mttp) REVERT: C 958 LYS cc_start: 0.7326 (tttt) cc_final: 0.7002 (tttp) REVERT: C 1131 MET cc_start: 0.8288 (mtt) cc_final: 0.7903 (mtt) REVERT: C 1180 MET cc_start: 0.8695 (ttp) cc_final: 0.8466 (ttp) REVERT: C 1315 MET cc_start: 0.8610 (ptm) cc_final: 0.8132 (ptp) REVERT: D 130 MET cc_start: 0.8563 (ttt) cc_final: 0.8356 (ttt) REVERT: D 147 ILE cc_start: 0.8155 (pt) cc_final: 0.7851 (mt) REVERT: D 200 GLN cc_start: 0.7439 (tt0) cc_final: 0.7041 (tm-30) REVERT: D 213 LYS cc_start: 0.8150 (tttt) cc_final: 0.7918 (tttt) REVERT: D 221 ILE cc_start: 0.8143 (mt) cc_final: 0.7930 (mt) REVERT: D 322 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7882 (mtp-110) REVERT: D 372 MET cc_start: 0.8779 (mtp) cc_final: 0.8117 (mtm) REVERT: D 375 GLU cc_start: 0.8275 (tp30) cc_final: 0.7968 (mm-30) REVERT: D 386 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6998 (mt-10) REVERT: D 525 MET cc_start: 0.8893 (ptp) cc_final: 0.8182 (ptm) REVERT: D 649 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7306 (mmtt) REVERT: D 712 GLN cc_start: 0.7320 (mt0) cc_final: 0.6912 (mm-40) REVERT: D 715 LYS cc_start: 0.8907 (ptmt) cc_final: 0.8665 (mtpt) REVERT: D 724 MET cc_start: 0.8137 (mtm) cc_final: 0.7703 (mtm) REVERT: D 743 MET cc_start: 0.8599 (ptp) cc_final: 0.8105 (ptp) REVERT: D 774 ILE cc_start: 0.8328 (mt) cc_final: 0.8106 (mp) REVERT: D 1095 MET cc_start: 0.5740 (ptp) cc_final: 0.5461 (ptt) REVERT: D 1149 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6814 (mtp-110) REVERT: D 1172 LYS cc_start: 0.7121 (mttm) cc_final: 0.6830 (ptpp) REVERT: D 1174 ARG cc_start: 0.7196 (ttm170) cc_final: 0.6446 (tmt90) REVERT: D 1188 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6828 (mm-30) REVERT: D 1189 MET cc_start: 0.8028 (mmm) cc_final: 0.7789 (mmp) REVERT: D 1193 TRP cc_start: 0.7614 (p-90) cc_final: 0.7271 (p90) REVERT: D 1205 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7684 (mp0) REVERT: D 1260 MET cc_start: 0.8948 (mtp) cc_final: 0.8736 (mtm) REVERT: D 1276 GLU cc_start: 0.7910 (mp0) cc_final: 0.7561 (mp0) REVERT: D 1372 ARG cc_start: 0.7291 (mmt180) cc_final: 0.5844 (tmm-80) REVERT: E 67 ARG cc_start: 0.7260 (tpt170) cc_final: 0.6814 (mtp-110) REVERT: E 70 GLN cc_start: 0.7158 (tt0) cc_final: 0.6744 (tm-30) REVERT: F 322 MET cc_start: 0.3810 (tpt) cc_final: 0.2712 (ppp) REVERT: F 456 MET cc_start: 0.7780 (tpp) cc_final: 0.7013 (tpt) REVERT: F 567 MET cc_start: 0.8175 (mtt) cc_final: 0.7847 (mtm) REVERT: F 581 ASP cc_start: 0.6961 (m-30) cc_final: 0.6363 (p0) outliers start: 2 outliers final: 3 residues processed: 404 average time/residue: 1.8861 time to fit residues: 869.0171 Evaluate side-chains 288 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 0.9990 chunk 283 optimal weight: 20.0000 chunk 157 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 293 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 218 optimal weight: 0.9990 chunk 339 optimal weight: 40.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 66 HIS B 103 ASN C 31 GLN C 46 GLN C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 276 GLN C 518 ASN C 582 ASN C 620 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS C1257 GLN C1268 GLN D 94 GLN D 274 ASN D 294 ASN D 364 HIS D 424 ASN D 489 ASN D 777 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 910 ASN D1084 GLN D1366 HIS E 62 GLN F 227 GLN F 258 GLN F 317 ASN F 331 HIS F 357 GLN F 383 ASN F 406 GLN F 446 GLN F 472 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31811 Z= 0.193 Angle : 0.534 9.122 43401 Z= 0.286 Chirality : 0.041 0.156 4958 Planarity : 0.004 0.051 5300 Dihedral : 15.871 139.074 5300 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 12.65 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -1.75 (0.13), residues: 3661 helix: -0.63 (0.13), residues: 1449 sheet: -1.62 (0.25), residues: 374 loop : -1.44 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1193 HIS 0.011 0.001 HIS A 117 PHE 0.014 0.001 PHE C 337 TYR 0.024 0.001 TYR F 137 ARG 0.011 0.000 ARG D1173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 327 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7821 (ttmm) REVERT: A 103 ASN cc_start: 0.8569 (m-40) cc_final: 0.8318 (m-40) REVERT: A 125 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7991 (tttt) REVERT: A 145 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8338 (ttpp) REVERT: A 181 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7288 (mt-10) REVERT: B 10 LYS cc_start: 0.9058 (mttp) cc_final: 0.8798 (mttm) REVERT: B 51 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8453 (mmm) REVERT: B 145 LYS cc_start: 0.8314 (tttt) cc_final: 0.7972 (ttmm) REVERT: B 152 TYR cc_start: 0.8814 (t80) cc_final: 0.8533 (t80) REVERT: B 156 SER cc_start: 0.8655 (m) cc_final: 0.8308 (p) REVERT: B 170 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.5958 (mpp-170) REVERT: C 74 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7399 (ttp-110) REVERT: C 119 GLU cc_start: 0.8522 (pp20) cc_final: 0.8131 (pp20) REVERT: C 200 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7775 (mmm-85) REVERT: C 299 LYS cc_start: 0.7439 (tttp) cc_final: 0.7208 (mtpt) REVERT: C 314 ASN cc_start: 0.8470 (t0) cc_final: 0.8063 (t0) REVERT: C 343 HIS cc_start: 0.6611 (m90) cc_final: 0.6236 (m90) REVERT: C 377 THR cc_start: 0.7998 (p) cc_final: 0.7749 (t) REVERT: C 470 ARG cc_start: 0.7438 (mtt-85) cc_final: 0.7063 (mtm-85) REVERT: C 479 LEU cc_start: 0.7328 (mt) cc_final: 0.6998 (mt) REVERT: C 492 MET cc_start: 0.8445 (mtp) cc_final: 0.8029 (mtp) REVERT: C 503 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7818 (mtpm) REVERT: C 515 MET cc_start: 0.8426 (ttp) cc_final: 0.8013 (ttm) REVERT: C 641 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7444 (pp20) REVERT: C 719 LYS cc_start: 0.8449 (mtmm) cc_final: 0.7522 (mmtt) REVERT: C 954 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7920 (mttp) REVERT: C 958 LYS cc_start: 0.7232 (tttt) cc_final: 0.6894 (tttp) REVERT: C 1085 MET cc_start: 0.8851 (mmp) cc_final: 0.8465 (mmp) REVERT: C 1088 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8032 (p0) REVERT: C 1131 MET cc_start: 0.8292 (mtt) cc_final: 0.7854 (mtt) REVERT: C 1315 MET cc_start: 0.8536 (ptm) cc_final: 0.8108 (ptp) REVERT: D 200 GLN cc_start: 0.7448 (tt0) cc_final: 0.7114 (tm-30) REVERT: D 217 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8252 (mp) REVERT: D 322 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8058 (mtp-110) REVERT: D 372 MET cc_start: 0.8745 (mtp) cc_final: 0.8185 (mtm) REVERT: D 375 GLU cc_start: 0.8031 (tp30) cc_final: 0.7746 (mm-30) REVERT: D 386 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6894 (mt-10) REVERT: D 393 THR cc_start: 0.8327 (m) cc_final: 0.7959 (p) REVERT: D 413 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: D 443 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7239 (mt-10) REVERT: D 525 MET cc_start: 0.8641 (ptp) cc_final: 0.8063 (ptm) REVERT: D 649 LYS cc_start: 0.7443 (mmmt) cc_final: 0.7212 (mmtt) REVERT: D 704 GLU cc_start: 0.4873 (OUTLIER) cc_final: 0.4501 (tm-30) REVERT: D 712 GLN cc_start: 0.7133 (mt0) cc_final: 0.6717 (mm-40) REVERT: D 715 LYS cc_start: 0.8881 (ptmt) cc_final: 0.8657 (mtpp) REVERT: D 724 MET cc_start: 0.7947 (mtm) cc_final: 0.7516 (mtm) REVERT: D 743 MET cc_start: 0.8428 (ptp) cc_final: 0.7893 (ptp) REVERT: D 1149 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6710 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7274 (ttm170) cc_final: 0.6510 (tmt90) REVERT: D 1205 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7683 (mp0) REVERT: D 1276 GLU cc_start: 0.7882 (mp0) cc_final: 0.7571 (mp0) REVERT: D 1370 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6591 (ptp) REVERT: E 21 LEU cc_start: 0.8089 (mt) cc_final: 0.7888 (mm) REVERT: E 67 ARG cc_start: 0.7199 (tpt170) cc_final: 0.6743 (mtp-110) REVERT: E 70 GLN cc_start: 0.7323 (tt0) cc_final: 0.6806 (tm-30) REVERT: F 567 MET cc_start: 0.8530 (mtt) cc_final: 0.8209 (mtm) outliers start: 44 outliers final: 12 residues processed: 353 average time/residue: 1.7379 time to fit residues: 706.2073 Evaluate side-chains 300 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 281 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 30.0000 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 340 optimal weight: 20.0000 chunk 367 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN C 20 GLN C 41 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN C 649 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 31811 Z= 0.590 Angle : 0.685 9.594 43401 Z= 0.357 Chirality : 0.048 0.229 4958 Planarity : 0.005 0.049 5300 Dihedral : 15.921 139.221 5298 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.36 % Allowed : 14.37 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -1.67 (0.13), residues: 3661 helix: -0.51 (0.13), residues: 1455 sheet: -1.66 (0.25), residues: 384 loop : -1.42 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 686 HIS 0.009 0.002 HIS C 447 PHE 0.017 0.002 PHE D 437 TYR 0.021 0.002 TYR C1281 ARG 0.009 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 283 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6435 (ttm110) REVERT: A 86 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7875 (ttmm) REVERT: A 103 ASN cc_start: 0.8613 (m-40) cc_final: 0.8367 (m-40) REVERT: A 125 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8007 (tttt) REVERT: A 145 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8197 (ttpp) REVERT: A 181 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7281 (mt-10) REVERT: B 7 GLU cc_start: 0.7086 (pp20) cc_final: 0.6797 (pm20) REVERT: B 10 LYS cc_start: 0.8988 (mttp) cc_final: 0.8698 (mttm) REVERT: B 51 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8615 (mmm) REVERT: B 78 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 145 LYS cc_start: 0.8306 (tttt) cc_final: 0.7910 (ttmm) REVERT: B 170 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6100 (mpp-170) REVERT: C 46 GLN cc_start: 0.8247 (mt0) cc_final: 0.7967 (tt0) REVERT: C 74 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7515 (ttp-110) REVERT: C 119 GLU cc_start: 0.8478 (pp20) cc_final: 0.8005 (pp20) REVERT: C 200 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7720 (mmm-85) REVERT: C 299 LYS cc_start: 0.7484 (tttp) cc_final: 0.7183 (mtpt) REVERT: C 314 ASN cc_start: 0.8509 (t0) cc_final: 0.8178 (t0) REVERT: C 343 HIS cc_start: 0.6620 (m90) cc_final: 0.6157 (m90) REVERT: C 377 THR cc_start: 0.7989 (p) cc_final: 0.7734 (t) REVERT: C 470 ARG cc_start: 0.7474 (mtt-85) cc_final: 0.7074 (mtm-85) REVERT: C 479 LEU cc_start: 0.7527 (mt) cc_final: 0.7203 (mt) REVERT: C 492 MET cc_start: 0.8441 (mtp) cc_final: 0.8023 (mtp) REVERT: C 503 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7861 (mtpm) REVERT: C 515 MET cc_start: 0.8635 (ttp) cc_final: 0.8178 (ttm) REVERT: C 529 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7290 (tpm170) REVERT: C 641 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: C 719 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7589 (mmtt) REVERT: C 779 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7931 (ttm110) REVERT: C 954 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7943 (mttp) REVERT: C 958 LYS cc_start: 0.7268 (tttt) cc_final: 0.6940 (tttp) REVERT: C 1088 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7966 (p0) REVERT: D 60 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8050 (ttp-170) REVERT: D 77 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7282 (mtm-85) REVERT: D 151 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7723 (mmm) REVERT: D 200 GLN cc_start: 0.7376 (tt0) cc_final: 0.7052 (tm-30) REVERT: D 217 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8260 (mp) REVERT: D 322 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8080 (ttp80) REVERT: D 372 MET cc_start: 0.8711 (mtp) cc_final: 0.8407 (ttp) REVERT: D 375 GLU cc_start: 0.8125 (tp30) cc_final: 0.7825 (mm-30) REVERT: D 413 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: D 525 MET cc_start: 0.8913 (ptp) cc_final: 0.8711 (ptp) REVERT: D 649 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7286 (mmtt) REVERT: D 704 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4407 (tm-30) REVERT: D 712 GLN cc_start: 0.7287 (mt0) cc_final: 0.6811 (mm-40) REVERT: D 715 LYS cc_start: 0.8909 (ptmt) cc_final: 0.8666 (mtpp) REVERT: D 724 MET cc_start: 0.7922 (mtm) cc_final: 0.7507 (mtm) REVERT: D 805 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.6842 (pp30) REVERT: D 1149 ARG cc_start: 0.7227 (ttm-80) cc_final: 0.6699 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7163 (ttm170) cc_final: 0.6339 (tmt90) REVERT: D 1188 GLU cc_start: 0.7551 (tm-30) cc_final: 0.6866 (tm-30) REVERT: D 1205 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7730 (mp0) REVERT: D 1220 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7782 (mm) REVERT: D 1276 GLU cc_start: 0.7784 (mp0) cc_final: 0.7469 (mp0) REVERT: E 35 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7092 (mtmm) REVERT: E 67 ARG cc_start: 0.7322 (tpt170) cc_final: 0.6876 (mtp-110) REVERT: E 70 GLN cc_start: 0.7197 (tt0) cc_final: 0.6772 (tm-30) REVERT: F 333 VAL cc_start: 0.2090 (OUTLIER) cc_final: 0.1834 (m) REVERT: F 567 MET cc_start: 0.8483 (mtt) cc_final: 0.8193 (mtm) outliers start: 106 outliers final: 42 residues processed: 355 average time/residue: 1.6909 time to fit residues: 693.9219 Evaluate side-chains 333 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 276 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 527 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 0.0980 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 228 optimal weight: 0.8980 chunk 341 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 323 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN C 20 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN D 777 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31811 Z= 0.168 Angle : 0.506 9.305 43401 Z= 0.269 Chirality : 0.041 0.160 4958 Planarity : 0.004 0.052 5300 Dihedral : 15.547 139.163 5298 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.51 % Allowed : 16.21 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3661 helix: 0.24 (0.14), residues: 1442 sheet: -1.38 (0.25), residues: 378 loop : -1.10 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 326 HIS 0.005 0.001 HIS D 865 PHE 0.015 0.001 PHE C 906 TYR 0.018 0.001 TYR F 137 ARG 0.010 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 309 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7805 (ttmm) REVERT: A 103 ASN cc_start: 0.8500 (m-40) cc_final: 0.8280 (m-40) REVERT: A 125 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7972 (tttt) REVERT: A 145 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8195 (ttpp) REVERT: A 181 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7265 (mt-10) REVERT: B 10 LYS cc_start: 0.8978 (mttp) cc_final: 0.8730 (mttp) REVERT: B 51 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: B 78 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7771 (mp) REVERT: B 145 LYS cc_start: 0.8315 (tttt) cc_final: 0.8053 (ttmm) REVERT: B 152 TYR cc_start: 0.8761 (t80) cc_final: 0.8531 (t80) REVERT: B 170 ARG cc_start: 0.6970 (mtm-85) cc_final: 0.5985 (mpp-170) REVERT: C 74 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7385 (ttp-110) REVERT: C 119 GLU cc_start: 0.8518 (pp20) cc_final: 0.8129 (pp20) REVERT: C 200 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7866 (mmm-85) REVERT: C 299 LYS cc_start: 0.7498 (tttp) cc_final: 0.7273 (mtpt) REVERT: C 314 ASN cc_start: 0.8450 (t0) cc_final: 0.8074 (t0) REVERT: C 337 PHE cc_start: 0.8054 (t80) cc_final: 0.7820 (t80) REVERT: C 343 HIS cc_start: 0.6469 (m90) cc_final: 0.6125 (m-70) REVERT: C 369 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6880 (tmm) REVERT: C 377 THR cc_start: 0.7881 (p) cc_final: 0.7645 (t) REVERT: C 470 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.6990 (mtm-85) REVERT: C 479 LEU cc_start: 0.7160 (mt) cc_final: 0.6813 (mt) REVERT: C 492 MET cc_start: 0.8592 (mtp) cc_final: 0.8223 (mtp) REVERT: C 503 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7873 (mtpm) REVERT: C 515 MET cc_start: 0.8425 (ttp) cc_final: 0.8080 (ttm) REVERT: C 641 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7283 (pp20) REVERT: C 954 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7910 (mttp) REVERT: C 958 LYS cc_start: 0.7239 (tttt) cc_final: 0.6892 (tttp) REVERT: C 1088 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8007 (p0) REVERT: D 151 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7773 (mmm) REVERT: D 200 GLN cc_start: 0.7340 (tt0) cc_final: 0.6995 (tm-30) REVERT: D 217 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8210 (mp) REVERT: D 372 MET cc_start: 0.8678 (mtp) cc_final: 0.8410 (ttp) REVERT: D 375 GLU cc_start: 0.7934 (tp30) cc_final: 0.7627 (mm-30) REVERT: D 386 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6849 (mt-10) REVERT: D 393 THR cc_start: 0.8298 (m) cc_final: 0.8071 (p) REVERT: D 443 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7426 (mt-10) REVERT: D 525 MET cc_start: 0.8581 (ptp) cc_final: 0.8040 (ptm) REVERT: D 649 LYS cc_start: 0.7446 (mmmt) cc_final: 0.7219 (mmtt) REVERT: D 704 GLU cc_start: 0.4740 (OUTLIER) cc_final: 0.4462 (tm-30) REVERT: D 712 GLN cc_start: 0.7092 (mt0) cc_final: 0.6720 (mm-40) REVERT: D 724 MET cc_start: 0.7904 (mtm) cc_final: 0.7462 (mtm) REVERT: D 792 ASN cc_start: 0.7988 (m110) cc_final: 0.7767 (m110) REVERT: D 1149 ARG cc_start: 0.7184 (ttm-80) cc_final: 0.6697 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7081 (ttm170) cc_final: 0.6165 (tmt90) REVERT: D 1188 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7100 (mt-10) REVERT: D 1276 GLU cc_start: 0.7819 (mp0) cc_final: 0.7583 (mp0) REVERT: E 67 ARG cc_start: 0.7277 (tpt170) cc_final: 0.6874 (mtp-110) REVERT: E 70 GLN cc_start: 0.7140 (tt0) cc_final: 0.6623 (tm-30) REVERT: F 485 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: F 500 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6224 (mp) REVERT: F 571 TYR cc_start: 0.7579 (m-80) cc_final: 0.7317 (m-80) outliers start: 79 outliers final: 26 residues processed: 363 average time/residue: 1.5732 time to fit residues: 663.2131 Evaluate side-chains 313 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 277 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 269 optimal weight: 0.0970 chunk 149 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 324 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31811 Z= 0.340 Angle : 0.568 8.303 43401 Z= 0.297 Chirality : 0.043 0.157 4958 Planarity : 0.004 0.048 5300 Dihedral : 15.581 138.888 5295 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.39 % Allowed : 17.06 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3661 helix: 0.29 (0.14), residues: 1447 sheet: -1.28 (0.26), residues: 374 loop : -1.06 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 33 HIS 0.005 0.001 HIS C 447 PHE 0.013 0.001 PHE D 437 TYR 0.019 0.002 TYR C1281 ARG 0.011 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 288 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6257 (ttm110) REVERT: A 86 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7827 (ttmm) REVERT: A 103 ASN cc_start: 0.8573 (m-40) cc_final: 0.8346 (m-40) REVERT: A 125 LYS cc_start: 0.8356 (ttpt) cc_final: 0.7986 (tttt) REVERT: A 145 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8193 (ttpp) REVERT: A 181 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7299 (mt-10) REVERT: B 10 LYS cc_start: 0.8980 (mttp) cc_final: 0.8715 (mttm) REVERT: B 51 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8428 (mmm) REVERT: B 78 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 145 LYS cc_start: 0.8295 (tttt) cc_final: 0.8030 (ttmm) REVERT: B 152 TYR cc_start: 0.8853 (t80) cc_final: 0.8552 (t80) REVERT: B 170 ARG cc_start: 0.6973 (mtm-85) cc_final: 0.5981 (mpp-170) REVERT: C 74 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7376 (ptm-80) REVERT: C 119 GLU cc_start: 0.8527 (pp20) cc_final: 0.8140 (pp20) REVERT: C 200 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7914 (mmm-85) REVERT: C 299 LYS cc_start: 0.7510 (tttp) cc_final: 0.7259 (mtpt) REVERT: C 314 ASN cc_start: 0.8490 (t0) cc_final: 0.8062 (t0) REVERT: C 343 HIS cc_start: 0.6459 (m90) cc_final: 0.6077 (m-70) REVERT: C 377 THR cc_start: 0.7863 (p) cc_final: 0.7624 (t) REVERT: C 470 ARG cc_start: 0.7317 (mtt-85) cc_final: 0.6987 (mtm-85) REVERT: C 479 LEU cc_start: 0.7240 (mt) cc_final: 0.6919 (mt) REVERT: C 492 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8225 (mtp) REVERT: C 503 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7882 (mtpm) REVERT: C 515 MET cc_start: 0.8560 (ttp) cc_final: 0.8149 (ttm) REVERT: C 529 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7451 (ttm170) REVERT: C 641 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7171 (pp20) REVERT: C 719 LYS cc_start: 0.8441 (mtmm) cc_final: 0.7575 (mmtt) REVERT: C 954 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7899 (mttp) REVERT: C 958 LYS cc_start: 0.7256 (tttt) cc_final: 0.6912 (tttp) REVERT: C 1020 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: C 1088 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8010 (p0) REVERT: D 147 ILE cc_start: 0.8277 (mt) cc_final: 0.7829 (mp) REVERT: D 151 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7767 (mmm) REVERT: D 200 GLN cc_start: 0.7359 (tt0) cc_final: 0.7026 (tm-30) REVERT: D 217 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (mp) REVERT: D 372 MET cc_start: 0.8692 (mtp) cc_final: 0.8407 (ttp) REVERT: D 375 GLU cc_start: 0.8104 (tp30) cc_final: 0.7539 (tp30) REVERT: D 386 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7017 (mt-10) REVERT: D 393 THR cc_start: 0.8366 (m) cc_final: 0.8008 (p) REVERT: D 413 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: D 443 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7615 (mt-10) REVERT: D 525 MET cc_start: 0.8752 (ptp) cc_final: 0.8012 (ptm) REVERT: D 649 LYS cc_start: 0.7466 (mmmt) cc_final: 0.7248 (mmtt) REVERT: D 704 GLU cc_start: 0.5031 (OUTLIER) cc_final: 0.4648 (tm-30) REVERT: D 712 GLN cc_start: 0.7111 (mt0) cc_final: 0.6746 (mm-40) REVERT: D 715 LYS cc_start: 0.8895 (ptmt) cc_final: 0.8679 (mtpt) REVERT: D 724 MET cc_start: 0.7965 (mtm) cc_final: 0.7558 (mtm) REVERT: D 792 ASN cc_start: 0.8098 (m110) cc_final: 0.7841 (m110) REVERT: D 805 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.6794 (pp30) REVERT: D 873 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5633 (mp0) REVERT: D 901 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7637 (ttm170) REVERT: D 1149 ARG cc_start: 0.7203 (ttm-80) cc_final: 0.6646 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6341 (tmt90) REVERT: D 1188 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7059 (mt-10) REVERT: D 1276 GLU cc_start: 0.7819 (mp0) cc_final: 0.7571 (mp0) REVERT: E 67 ARG cc_start: 0.7306 (tpt170) cc_final: 0.6890 (mtp-110) REVERT: E 70 GLN cc_start: 0.7163 (tt0) cc_final: 0.6713 (tm-30) REVERT: F 322 MET cc_start: 0.2821 (mmm) cc_final: 0.2394 (ppp) REVERT: F 485 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: F 500 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6280 (mp) REVERT: F 561 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7672 (tmt) outliers start: 107 outliers final: 49 residues processed: 363 average time/residue: 1.6415 time to fit residues: 691.7940 Evaluate side-chains 345 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 278 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 561 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 212 optimal weight: 0.0010 chunk 89 optimal weight: 0.8980 chunk 361 optimal weight: 7.9990 chunk 300 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 301 ASN F 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31811 Z= 0.214 Angle : 0.517 8.325 43401 Z= 0.273 Chirality : 0.041 0.159 4958 Planarity : 0.004 0.051 5300 Dihedral : 15.456 138.868 5295 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.08 % Allowed : 18.30 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3661 helix: 0.52 (0.14), residues: 1453 sheet: -1.18 (0.26), residues: 359 loop : -0.88 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 33 HIS 0.004 0.001 HIS D 865 PHE 0.025 0.001 PHE F 266 TYR 0.016 0.001 TYR F 137 ARG 0.012 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 288 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7808 (ttmm) REVERT: A 103 ASN cc_start: 0.8535 (m-40) cc_final: 0.8300 (m-40) REVERT: A 125 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7982 (tttt) REVERT: A 145 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8235 (ttpp) REVERT: A 181 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7284 (mt-10) REVERT: B 10 LYS cc_start: 0.8950 (mttp) cc_final: 0.8686 (mttm) REVERT: B 51 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8409 (mmm) REVERT: B 78 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7862 (mp) REVERT: B 145 LYS cc_start: 0.8316 (tttt) cc_final: 0.8087 (ttmm) REVERT: B 152 TYR cc_start: 0.8896 (t80) cc_final: 0.8580 (t80) REVERT: B 170 ARG cc_start: 0.6976 (mtm-85) cc_final: 0.5980 (mpp-170) REVERT: C 74 ARG cc_start: 0.7804 (ttp-110) cc_final: 0.7420 (ttp-110) REVERT: C 119 GLU cc_start: 0.8507 (pp20) cc_final: 0.8134 (pp20) REVERT: C 200 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7572 (mmm-85) REVERT: C 299 LYS cc_start: 0.7511 (tttp) cc_final: 0.7274 (mtpt) REVERT: C 314 ASN cc_start: 0.8455 (t0) cc_final: 0.8022 (t0) REVERT: C 343 HIS cc_start: 0.6419 (m90) cc_final: 0.6026 (m90) REVERT: C 369 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7066 (tmt) REVERT: C 377 THR cc_start: 0.7777 (p) cc_final: 0.7553 (t) REVERT: C 470 ARG cc_start: 0.7301 (mtt-85) cc_final: 0.6974 (mtm-85) REVERT: C 479 LEU cc_start: 0.7131 (mt) cc_final: 0.6792 (mt) REVERT: C 492 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: C 496 LYS cc_start: 0.7685 (mmmm) cc_final: 0.7022 (tttt) REVERT: C 503 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7892 (mtpm) REVERT: C 515 MET cc_start: 0.8504 (ttp) cc_final: 0.8128 (ttm) REVERT: C 641 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7154 (pp20) REVERT: C 940 GLU cc_start: 0.7614 (pp20) cc_final: 0.7397 (pp20) REVERT: C 954 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7905 (mttp) REVERT: C 958 LYS cc_start: 0.7241 (tttt) cc_final: 0.6896 (tttp) REVERT: C 1020 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: C 1088 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7991 (p0) REVERT: D 147 ILE cc_start: 0.8182 (mt) cc_final: 0.7812 (mp) REVERT: D 151 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7768 (mmm) REVERT: D 200 GLN cc_start: 0.7350 (tt0) cc_final: 0.7001 (tm-30) REVERT: D 372 MET cc_start: 0.8690 (mtp) cc_final: 0.8406 (ttp) REVERT: D 375 GLU cc_start: 0.7987 (tp30) cc_final: 0.7431 (tp30) REVERT: D 386 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6930 (mt-10) REVERT: D 393 THR cc_start: 0.8200 (m) cc_final: 0.7921 (p) REVERT: D 443 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7541 (mt-10) REVERT: D 525 MET cc_start: 0.8638 (ptp) cc_final: 0.7946 (ptm) REVERT: D 704 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4699 (tm-30) REVERT: D 712 GLN cc_start: 0.7119 (mt0) cc_final: 0.6700 (mm-40) REVERT: D 715 LYS cc_start: 0.8887 (ptmt) cc_final: 0.8675 (mtpt) REVERT: D 724 MET cc_start: 0.7912 (mtm) cc_final: 0.7491 (mtm) REVERT: D 792 ASN cc_start: 0.8025 (m110) cc_final: 0.7793 (m110) REVERT: D 873 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5600 (mp0) REVERT: D 901 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7636 (ttm170) REVERT: D 1149 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6695 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6133 (tmt90) REVERT: D 1188 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7041 (mt-10) REVERT: D 1276 GLU cc_start: 0.7762 (mp0) cc_final: 0.7548 (mp0) REVERT: E 35 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6570 (mtmm) REVERT: E 67 ARG cc_start: 0.7242 (tpt170) cc_final: 0.6809 (mtp-110) REVERT: E 70 GLN cc_start: 0.7152 (tt0) cc_final: 0.6691 (tm-30) REVERT: E 72 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7038 (tm-30) REVERT: F 322 MET cc_start: 0.2846 (mmm) cc_final: 0.2357 (ppp) REVERT: F 485 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: F 500 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6326 (mp) REVERT: F 561 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7583 (tmt) REVERT: F 567 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8391 (ptp) REVERT: F 605 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7155 (mp0) outliers start: 97 outliers final: 49 residues processed: 357 average time/residue: 1.6383 time to fit residues: 679.4488 Evaluate side-chains 341 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 275 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 605 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 chunk 304 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 chunk 225 optimal weight: 0.0170 chunk 219 optimal weight: 0.2980 chunk 166 optimal weight: 1.9990 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31811 Z= 0.250 Angle : 0.535 10.571 43401 Z= 0.279 Chirality : 0.042 0.158 4958 Planarity : 0.004 0.055 5300 Dihedral : 15.423 138.726 5295 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.92 % Allowed : 18.68 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3661 helix: 0.58 (0.14), residues: 1458 sheet: -1.11 (0.26), residues: 370 loop : -0.85 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D1193 HIS 0.004 0.001 HIS D 865 PHE 0.010 0.001 PHE D 437 TYR 0.018 0.001 TYR C1281 ARG 0.012 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 288 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6223 (ttm110) REVERT: A 86 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7803 (ttmm) REVERT: A 97 GLU cc_start: 0.8142 (tt0) cc_final: 0.7613 (tt0) REVERT: A 103 ASN cc_start: 0.8564 (m-40) cc_final: 0.8314 (m-40) REVERT: A 125 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7986 (tttt) REVERT: B 10 LYS cc_start: 0.8946 (mttp) cc_final: 0.8683 (mttm) REVERT: B 51 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8430 (mmm) REVERT: B 78 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7800 (mp) REVERT: B 145 LYS cc_start: 0.8344 (tttt) cc_final: 0.8102 (ttmm) REVERT: B 152 TYR cc_start: 0.8779 (t80) cc_final: 0.8525 (t80) REVERT: B 170 ARG cc_start: 0.6972 (mtm-85) cc_final: 0.5977 (mpp-170) REVERT: C 74 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7444 (ttp-110) REVERT: C 119 GLU cc_start: 0.8499 (pp20) cc_final: 0.8154 (pp20) REVERT: C 200 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7579 (mmm-85) REVERT: C 299 LYS cc_start: 0.7554 (tttp) cc_final: 0.7246 (mtpt) REVERT: C 314 ASN cc_start: 0.8454 (t0) cc_final: 0.8021 (t0) REVERT: C 343 HIS cc_start: 0.6697 (m90) cc_final: 0.6185 (m90) REVERT: C 377 THR cc_start: 0.7803 (p) cc_final: 0.7582 (t) REVERT: C 470 ARG cc_start: 0.7300 (mtt-85) cc_final: 0.6969 (mtm-85) REVERT: C 479 LEU cc_start: 0.7122 (mt) cc_final: 0.6782 (mt) REVERT: C 492 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8213 (mtp) REVERT: C 496 LYS cc_start: 0.7520 (mmmm) cc_final: 0.6811 (tttt) REVERT: C 503 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7893 (mtpm) REVERT: C 515 MET cc_start: 0.8485 (ttp) cc_final: 0.8068 (ttm) REVERT: C 529 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7488 (ttm170) REVERT: C 954 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7903 (mttp) REVERT: C 958 LYS cc_start: 0.7249 (tttt) cc_final: 0.6902 (tttp) REVERT: C 1020 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6988 (tm-30) REVERT: C 1088 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8001 (p0) REVERT: C 1232 MET cc_start: 0.9040 (mmm) cc_final: 0.8770 (mmm) REVERT: D 147 ILE cc_start: 0.8186 (mt) cc_final: 0.7831 (mp) REVERT: D 151 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: D 200 GLN cc_start: 0.7354 (tt0) cc_final: 0.7026 (tm-30) REVERT: D 372 MET cc_start: 0.8698 (mtp) cc_final: 0.8404 (ttp) REVERT: D 375 GLU cc_start: 0.8003 (tp30) cc_final: 0.7444 (tp30) REVERT: D 386 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7021 (mt-10) REVERT: D 393 THR cc_start: 0.8237 (m) cc_final: 0.7923 (p) REVERT: D 443 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7589 (mt-10) REVERT: D 525 MET cc_start: 0.8704 (ptp) cc_final: 0.7993 (ptm) REVERT: D 704 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.4669 (tm-30) REVERT: D 712 GLN cc_start: 0.7139 (mt0) cc_final: 0.6714 (mm-40) REVERT: D 724 MET cc_start: 0.7915 (mtm) cc_final: 0.7487 (mtm) REVERT: D 792 ASN cc_start: 0.8102 (m110) cc_final: 0.7836 (m110) REVERT: D 873 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5599 (mp0) REVERT: D 901 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7610 (ttm170) REVERT: D 1060 VAL cc_start: 0.3286 (OUTLIER) cc_final: 0.2638 (t) REVERT: D 1149 ARG cc_start: 0.7202 (ttm-80) cc_final: 0.6699 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7243 (ttm170) cc_final: 0.6347 (tmt90) REVERT: D 1187 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: D 1188 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7041 (mt-10) REVERT: D 1276 GLU cc_start: 0.7775 (mp0) cc_final: 0.7551 (mp0) REVERT: E 35 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6595 (mtmm) REVERT: E 67 ARG cc_start: 0.7302 (tpt170) cc_final: 0.6880 (mtp-110) REVERT: E 70 GLN cc_start: 0.7150 (tt0) cc_final: 0.6679 (tm-30) REVERT: E 72 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7037 (tm-30) REVERT: F 131 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6792 (tm-30) REVERT: F 322 MET cc_start: 0.2858 (mmm) cc_final: 0.2360 (ppp) REVERT: F 485 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: F 500 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6246 (mp) REVERT: F 561 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7665 (ppp) REVERT: F 567 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8343 (ptp) outliers start: 92 outliers final: 55 residues processed: 353 average time/residue: 1.6573 time to fit residues: 680.9198 Evaluate side-chains 348 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 274 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 567 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 0.6980 chunk 143 optimal weight: 30.0000 chunk 215 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 283 optimal weight: 30.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31811 Z= 0.272 Angle : 0.542 10.341 43401 Z= 0.283 Chirality : 0.042 0.173 4958 Planarity : 0.004 0.054 5300 Dihedral : 15.399 138.731 5295 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.33 % Allowed : 18.65 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3661 helix: 0.59 (0.14), residues: 1459 sheet: -1.07 (0.26), residues: 371 loop : -0.80 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 326 HIS 0.004 0.001 HIS D 865 PHE 0.021 0.001 PHE F 266 TYR 0.018 0.001 TYR C1281 ARG 0.014 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 281 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6227 (ttm110) REVERT: A 86 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7791 (ttmm) REVERT: A 103 ASN cc_start: 0.8557 (m-40) cc_final: 0.8335 (m-40) REVERT: A 125 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7980 (tttt) REVERT: A 145 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8171 (ttpp) REVERT: B 10 LYS cc_start: 0.8936 (mttp) cc_final: 0.8670 (mttm) REVERT: B 51 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8457 (mmm) REVERT: B 78 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7824 (mp) REVERT: B 145 LYS cc_start: 0.8310 (tttt) cc_final: 0.8086 (ttmm) REVERT: B 152 TYR cc_start: 0.8815 (t80) cc_final: 0.8567 (t80) REVERT: B 170 ARG cc_start: 0.6964 (mtm-85) cc_final: 0.5972 (mpp-170) REVERT: C 74 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7467 (ttp-110) REVERT: C 119 GLU cc_start: 0.8504 (pp20) cc_final: 0.8161 (pp20) REVERT: C 200 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7589 (mmm-85) REVERT: C 299 LYS cc_start: 0.7430 (tttp) cc_final: 0.7165 (mtpt) REVERT: C 314 ASN cc_start: 0.8461 (t0) cc_final: 0.8038 (t0) REVERT: C 343 HIS cc_start: 0.6733 (m90) cc_final: 0.6212 (m90) REVERT: C 377 THR cc_start: 0.7800 (p) cc_final: 0.7576 (t) REVERT: C 470 ARG cc_start: 0.7304 (mtt-85) cc_final: 0.6966 (mtm-85) REVERT: C 479 LEU cc_start: 0.7150 (mt) cc_final: 0.6823 (mt) REVERT: C 492 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8211 (mtp) REVERT: C 496 LYS cc_start: 0.7484 (mmmm) cc_final: 0.6957 (tttt) REVERT: C 503 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7897 (mtpm) REVERT: C 515 MET cc_start: 0.8496 (ttp) cc_final: 0.8067 (ttm) REVERT: C 529 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7484 (ttm170) REVERT: C 641 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7068 (pp20) REVERT: C 719 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7525 (mmtt) REVERT: C 954 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7903 (mttp) REVERT: C 958 LYS cc_start: 0.7252 (tttt) cc_final: 0.6908 (tttp) REVERT: C 1020 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 1088 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8003 (p0) REVERT: D 147 ILE cc_start: 0.8135 (mt) cc_final: 0.7801 (mp) REVERT: D 151 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7791 (mmm) REVERT: D 200 GLN cc_start: 0.7353 (tt0) cc_final: 0.7016 (tm-30) REVERT: D 213 LYS cc_start: 0.8045 (tttt) cc_final: 0.7712 (ttmm) REVERT: D 372 MET cc_start: 0.8688 (mtp) cc_final: 0.8388 (ttp) REVERT: D 375 GLU cc_start: 0.8067 (tp30) cc_final: 0.7506 (tp30) REVERT: D 386 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7020 (mt-10) REVERT: D 393 THR cc_start: 0.8263 (m) cc_final: 0.7919 (p) REVERT: D 443 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7555 (mt-10) REVERT: D 525 MET cc_start: 0.8730 (ptp) cc_final: 0.8013 (ptm) REVERT: D 704 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4725 (tm-30) REVERT: D 712 GLN cc_start: 0.7129 (mt0) cc_final: 0.6718 (mm-40) REVERT: D 724 MET cc_start: 0.7919 (mtm) cc_final: 0.7513 (mtm) REVERT: D 792 ASN cc_start: 0.8100 (m110) cc_final: 0.7854 (m110) REVERT: D 805 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.6716 (pp30) REVERT: D 873 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5574 (mp0) REVERT: D 901 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7608 (ttm170) REVERT: D 1060 VAL cc_start: 0.3284 (OUTLIER) cc_final: 0.2610 (t) REVERT: D 1149 ARG cc_start: 0.7200 (ttm-80) cc_final: 0.6701 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7454 (ttm170) cc_final: 0.6563 (tmt90) REVERT: D 1188 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7035 (mt-10) REVERT: D 1276 GLU cc_start: 0.7789 (mp0) cc_final: 0.7556 (mp0) REVERT: E 35 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6612 (mtmm) REVERT: E 67 ARG cc_start: 0.7304 (tpt170) cc_final: 0.6884 (mtp-110) REVERT: E 70 GLN cc_start: 0.7144 (tt0) cc_final: 0.6674 (tm-30) REVERT: E 72 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7108 (tm-30) REVERT: F 131 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6555 (tm-30) REVERT: F 322 MET cc_start: 0.2944 (mmm) cc_final: 0.2419 (ppp) REVERT: F 485 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: F 500 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6199 (mp) REVERT: F 567 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8369 (ptp) outliers start: 105 outliers final: 61 residues processed: 362 average time/residue: 1.6367 time to fit residues: 692.4591 Evaluate side-chains 354 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 274 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 567 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 303 optimal weight: 0.3980 chunk 317 optimal weight: 6.9990 chunk 334 optimal weight: 0.2980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31811 Z= 0.313 Angle : 0.564 10.094 43401 Z= 0.294 Chirality : 0.043 0.191 4958 Planarity : 0.004 0.063 5300 Dihedral : 15.398 138.710 5295 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.89 % Allowed : 19.47 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3661 helix: 0.55 (0.14), residues: 1457 sheet: -1.05 (0.26), residues: 371 loop : -0.80 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 409 HIS 0.004 0.001 HIS C 447 PHE 0.012 0.001 PHE D 437 TYR 0.021 0.001 TYR F 137 ARG 0.014 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 278 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6239 (ttm110) REVERT: A 86 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7799 (ttmm) REVERT: A 103 ASN cc_start: 0.8571 (m-40) cc_final: 0.8346 (m-40) REVERT: A 125 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7984 (tttt) REVERT: B 10 LYS cc_start: 0.8996 (mttp) cc_final: 0.8736 (mttm) REVERT: B 51 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8468 (mmm) REVERT: B 78 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7831 (mp) REVERT: B 145 LYS cc_start: 0.8353 (tttt) cc_final: 0.8108 (ttmm) REVERT: B 170 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.5971 (mpp-170) REVERT: C 74 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7464 (ttp-110) REVERT: C 119 GLU cc_start: 0.8512 (pp20) cc_final: 0.8166 (pp20) REVERT: C 200 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7615 (mmm-85) REVERT: C 239 MET cc_start: 0.5604 (tmm) cc_final: 0.5358 (ttt) REVERT: C 299 LYS cc_start: 0.7483 (tttp) cc_final: 0.7204 (mtpt) REVERT: C 314 ASN cc_start: 0.8480 (t0) cc_final: 0.8042 (t0) REVERT: C 343 HIS cc_start: 0.6721 (m90) cc_final: 0.6185 (m90) REVERT: C 470 ARG cc_start: 0.7314 (mtt-85) cc_final: 0.6968 (mtm-85) REVERT: C 479 LEU cc_start: 0.7211 (mt) cc_final: 0.6898 (mt) REVERT: C 492 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8131 (mtp) REVERT: C 496 LYS cc_start: 0.7514 (mmmm) cc_final: 0.6990 (tttt) REVERT: C 503 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7865 (mtpm) REVERT: C 515 MET cc_start: 0.8525 (ttp) cc_final: 0.8094 (ttm) REVERT: C 529 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7440 (ttm170) REVERT: C 641 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7062 (pp20) REVERT: C 719 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7523 (mmtt) REVERT: C 954 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7904 (mttp) REVERT: C 958 LYS cc_start: 0.7255 (tttt) cc_final: 0.6911 (tttp) REVERT: C 1020 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: C 1088 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8002 (p0) REVERT: D 147 ILE cc_start: 0.8153 (mt) cc_final: 0.7818 (mp) REVERT: D 151 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7825 (mmm) REVERT: D 200 GLN cc_start: 0.7354 (tt0) cc_final: 0.7021 (tm-30) REVERT: D 213 LYS cc_start: 0.8107 (tttt) cc_final: 0.7763 (ttmm) REVERT: D 372 MET cc_start: 0.8693 (mtp) cc_final: 0.8394 (ttp) REVERT: D 375 GLU cc_start: 0.8026 (tp30) cc_final: 0.7701 (mm-30) REVERT: D 393 THR cc_start: 0.8304 (m) cc_final: 0.7927 (p) REVERT: D 413 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: D 443 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7578 (mt-10) REVERT: D 525 MET cc_start: 0.8749 (ptp) cc_final: 0.7993 (ptm) REVERT: D 704 GLU cc_start: 0.5087 (OUTLIER) cc_final: 0.4728 (tm-30) REVERT: D 712 GLN cc_start: 0.7135 (mt0) cc_final: 0.6736 (mm-40) REVERT: D 715 LYS cc_start: 0.8908 (ptmt) cc_final: 0.8682 (mtpt) REVERT: D 724 MET cc_start: 0.7926 (mtm) cc_final: 0.7521 (mtm) REVERT: D 792 ASN cc_start: 0.8128 (m110) cc_final: 0.7846 (m110) REVERT: D 805 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.6715 (pp30) REVERT: D 873 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5557 (mp0) REVERT: D 901 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.7609 (ttm170) REVERT: D 954 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7744 (t0) REVERT: D 1060 VAL cc_start: 0.3069 (OUTLIER) cc_final: 0.2425 (t) REVERT: D 1149 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6705 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7584 (ttm170) cc_final: 0.6595 (tmt90) REVERT: D 1188 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7054 (mt-10) REVERT: E 35 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6660 (mtmm) REVERT: E 67 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6888 (mtp-110) REVERT: E 70 GLN cc_start: 0.7145 (tt0) cc_final: 0.6672 (tm-30) REVERT: E 72 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7145 (tm-30) REVERT: F 131 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: F 322 MET cc_start: 0.2951 (mmm) cc_final: 0.2402 (ppp) REVERT: F 485 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: F 500 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6267 (mp) REVERT: F 567 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8424 (ptp) outliers start: 91 outliers final: 63 residues processed: 346 average time/residue: 1.7406 time to fit residues: 702.5448 Evaluate side-chains 350 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 266 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 567 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 216 optimal weight: 0.0270 chunk 168 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 342 optimal weight: 0.9980 chunk 296 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31811 Z= 0.224 Angle : 0.534 9.722 43401 Z= 0.279 Chirality : 0.042 0.201 4958 Planarity : 0.004 0.068 5300 Dihedral : 15.332 138.507 5295 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.57 % Allowed : 19.95 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3661 helix: 0.69 (0.14), residues: 1455 sheet: -1.03 (0.27), residues: 370 loop : -0.73 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 33 HIS 0.004 0.001 HIS D 865 PHE 0.021 0.001 PHE F 266 TYR 0.020 0.001 TYR F 137 ARG 0.015 0.000 ARG D 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 275 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7796 (ttmm) REVERT: A 97 GLU cc_start: 0.8153 (tt0) cc_final: 0.7631 (tt0) REVERT: A 103 ASN cc_start: 0.8558 (m-40) cc_final: 0.8317 (m-40) REVERT: A 125 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7975 (tttt) REVERT: B 10 LYS cc_start: 0.8931 (mttp) cc_final: 0.8677 (mttm) REVERT: B 51 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8414 (mmm) REVERT: B 78 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 145 LYS cc_start: 0.8346 (tttt) cc_final: 0.8115 (ttmm) REVERT: B 170 ARG cc_start: 0.7028 (mtm-85) cc_final: 0.5995 (mpp-170) REVERT: C 74 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7452 (ttp-110) REVERT: C 119 GLU cc_start: 0.8411 (pp20) cc_final: 0.8057 (pp20) REVERT: C 151 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.8080 (mtm-85) REVERT: C 200 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7603 (mmm-85) REVERT: C 239 MET cc_start: 0.5582 (tmm) cc_final: 0.5356 (ttt) REVERT: C 343 HIS cc_start: 0.6723 (m90) cc_final: 0.6166 (m90) REVERT: C 377 THR cc_start: 0.7739 (p) cc_final: 0.7536 (t) REVERT: C 470 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.6960 (mtm-85) REVERT: C 479 LEU cc_start: 0.7115 (mt) cc_final: 0.6777 (mt) REVERT: C 492 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8200 (mtp) REVERT: C 496 LYS cc_start: 0.7489 (mmmm) cc_final: 0.6980 (tttt) REVERT: C 503 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7897 (mtpm) REVERT: C 515 MET cc_start: 0.8467 (ttp) cc_final: 0.8060 (ttm) REVERT: C 529 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7503 (ttm170) REVERT: C 954 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7902 (mttp) REVERT: C 958 LYS cc_start: 0.7245 (tttt) cc_final: 0.6897 (tttp) REVERT: C 1020 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: C 1088 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7996 (p0) REVERT: D 147 ILE cc_start: 0.8117 (mt) cc_final: 0.7813 (mp) REVERT: D 151 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7810 (mmm) REVERT: D 200 GLN cc_start: 0.7360 (tt0) cc_final: 0.7021 (tm-30) REVERT: D 372 MET cc_start: 0.8676 (mtp) cc_final: 0.8375 (ttp) REVERT: D 375 GLU cc_start: 0.8056 (tp30) cc_final: 0.7505 (tp30) REVERT: D 386 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7038 (mt-10) REVERT: D 393 THR cc_start: 0.8274 (m) cc_final: 0.7945 (p) REVERT: D 443 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7449 (mt-10) REVERT: D 525 MET cc_start: 0.8673 (ptp) cc_final: 0.7963 (ptm) REVERT: D 704 GLU cc_start: 0.4961 (OUTLIER) cc_final: 0.4677 (tm-30) REVERT: D 712 GLN cc_start: 0.7125 (mt0) cc_final: 0.6717 (mm-40) REVERT: D 724 MET cc_start: 0.7892 (mtm) cc_final: 0.7468 (mtm) REVERT: D 792 ASN cc_start: 0.8123 (m110) cc_final: 0.7854 (m110) REVERT: D 805 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.6739 (pp30) REVERT: D 873 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5575 (mp0) REVERT: D 901 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: D 954 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7762 (t0) REVERT: D 955 LYS cc_start: 0.7168 (tmtm) cc_final: 0.6754 (pttm) REVERT: D 1149 ARG cc_start: 0.7192 (ttm-80) cc_final: 0.6693 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7599 (ttm170) cc_final: 0.6633 (tmt90) REVERT: D 1188 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7057 (mt-10) REVERT: E 35 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6579 (mtmm) REVERT: E 67 ARG cc_start: 0.7292 (tpt170) cc_final: 0.6875 (mtp-110) REVERT: E 70 GLN cc_start: 0.7138 (tt0) cc_final: 0.6718 (tm-30) REVERT: E 72 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7178 (tm-30) REVERT: F 131 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: F 322 MET cc_start: 0.2886 (mmm) cc_final: 0.2343 (ppp) REVERT: F 485 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: F 500 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6203 (mp) REVERT: F 567 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8265 (ptp) outliers start: 81 outliers final: 59 residues processed: 336 average time/residue: 1.6095 time to fit residues: 628.8037 Evaluate side-chains 343 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 267 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 567 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 305 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101249 restraints weight = 39081.602| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.19 r_work: 0.3140 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31811 Z= 0.260 Angle : 0.546 9.401 43401 Z= 0.284 Chirality : 0.042 0.201 4958 Planarity : 0.004 0.071 5300 Dihedral : 15.322 138.409 5295 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.70 % Allowed : 20.01 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3661 helix: 0.68 (0.14), residues: 1456 sheet: -0.96 (0.27), residues: 366 loop : -0.72 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 33 HIS 0.004 0.001 HIS D 865 PHE 0.011 0.001 PHE D 437 TYR 0.018 0.001 TYR C1281 ARG 0.015 0.000 ARG D 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12076.25 seconds wall clock time: 214 minutes 36.33 seconds (12876.33 seconds total)