Starting phenix.real_space_refine on Mon Mar 18 00:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8h_10401/03_2024/6t8h_10401_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8h_10401/03_2024/6t8h_10401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8h_10401/03_2024/6t8h_10401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8h_10401/03_2024/6t8h_10401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8h_10401/03_2024/6t8h_10401_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8h_10401/03_2024/6t8h_10401_neut.pdb" } resolution = 3.77 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= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 4 6.06 5 P 34 5.49 5 S 75 5.16 5 C 12297 2.51 5 N 3244 2.21 5 O 3710 1.98 5 H 33 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 167": "NH1" <-> "NH2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1089": "NH1" <-> "NH2" Residue "B ARG 1122": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19398 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1950 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3345 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 390} Chain breaks: 1 Chain: "B" Number of atoms: 9501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9501 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1121} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1950 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "D" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1950 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "P" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "T" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 347 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10706 SG CYS B 706 102.750 43.270 74.558 1.00 99.36 S ATOM 10728 SG CYS B 709 101.852 42.311 76.372 1.00104.89 S ATOM 10793 SG CYS B 718 101.528 45.234 76.055 1.00 95.92 S ATOM 10814 SG CYS B 721 105.014 45.227 75.754 1.00 97.36 S ATOM 10897 SG CYS B 731 89.968 28.756 58.650 1.00106.91 S ATOM 10921 SG CYS B 734 91.346 27.074 60.823 1.00111.08 S ATOM 11049 SG CYS B 750 93.383 26.785 58.444 1.00114.17 S ATOM 11071 SG CYS B 753 90.050 25.063 58.121 1.00118.66 S ATOM 14062 SG CYS B1123 57.561 45.023 65.105 1.00118.28 S ATOM 14084 SG CYS B1126 58.252 41.730 63.166 1.00120.23 S ATOM 14190 SG CYS B1139 54.932 41.922 65.603 1.00110.09 S ATOM 14210 SG CYS B1142 59.188 42.029 66.786 1.00110.26 S Time building chain proxies: 10.43, per 1000 atoms: 0.54 Number of scatterers: 19398 At special positions: 0 Unit cell: (119.52, 135.29, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Fe 1 26.01 S 75 16.00 P 34 15.00 O 3710 8.00 N 3244 7.00 C 12297 6.00 H 33 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" ND1 HIS A 560 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 497 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 709 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 706 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 718 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 721 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 734 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 753 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 731 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1126 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1142 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1123 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1139 " Number of angles added : 18 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4376 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 21 sheets defined 35.0% alpha, 20.6% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'E' and resid 9 through 22 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 73 through 82 Processing helix chain 'E' and resid 138 through 152 removed outlier: 3.922A pdb=" N LEU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 209 Processing helix chain 'A' and resid 219 through 244 removed outlier: 4.194A pdb=" N ILE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 464 through 473 Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.895A pdb=" N MET A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'B' and resid 5 through 31 removed outlier: 3.692A pdb=" N GLN B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 59 through 72 removed outlier: 3.931A pdb=" N ARG B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.719A pdb=" N ALA B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 150 through 169 removed outlier: 4.154A pdb=" N ALA B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.509A pdb=" N MET B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 459 through 476 removed outlier: 4.120A pdb=" N LEU B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 517 through 529 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.738A pdb=" N VAL B 543 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.500A pdb=" N VAL B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 584 through 592 removed outlier: 3.930A pdb=" N THR B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 removed outlier: 3.650A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 631 through 640 Processing helix chain 'B' and resid 677 through 682 removed outlier: 4.249A pdb=" N GLY B 681 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 693 removed outlier: 3.551A pdb=" N ALA B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 Processing helix chain 'B' and resid 766 through 779 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.831A pdb=" N GLY B 805 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.935A pdb=" N ILE B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 Processing helix chain 'B' and resid 877 through 897 removed outlier: 4.213A pdb=" N LYS B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 912 Processing helix chain 'B' and resid 944 through 951 Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 973 through 977 Processing helix chain 'B' and resid 1002 through 1007 removed outlier: 3.736A pdb=" N ASN B1006 " --> pdb=" O GLU B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1022 removed outlier: 3.571A pdb=" N TYR B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR B1022 " --> pdb=" O TYR B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 3.596A pdb=" N VAL B1031 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1041 removed outlier: 3.735A pdb=" N LEU B1041 " --> pdb=" O GLU B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1085 removed outlier: 4.006A pdb=" N ARG B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B1085 " --> pdb=" O GLN B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1117 Proline residue: B1107 - end of helix removed outlier: 3.999A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1156 removed outlier: 3.669A pdb=" N ILE B1155 " --> pdb=" O SER B1151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B1156 " --> pdb=" O LYS B1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1151 through 1156' Processing helix chain 'B' and resid 1158 through 1169 Processing helix chain 'B' and resid 1172 through 1190 removed outlier: 3.717A pdb=" N PHE B1190 " --> pdb=" O ILE B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1214 Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 138 through 152 removed outlier: 3.922A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'D' and resid 9 through 22 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 73 through 82 Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.922A pdb=" N LEU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 209 Processing sheet with id=AA1, first strand: chain 'E' and resid 60 through 62 removed outlier: 4.652A pdb=" N THR E 108 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS C 178 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU C 169 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 154 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.647A pdb=" N ALA E 27 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU E 26 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET E 41 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA E 28 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG E 39 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN E 52 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 238 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR E 232 " --> pdb=" O GLU E 216 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 216 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 195 through 200 removed outlier: 6.557A pdb=" N SER E 154 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU E 169 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS E 178 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 108 " --> pdb=" O LYS E 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 201 removed outlier: 5.344A pdb=" N VAL A 199 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 487 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 565 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 278 removed outlier: 5.462A pdb=" N VAL A 273 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A 288 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 275 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N PHE A 329 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 295 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA A 331 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 297 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS A 333 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N TYR A 335 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE A 329 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER A 324 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA A 331 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 322 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.137A pdb=" N MET A 444 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A 354 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU A 399 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 356 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE A 401 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE A 358 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL A 599 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 612 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 601 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 608 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.640A pdb=" N GLY B 927 " --> pdb=" O THR B 992 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 875 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B 935 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.640A pdb=" N GLY B 927 " --> pdb=" O THR B 992 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR B 826 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ALA B 943 " --> pdb=" O THR B 826 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 828 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 129 removed outlier: 9.164A pdb=" N GLU B 217 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 139 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 219 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 141 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 340 through 342 removed outlier: 6.033A pdb=" N ALA B 654 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.022A pdb=" N ARG B 353 " --> pdb=" O ILE B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 414 through 416 removed outlier: 6.427A pdb=" N ILE B 406 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 560 through 562 removed outlier: 3.677A pdb=" N LYS B 574 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AB6, first strand: chain 'B' and resid 697 through 701 Processing sheet with id=AB7, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AB8, first strand: chain 'B' and resid 832 through 833 Processing sheet with id=AB9, first strand: chain 'B' and resid 1121 through 1122 Processing sheet with id=AC1, first strand: chain 'C' and resid 60 through 62 removed outlier: 4.451A pdb=" N THR C 108 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS D 178 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU D 169 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER D 154 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.647A pdb=" N ALA C 27 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU C 26 " --> pdb=" O MET C 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET C 41 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA C 28 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG C 39 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 52 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 238 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR C 232 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 216 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.647A pdb=" N ALA D 27 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU D 26 " --> pdb=" O MET D 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET D 41 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA D 28 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG D 39 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 52 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 238 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR D 232 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU D 216 " --> pdb=" O TYR D 232 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 8.94 Time building geometry restraints manager: 8.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 33 1.04 - 1.24: 2164 1.24 - 1.43: 5982 1.43 - 1.62: 11524 1.62 - 1.82: 132 Bond restraints: 19835 Sorted by residual: bond pdb=" C GLN A 345 " pdb=" N LYS A 346 " ideal model delta sigma weight residual 1.327 1.167 0.159 1.39e-02 5.18e+03 1.32e+02 bond pdb=" CA ASN B 541 " pdb=" C ASN B 541 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.41e-02 5.03e+03 2.75e+01 bond pdb=" C TRP B 365 " pdb=" N GLY B 366 " ideal model delta sigma weight residual 1.333 1.289 0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" C ARG B 338 " pdb=" N PRO B 339 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.22e-02 6.72e+03 1.57e+01 bond pdb=" C VAL B 514 " pdb=" N LYS B 515 " ideal model delta sigma weight residual 1.331 1.283 0.047 1.24e-02 6.50e+03 1.45e+01 ... (remaining 19830 not shown) Histogram of bond angle deviations from ideal: 79.47 - 90.40: 2 90.40 - 101.32: 76 101.32 - 112.25: 10821 112.25 - 123.17: 14719 123.17 - 134.10: 1334 Bond angle restraints: 26952 Sorted by residual: angle pdb=" O3' DA T 10 " pdb=" P DC T 11 " pdb=" OP1 DC T 11 " ideal model delta sigma weight residual 108.00 79.47 28.53 3.00e+00 1.11e-01 9.04e+01 angle pdb=" O3' DA T 10 " pdb=" P DC T 11 " pdb=" OP2 DC T 11 " ideal model delta sigma weight residual 108.00 86.19 21.81 3.00e+00 1.11e-01 5.28e+01 angle pdb=" C TRP B 540 " pdb=" N ASN B 541 " pdb=" CA ASN B 541 " ideal model delta sigma weight residual 122.38 110.02 12.36 1.81e+00 3.05e-01 4.66e+01 angle pdb=" CA ILE B1106 " pdb=" C ILE B1106 " pdb=" N PRO B1107 " ideal model delta sigma weight residual 121.00 116.63 4.37 8.30e-01 1.45e+00 2.77e+01 angle pdb=" CA ASN B 541 " pdb=" C ASN B 541 " pdb=" N SER B 542 " ideal model delta sigma weight residual 118.32 125.33 -7.01 1.35e+00 5.49e-01 2.69e+01 ... (remaining 26947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 11318 15.01 - 30.01: 473 30.01 - 45.02: 156 45.02 - 60.02: 98 60.02 - 75.03: 6 Dihedral angle restraints: 12051 sinusoidal: 5253 harmonic: 6798 Sorted by residual: dihedral pdb=" CA GLY B 437 " pdb=" C GLY B 437 " pdb=" N ASP B 438 " pdb=" CA ASP B 438 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LYS B 668 " pdb=" C LYS B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLU B1093 " pdb=" C GLU B1093 " pdb=" N HIS B1094 " pdb=" CA HIS B1094 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 12048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.386: 3012 0.386 - 0.772: 1 0.772 - 1.158: 0 1.158 - 1.544: 0 1.544 - 1.931: 1 Chirality restraints: 3014 Sorted by residual: chirality pdb=" P DC T 11 " pdb=" OP1 DC T 11 " pdb=" OP2 DC T 11 " pdb=" O5' DC T 11 " both_signs ideal model delta sigma weight residual True 2.35 0.41 1.93 2.00e-01 2.50e+01 9.32e+01 chirality pdb=" CB VAL B1141 " pdb=" CA VAL B1141 " pdb=" CG1 VAL B1141 " pdb=" CG2 VAL B1141 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE B 830 " pdb=" CA ILE B 830 " pdb=" CG1 ILE B 830 " pdb=" CG2 ILE B 830 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 3011 not shown) Planarity restraints: 3378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 462 " -0.027 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP B 462 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 462 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP B 462 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 462 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 462 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 462 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 462 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 462 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 462 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1093 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C GLU B1093 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU B1093 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS B1094 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 435 " -0.007 2.00e-02 2.50e+03 2.17e-02 9.42e+00 pdb=" CG TYR B 435 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 435 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR B 435 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 435 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 435 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 435 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 435 " 0.004 2.00e-02 2.50e+03 ... (remaining 3375 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 64 2.28 - 2.86: 7020 2.86 - 3.44: 23165 3.44 - 4.02: 36905 4.02 - 4.60: 53699 Nonbonded interactions: 120853 Sorted by model distance: nonbonded pdb=" O SER B1103 " pdb=" CD PRO B1107 " model vdw 1.696 3.100 nonbonded pdb=" O PHE B1121 " pdb=" CB LYS B1129 " model vdw 1.704 3.100 nonbonded pdb=" CB PHE B 443 " pdb=" OD2 ASP B1008 " model vdw 1.745 3.100 nonbonded pdb=" CD1 ILE B1106 " pdb=" CD1 ILE B1179 " model vdw 1.819 3.400 nonbonded pdb=" NE2 HIS A 562 " pdb="FE FE A 701 " model vdw 1.875 2.290 ... (remaining 120848 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 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.490 Extract box with map and model: 6.630 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 62.030 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.012 0.159 19802 Z= 0.775 Angle : 1.095 28.527 26886 Z= 0.605 Chirality : 0.065 1.931 3014 Planarity : 0.006 0.074 3345 Dihedral : 11.304 75.030 7642 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 39.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.62 % Favored : 91.25 % Rotamer: Outliers : 0.94 % Allowed : 2.61 % Favored : 96.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.59 % 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: -3.78 (0.15), residues: 2332 helix: -2.74 (0.15), residues: 690 sheet: -1.95 (0.21), residues: 514 loop : -2.56 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.006 TRP B 462 HIS 0.023 0.003 HIS B1005 PHE 0.034 0.004 PHE B 524 TYR 0.046 0.004 TYR B 435 ARG 0.017 0.002 ARG B 931 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 613 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 594 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 ILE cc_start: 0.8266 (pt) cc_final: 0.8002 (tt) REVERT: E 109 ARG cc_start: 0.7218 (mtm180) cc_final: 0.6460 (mtm-85) REVERT: E 181 LEU cc_start: 0.7589 (mt) cc_final: 0.7219 (tp) REVERT: A 212 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.4505 (tptt) REVERT: A 262 SER cc_start: 0.6350 (m) cc_final: 0.6078 (t) REVERT: A 418 ASP cc_start: 0.7675 (t70) cc_final: 0.7459 (t0) REVERT: B 111 THR cc_start: 0.8698 (p) cc_final: 0.8305 (t) REVERT: B 149 SER cc_start: 0.7570 (m) cc_final: 0.7212 (p) REVERT: B 332 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8305 (tppt) REVERT: B 552 TRP cc_start: 0.9098 (t60) cc_final: 0.8878 (t60) REVERT: B 705 LYS cc_start: 0.8718 (tttt) cc_final: 0.8358 (tmtt) REVERT: B 772 ASN cc_start: 0.8433 (t160) cc_final: 0.8203 (t0) REVERT: B 776 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 1099 LYS cc_start: 0.8063 (tptp) cc_final: 0.7178 (tptt) REVERT: B 1103 SER cc_start: 0.3333 (OUTLIER) cc_final: 0.2871 (t) REVERT: B 1145 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5065 (mmtt) REVERT: C 36 ILE cc_start: 0.7466 (mt) cc_final: 0.7186 (mm) REVERT: C 90 ILE cc_start: 0.8629 (mp) cc_final: 0.7844 (mt) REVERT: C 147 ASP cc_start: 0.7891 (m-30) cc_final: 0.6837 (m-30) REVERT: D 22 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8196 (mpp80) REVERT: D 45 ARG cc_start: 0.8201 (mpt180) cc_final: 0.7970 (mmt180) REVERT: D 167 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7130 (ttm170) REVERT: D 238 ARG cc_start: 0.7604 (pmt-80) cc_final: 0.7285 (pmt-80) REVERT: D 240 ILE cc_start: 0.7935 (mt) cc_final: 0.6882 (mt) outliers start: 19 outliers final: 4 residues processed: 609 average time/residue: 0.4008 time to fit residues: 340.0471 Evaluate side-chains 310 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 302 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain D residue 167 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 362 HIS A 514 HIS A 587 GLN B 180 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN B 478 HIS ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN B 602 ASN ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 ASN B 811 ASN ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 ASN B1094 HIS B1102 ASN B1104 HIS ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN D 75 HIS D 97 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19802 Z= 0.180 Angle : 0.587 26.562 26886 Z= 0.299 Chirality : 0.056 1.987 3014 Planarity : 0.004 0.061 3345 Dihedral : 12.779 78.214 2913 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 47.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.35 % Allowed : 10.71 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -2.06 (0.16), residues: 2332 helix: -0.55 (0.18), residues: 716 sheet: -1.37 (0.21), residues: 541 loop : -1.87 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 274 HIS 0.004 0.001 HIS A 497 PHE 0.014 0.001 PHE C 7 TYR 0.014 0.001 TYR B 435 ARG 0.006 0.000 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 426 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 358 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 GLN cc_start: 0.8600 (mt0) cc_final: 0.8288 (mp10) REVERT: E 143 GLU cc_start: 0.6279 (tp30) cc_final: 0.6062 (tp30) REVERT: A 212 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.4855 (tptt) REVERT: A 418 ASP cc_start: 0.7471 (t70) cc_final: 0.7157 (t0) REVERT: A 491 ARG cc_start: 0.7022 (mpt180) cc_final: 0.6684 (mpt90) REVERT: A 525 LYS cc_start: 0.7434 (mttt) cc_final: 0.6078 (mmtt) REVERT: B 13 MET cc_start: 0.8278 (ttp) cc_final: 0.7964 (ttm) REVERT: B 34 ASP cc_start: 0.7212 (m-30) cc_final: 0.6701 (m-30) REVERT: B 166 ARG cc_start: 0.6397 (ppt170) cc_final: 0.5871 (tmm-80) REVERT: B 310 MET cc_start: 0.8064 (ttp) cc_final: 0.7799 (ttp) REVERT: B 332 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8396 (tppt) REVERT: B 388 GLU cc_start: 0.8333 (pp20) cc_final: 0.8129 (pt0) REVERT: B 552 TRP cc_start: 0.9050 (t60) cc_final: 0.8748 (t60) REVERT: B 705 LYS cc_start: 0.8690 (tttt) cc_final: 0.8392 (tmtt) REVERT: B 772 ASN cc_start: 0.8540 (t0) cc_final: 0.8162 (t0) REVERT: B 776 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 827 ASP cc_start: 0.9048 (p0) cc_final: 0.8817 (p0) REVERT: B 1099 LYS cc_start: 0.8566 (tptp) cc_final: 0.8151 (tptp) REVERT: B 1103 SER cc_start: 0.6126 (OUTLIER) cc_final: 0.5197 (m) REVERT: C 3 PHE cc_start: 0.7592 (p90) cc_final: 0.7376 (p90) REVERT: C 15 GLN cc_start: 0.8251 (mt0) cc_final: 0.7926 (mm-40) REVERT: C 22 ARG cc_start: 0.8408 (ttm110) cc_final: 0.8177 (ttm-80) REVERT: C 177 VAL cc_start: 0.9096 (t) cc_final: 0.8835 (m) REVERT: D 238 ARG cc_start: 0.7798 (pmt-80) cc_final: 0.7573 (pmt-80) outliers start: 68 outliers final: 43 residues processed: 399 average time/residue: 0.3611 time to fit residues: 210.0317 Evaluate side-chains 310 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 265 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 230 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 58 optimal weight: 0.0050 chunk 212 optimal weight: 0.2980 chunk 229 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 HIS ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19802 Z= 0.216 Angle : 0.571 26.391 26886 Z= 0.285 Chirality : 0.055 1.944 3014 Planarity : 0.004 0.042 3345 Dihedral : 12.509 74.941 2901 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 48.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.95 % Allowed : 13.62 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.28 (0.17), residues: 2332 helix: 0.36 (0.19), residues: 722 sheet: -0.96 (0.22), residues: 549 loop : -1.60 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 274 HIS 0.003 0.001 HIS B1005 PHE 0.015 0.001 PHE B 947 TYR 0.018 0.001 TYR C 231 ARG 0.010 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 359 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 279 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 GLN cc_start: 0.8589 (mt0) cc_final: 0.8279 (mp10) REVERT: A 212 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.5205 (tptt) REVERT: A 418 ASP cc_start: 0.7471 (t70) cc_final: 0.7178 (t0) REVERT: A 525 LYS cc_start: 0.7453 (mttt) cc_final: 0.6106 (mmtt) REVERT: B 7 MET cc_start: 0.8428 (tpp) cc_final: 0.7907 (mmm) REVERT: B 310 MET cc_start: 0.8153 (ttp) cc_final: 0.7886 (ttp) REVERT: B 332 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8440 (tppt) REVERT: B 392 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7598 (mttt) REVERT: B 520 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 552 TRP cc_start: 0.9107 (t60) cc_final: 0.8733 (t60) REVERT: B 663 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8590 (mtmm) REVERT: B 705 LYS cc_start: 0.8793 (tttt) cc_final: 0.8426 (tmtt) REVERT: B 772 ASN cc_start: 0.8414 (t0) cc_final: 0.8119 (t0) REVERT: B 776 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7437 (mt-10) REVERT: B 827 ASP cc_start: 0.8982 (p0) cc_final: 0.8768 (p0) REVERT: B 1082 LEU cc_start: 0.9065 (tt) cc_final: 0.8684 (mt) REVERT: B 1099 LYS cc_start: 0.8615 (tptp) cc_final: 0.8296 (tptp) REVERT: C 15 GLN cc_start: 0.8277 (mt0) cc_final: 0.7896 (mm-40) REVERT: C 22 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8287 (ttm-80) REVERT: C 110 THR cc_start: 0.7561 (m) cc_final: 0.7346 (t) REVERT: C 166 MET cc_start: 0.7704 (mtm) cc_final: 0.7081 (mtm) REVERT: C 177 VAL cc_start: 0.9173 (t) cc_final: 0.8815 (m) outliers start: 80 outliers final: 56 residues processed: 332 average time/residue: 0.3386 time to fit residues: 165.0640 Evaluate side-chains 300 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 240 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19802 Z= 0.261 Angle : 0.585 25.975 26886 Z= 0.291 Chirality : 0.055 1.925 3014 Planarity : 0.004 0.046 3345 Dihedral : 12.451 72.366 2900 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 50.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.39 % Allowed : 14.95 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.05 (0.17), residues: 2332 helix: 0.54 (0.19), residues: 736 sheet: -0.84 (0.21), residues: 583 loop : -1.47 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 274 HIS 0.003 0.001 HIS B1104 PHE 0.017 0.001 PHE B 947 TYR 0.019 0.001 TYR C 231 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 254 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ARG cc_start: 0.6699 (mtm-85) cc_final: 0.6477 (mtm-85) REVERT: A 212 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.5219 (tptt) REVERT: A 513 HIS cc_start: 0.5989 (p-80) cc_final: 0.5675 (p-80) REVERT: B 7 MET cc_start: 0.8529 (tpp) cc_final: 0.7955 (mmm) REVERT: B 310 MET cc_start: 0.8136 (ttp) cc_final: 0.7876 (ttp) REVERT: B 332 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8478 (tppt) REVERT: B 392 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7693 (mttt) REVERT: B 552 TRP cc_start: 0.9153 (t60) cc_final: 0.8739 (t60) REVERT: B 663 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8521 (mtmm) REVERT: B 772 ASN cc_start: 0.8348 (t0) cc_final: 0.7980 (t0) REVERT: B 776 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7476 (mt-10) REVERT: B 1082 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8864 (mt) REVERT: B 1099 LYS cc_start: 0.8543 (tptp) cc_final: 0.8137 (tptp) REVERT: B 1145 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.5432 (pptt) REVERT: C 15 GLN cc_start: 0.8296 (mt0) cc_final: 0.7909 (mm-40) REVERT: C 22 ARG cc_start: 0.8611 (ttm110) cc_final: 0.7603 (ttm-80) outliers start: 89 outliers final: 67 residues processed: 308 average time/residue: 0.3617 time to fit residues: 164.7654 Evaluate side-chains 305 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 233 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1186 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 489 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19802 Z= 0.130 Angle : 0.512 26.074 26886 Z= 0.249 Chirality : 0.054 1.903 3014 Planarity : 0.003 0.041 3345 Dihedral : 12.315 73.131 2900 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 47.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.26 % Allowed : 16.43 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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 (0.18), residues: 2332 helix: 1.16 (0.20), residues: 729 sheet: -0.67 (0.21), residues: 585 loop : -1.17 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 365 HIS 0.003 0.000 HIS B 180 PHE 0.011 0.001 PHE A 309 TYR 0.022 0.001 TYR C 231 ARG 0.003 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 269 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 GLU cc_start: 0.4675 (tt0) cc_final: 0.4313 (tt0) REVERT: E 238 ARG cc_start: 0.7639 (pmt-80) cc_final: 0.7194 (ppt170) REVERT: A 212 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.5307 (tptt) REVERT: A 249 ILE cc_start: 0.7540 (mt) cc_final: 0.7322 (tp) REVERT: A 381 ASN cc_start: 0.7331 (m-40) cc_final: 0.6194 (t0) REVERT: A 513 HIS cc_start: 0.5861 (p-80) cc_final: 0.5587 (p-80) REVERT: A 525 LYS cc_start: 0.7501 (mttt) cc_final: 0.6829 (mttt) REVERT: B 7 MET cc_start: 0.8482 (tpp) cc_final: 0.7915 (mmm) REVERT: B 310 MET cc_start: 0.8093 (ttp) cc_final: 0.7876 (ttp) REVERT: B 392 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7545 (mttt) REVERT: B 663 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8476 (mtmm) REVERT: B 772 ASN cc_start: 0.8342 (t0) cc_final: 0.7963 (t0) REVERT: B 776 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 951 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8364 (ttpp) REVERT: B 953 ARG cc_start: 0.7558 (mmm160) cc_final: 0.7073 (mmm160) REVERT: B 1099 LYS cc_start: 0.8533 (tptp) cc_final: 0.8118 (tptp) REVERT: C 15 GLN cc_start: 0.8265 (mt0) cc_final: 0.7889 (mm-40) outliers start: 66 outliers final: 48 residues processed: 307 average time/residue: 0.3341 time to fit residues: 153.1825 Evaluate side-chains 297 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 245 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 19802 Z= 0.498 Angle : 0.753 26.737 26886 Z= 0.375 Chirality : 0.058 1.892 3014 Planarity : 0.005 0.052 3345 Dihedral : 12.608 66.969 2898 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 60.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.33 % Allowed : 16.18 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.22 (0.17), residues: 2332 helix: 0.20 (0.18), residues: 740 sheet: -0.74 (0.21), residues: 561 loop : -1.54 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 796 HIS 0.006 0.001 HIS B1104 PHE 0.027 0.002 PHE B 947 TYR 0.028 0.002 TYR B 420 ARG 0.005 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 233 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.5384 (tptt) REVERT: B 388 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: B 392 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7891 (mttt) REVERT: B 663 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8664 (mtmm) REVERT: B 772 ASN cc_start: 0.8382 (t0) cc_final: 0.7945 (t0) REVERT: B 776 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 1098 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: B 1145 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5612 (pptt) REVERT: B 1214 MET cc_start: 0.7678 (tpp) cc_final: 0.7408 (tpp) REVERT: C 72 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7570 (p0) outliers start: 108 outliers final: 73 residues processed: 298 average time/residue: 0.3697 time to fit residues: 162.1950 Evaluate side-chains 300 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 220 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1010 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1186 ILE Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 190 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19802 Z= 0.137 Angle : 0.530 25.967 26886 Z= 0.258 Chirality : 0.054 1.879 3014 Planarity : 0.003 0.034 3345 Dihedral : 12.381 71.973 2898 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 51.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.40 % Allowed : 18.25 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -0.59 (0.18), residues: 2332 helix: 0.94 (0.19), residues: 743 sheet: -0.62 (0.22), residues: 569 loop : -1.20 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 609 HIS 0.003 0.001 HIS B 180 PHE 0.012 0.001 PHE A 309 TYR 0.019 0.001 TYR C 231 ARG 0.006 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 252 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 ARG cc_start: 0.7874 (pmt-80) cc_final: 0.7558 (ppt170) REVERT: A 212 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.5346 (tptt) REVERT: A 381 ASN cc_start: 0.7334 (m-40) cc_final: 0.6362 (t0) REVERT: A 525 LYS cc_start: 0.7542 (mttt) cc_final: 0.6626 (mmtt) REVERT: B 7 MET cc_start: 0.8432 (tpp) cc_final: 0.8019 (mmm) REVERT: B 63 ARG cc_start: 0.8800 (tpt170) cc_final: 0.8538 (tpm170) REVERT: B 114 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 392 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7638 (mttt) REVERT: B 663 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8488 (mtmm) REVERT: B 667 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6188 (mmt) REVERT: B 772 ASN cc_start: 0.8355 (t0) cc_final: 0.7966 (t0) REVERT: B 776 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 1099 LYS cc_start: 0.8437 (tptp) cc_final: 0.8185 (tptp) REVERT: B 1145 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5280 (pptt) REVERT: B 1181 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7522 (tm) REVERT: B 1214 MET cc_start: 0.7526 (tpp) cc_final: 0.7242 (tpp) REVERT: D 39 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7531 (mtp-110) outliers start: 69 outliers final: 52 residues processed: 292 average time/residue: 0.3478 time to fit residues: 150.6901 Evaluate side-chains 289 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 21 optimal weight: 0.1980 chunk 177 optimal weight: 0.0970 chunk 205 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 HIS ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19802 Z= 0.118 Angle : 0.511 25.926 26886 Z= 0.247 Chirality : 0.053 1.880 3014 Planarity : 0.003 0.055 3345 Dihedral : 12.244 72.566 2898 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 50.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.47 % Allowed : 19.54 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -0.20 (0.18), residues: 2332 helix: 1.34 (0.20), residues: 737 sheet: -0.46 (0.22), residues: 563 loop : -0.97 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 274 HIS 0.003 0.000 HIS B 180 PHE 0.011 0.001 PHE A 309 TYR 0.021 0.001 TYR C 231 ARG 0.011 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 256 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 ARG cc_start: 0.7791 (pmt-80) cc_final: 0.7442 (ppt170) REVERT: A 212 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.5463 (tptt) REVERT: A 381 ASN cc_start: 0.7299 (m-40) cc_final: 0.6255 (t0) REVERT: A 525 LYS cc_start: 0.7513 (mttt) cc_final: 0.6941 (mttt) REVERT: B 7 MET cc_start: 0.8338 (tpp) cc_final: 0.7958 (mmm) REVERT: B 211 MET cc_start: 0.4611 (mtm) cc_final: 0.3172 (ttp) REVERT: B 392 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7771 (pttm) REVERT: B 663 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8491 (mttp) REVERT: B 772 ASN cc_start: 0.8329 (t0) cc_final: 0.7969 (t0) REVERT: B 776 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7497 (mt-10) REVERT: B 1099 LYS cc_start: 0.8468 (tptp) cc_final: 0.8264 (tptp) REVERT: B 1214 MET cc_start: 0.7531 (tpp) cc_final: 0.7247 (tpp) REVERT: D 39 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7549 (mtp-110) outliers start: 50 outliers final: 37 residues processed: 286 average time/residue: 0.3803 time to fit residues: 161.2600 Evaluate side-chains 283 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 243 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 218 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 210 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19802 Z= 0.126 Angle : 0.501 25.837 26886 Z= 0.242 Chirality : 0.053 1.878 3014 Planarity : 0.003 0.048 3345 Dihedral : 12.151 70.454 2898 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 52.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.37 % Allowed : 19.63 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2332 helix: 1.54 (0.20), residues: 735 sheet: -0.37 (0.22), residues: 580 loop : -0.86 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 274 HIS 0.005 0.001 HIS C 75 PHE 0.013 0.001 PHE A 309 TYR 0.020 0.001 TYR C 231 ARG 0.011 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 258 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 MET cc_start: 0.6612 (ttt) cc_final: 0.6139 (ttt) REVERT: E 238 ARG cc_start: 0.7776 (pmt-80) cc_final: 0.7439 (ppt170) REVERT: A 212 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.5367 (tptt) REVERT: A 381 ASN cc_start: 0.7358 (m-40) cc_final: 0.6312 (t0) REVERT: A 525 LYS cc_start: 0.7511 (mttt) cc_final: 0.6942 (mttt) REVERT: B 7 MET cc_start: 0.8350 (tpp) cc_final: 0.7961 (mmm) REVERT: B 392 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7747 (pttm) REVERT: B 663 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8403 (mttp) REVERT: B 772 ASN cc_start: 0.8299 (t0) cc_final: 0.7931 (t0) REVERT: B 776 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 1145 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.4918 (pptt) REVERT: B 1181 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7474 (tm) REVERT: B 1214 MET cc_start: 0.7536 (tpp) cc_final: 0.7258 (tpp) REVERT: C 15 GLN cc_start: 0.8286 (mt0) cc_final: 0.7939 (mm-40) outliers start: 48 outliers final: 38 residues processed: 292 average time/residue: 0.3654 time to fit residues: 155.5047 Evaluate side-chains 293 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 0.0770 chunk 233 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 143 optimal weight: 0.0970 chunk 113 optimal weight: 0.7980 chunk 147 optimal weight: 0.0670 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19802 Z= 0.146 Angle : 0.510 25.925 26886 Z= 0.247 Chirality : 0.053 1.873 3014 Planarity : 0.003 0.045 3345 Dihedral : 12.065 68.625 2898 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 52.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.37 % Allowed : 19.93 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: 0.08 (0.18), residues: 2332 helix: 1.53 (0.20), residues: 740 sheet: -0.25 (0.22), residues: 573 loop : -0.83 (0.21), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 274 HIS 0.006 0.001 HIS C 75 PHE 0.016 0.001 PHE A 309 TYR 0.021 0.001 TYR C 231 ARG 0.011 0.000 ARG C 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue ILE 121 is missing expected H atoms. Skipping. Residue VAL 123 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 MET cc_start: 0.6568 (ttt) cc_final: 0.6162 (ttt) REVERT: E 73 MET cc_start: 0.7158 (mtp) cc_final: 0.6754 (mtp) REVERT: A 212 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.5412 (tptt) REVERT: A 381 ASN cc_start: 0.7439 (m-40) cc_final: 0.6342 (t0) REVERT: A 525 LYS cc_start: 0.7527 (mttt) cc_final: 0.6956 (mttt) REVERT: B 7 MET cc_start: 0.8405 (tpp) cc_final: 0.8019 (mmm) REVERT: B 83 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: B 211 MET cc_start: 0.4525 (mtm) cc_final: 0.3098 (ttp) REVERT: B 392 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7769 (pttm) REVERT: B 663 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8407 (mttp) REVERT: B 772 ASN cc_start: 0.8306 (t0) cc_final: 0.7932 (t0) REVERT: B 776 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 1145 LYS cc_start: 0.5575 (OUTLIER) cc_final: 0.4925 (pptt) REVERT: B 1181 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7528 (tm) REVERT: B 1214 MET cc_start: 0.7533 (tpp) cc_final: 0.7252 (tpp) REVERT: C 15 GLN cc_start: 0.8260 (mt0) cc_final: 0.7903 (mm-40) outliers start: 48 outliers final: 41 residues processed: 288 average time/residue: 0.3700 time to fit residues: 155.9071 Evaluate side-chains 294 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 685 ARG Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1145 LYS Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 190 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100485 restraints weight = 35906.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098948 restraints weight = 28998.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099865 restraints weight = 30659.190| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19802 Z= 0.234 Angle : 0.563 26.386 26886 Z= 0.275 Chirality : 0.054 1.859 3014 Planarity : 0.003 0.046 3345 Dihedral : 12.136 65.455 2898 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 54.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.76 % Allowed : 19.83 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -0.15 (0.18), residues: 2332 helix: 1.26 (0.19), residues: 744 sheet: -0.32 (0.22), residues: 573 loop : -0.93 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 274 HIS 0.007 0.001 HIS C 75 PHE 0.023 0.001 PHE C 3 TYR 0.021 0.001 TYR C 231 ARG 0.010 0.000 ARG C 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4190.01 seconds wall clock time: 76 minutes 42.03 seconds (4602.03 seconds total)