Starting phenix.real_space_refine on Sun Feb 18 23:45:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usd_26733/02_2024/7usd_26733_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usd_26733/02_2024/7usd_26733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usd_26733/02_2024/7usd_26733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usd_26733/02_2024/7usd_26733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usd_26733/02_2024/7usd_26733_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usd_26733/02_2024/7usd_26733_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 155 5.16 5 C 14794 2.51 5 N 3960 2.21 5 O 4313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 931": "OE1" <-> "OE2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A ARG 1049": "NH1" <-> "NH2" Residue "A GLU 1064": "OE1" <-> "OE2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B GLU 713": "OE1" <-> "OE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B GLU 828": "OE1" <-> "OE2" Residue "B GLU 829": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B ARG 948": "NH1" <-> "NH2" Residue "B GLU 960": "OE1" <-> "OE2" Residue "B GLU 970": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 991": "OE1" <-> "OE2" Residue "B GLU 1057": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23226 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9709 Classifications: {'peptide': 1185} Link IDs: {'PTRANS': 45, 'TRANS': 1139} Chain breaks: 6 Chain: "B" Number of atoms: 8773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8773 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 38, 'TRANS': 1055} Chain breaks: 3 Chain: "C" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1576 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain breaks: 2 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 515 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "F" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1412 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'peptide': 177, 'undetermined': 2} Link IDs: {'PTRANS': 10, 'TRANS': 166, None: 2} Not linked: pdbres="CYS F 178 " pdbres="GTP F 201 " Not linked: pdbres="GTP F 201 " pdbres=" MG F 202 " Time building chain proxies: 12.00, per 1000 atoms: 0.52 Number of scatterers: 23226 At special positions: 0 Unit cell: (141.863, 141.863, 207.541, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 155 16.00 P 3 15.00 Mg 1 11.99 O 4313 8.00 N 3960 7.00 C 14794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.17 Conformation dependent library (CDL) restraints added in 4.1 seconds 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 6 sheets defined 68.4% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 59 through 84 Processing helix chain 'A' and resid 104 through 144 removed outlier: 3.986A pdb=" N TYR A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.724A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 155 through 177 Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.575A pdb=" N LEU A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 234 through 250 Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.628A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.170A pdb=" N ILE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 4.121A pdb=" N LYS A 329 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER A 330 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 384 through 417 Processing helix chain 'A' and resid 434 through 442 removed outlier: 4.573A pdb=" N TYR A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 501 removed outlier: 3.648A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ARG A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Proline residue: A 495 - end of helix Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.541A pdb=" N VAL A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 534 No H-bonds generated for 'chain 'A' and resid 531 through 534' Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.675A pdb=" N LEU A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 583 Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.721A pdb=" N PHE A 600 " --> pdb=" O HIS A 596 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N HIS A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 659 through 663 removed outlier: 4.246A pdb=" N GLU A 662 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 685 through 722 removed outlier: 3.701A pdb=" N LEU A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 764 through 788 Processing helix chain 'A' and resid 792 through 814 removed outlier: 3.986A pdb=" N VAL A 796 " --> pdb=" O THR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 829 Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 892 through 905 removed outlier: 4.414A pdb=" N SER A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TYR A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 924 through 941 Processing helix chain 'A' and resid 944 through 955 removed outlier: 3.549A pdb=" N GLU A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 955 " --> pdb=" O THR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'A' and resid 981 through 985 Processing helix chain 'A' and resid 988 through 990 No H-bonds generated for 'chain 'A' and resid 988 through 990' Processing helix chain 'A' and resid 993 through 1029 Proline residue: A1027 - end of helix Processing helix chain 'A' and resid 1043 through 1053 Processing helix chain 'A' and resid 1055 through 1057 No H-bonds generated for 'chain 'A' and resid 1055 through 1057' Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1069 through 1083 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1093 through 1103 Processing helix chain 'A' and resid 1107 through 1109 No H-bonds generated for 'chain 'A' and resid 1107 through 1109' Processing helix chain 'A' and resid 1127 through 1138 Processing helix chain 'A' and resid 1149 through 1152 No H-bonds generated for 'chain 'A' and resid 1149 through 1152' Processing helix chain 'A' and resid 1156 through 1167 Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1179 through 1190 Processing helix chain 'A' and resid 1201 through 1226 Processing helix chain 'B' and resid 8 through 11 No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.848A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.674A pdb=" N LYS B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 81' Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 117 Processing helix chain 'B' and resid 127 through 149 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.979A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 212 removed outlier: 3.692A pdb=" N SER B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N MET B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 217 No H-bonds generated for 'chain 'B' and resid 214 through 217' Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.944A pdb=" N ASN B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 318 through 359 removed outlier: 5.764A pdb=" N GLY B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.763A pdb=" N GLY B 365 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Proline residue: B 366 - end of helix Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.720A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.585A pdb=" N GLN B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.825A pdb=" N GLU B 476 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 Processing helix chain 'B' and resid 506 through 508 No H-bonds generated for 'chain 'B' and resid 506 through 508' Processing helix chain 'B' and resid 510 through 527 Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 546 through 558 Processing helix chain 'B' and resid 562 through 578 removed outlier: 5.174A pdb=" N ILE B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) Proline residue: B 570 - end of helix removed outlier: 4.245A pdb=" N MET B 577 " --> pdb=" O THR B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 628 removed outlier: 4.344A pdb=" N HIS B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.775A pdb=" N ALA B 634 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS B 635 " --> pdb=" O HIS B 632 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 636 " --> pdb=" O CYS B 633 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN B 642 " --> pdb=" O GLN B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 674 through 691 Processing helix chain 'B' and resid 704 through 724 removed outlier: 4.085A pdb=" N THR B 724 " --> pdb=" O ILE B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 755 removed outlier: 3.554A pdb=" N SER B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 755 " --> pdb=" O GLN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 773 removed outlier: 3.568A pdb=" N GLN B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 Processing helix chain 'B' and resid 797 through 802 removed outlier: 3.507A pdb=" N SER B 801 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 802 " --> pdb=" O ARG B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 802' Processing helix chain 'B' and resid 827 through 829 No H-bonds generated for 'chain 'B' and resid 827 through 829' Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 845 through 882 removed outlier: 3.574A pdb=" N LYS B 868 " --> pdb=" O ALA B 864 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 874 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP B 875 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 876 " --> pdb=" O GLU B 872 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 896 removed outlier: 3.874A pdb=" N ALA B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 895 " --> pdb=" O ALA B 891 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 931 removed outlier: 4.076A pdb=" N LEU B 904 " --> pdb=" O VAL B 900 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR B 930 " --> pdb=" O ASP B 926 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 931 " --> pdb=" O VAL B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 944 Processing helix chain 'B' and resid 952 through 965 removed outlier: 3.893A pdb=" N ASN B 957 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 965 " --> pdb=" O LEU B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 989 through 1012 removed outlier: 3.673A pdb=" N MET B1000 " --> pdb=" O ALA B 996 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B1001 " --> pdb=" O CYS B 997 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B1006 " --> pdb=" O PHE B1002 " (cutoff:3.500A) Proline residue: B1008 - end of helix removed outlier: 4.374A pdb=" N ALA B1011 " --> pdb=" O LEU B1007 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B1012 " --> pdb=" O PRO B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1029 through 1046 removed outlier: 3.705A pdb=" N ALA B1033 " --> pdb=" O HIS B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1071 removed outlier: 3.785A pdb=" N GLN B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1094 removed outlier: 3.660A pdb=" N LEU B1086 " --> pdb=" O GLU B1082 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B1088 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP B1089 " --> pdb=" O TYR B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1106 Processing helix chain 'B' and resid 1109 through 1118 Processing helix chain 'C' and resid 25 through 82 removed outlier: 4.009A pdb=" N ILE C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 93 through 97 removed outlier: 4.223A pdb=" N THR C 96 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.692A pdb=" N THR C 138 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Proline residue: C 139 - end of helix Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 154 through 176 removed outlier: 3.790A pdb=" N PHE C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 160 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 173 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 Processing helix chain 'C' and resid 531 through 541 Processing helix chain 'D' and resid 11 through 68 removed outlier: 3.570A pdb=" N SER D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 12 through 38 removed outlier: 3.686A pdb=" N ILE E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 112 removed outlier: 3.531A pdb=" N LEU E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 25 Processing helix chain 'F' and resid 62 through 71 removed outlier: 3.827A pdb=" N ASP F 65 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Proline residue: F 69 - end of helix Processing helix chain 'F' and resid 87 through 104 removed outlier: 4.157A pdb=" N ARG F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Proline residue: F 99 - end of helix Processing helix chain 'F' and resid 123 through 132 removed outlier: 3.948A pdb=" N LYS F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'F' and resid 166 through 177 Processing sheet with id= A, first strand: chain 'A' and resid 755 through 757 removed outlier: 3.649A pdb=" N VAL A 755 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 855 through 858 removed outlier: 3.524A pdb=" N VAL A 865 " --> pdb=" O CYS A 856 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 304 through 308 removed outlier: 7.175A pdb=" N MET A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 695 through 697 Processing sheet with id= E, first strand: chain 'B' and resid 805 through 808 Processing sheet with id= F, first strand: chain 'F' and resid 109 through 115 removed outlier: 3.573A pdb=" N VAL F 77 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE F 4 " --> pdb=" O PRO F 50 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN F 52 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS F 6 " --> pdb=" O ASN F 52 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY F 54 " --> pdb=" O CYS F 6 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL F 8 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP F 56 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY F 10 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR F 58 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP F 38 " --> pdb=" O ASP F 57 " (cutoff:3.500A) 1335 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4037 1.32 - 1.45: 5953 1.45 - 1.57: 13434 1.57 - 1.69: 5 1.69 - 1.81: 249 Bond restraints: 23678 Sorted by residual: bond pdb=" C ALA F 172 " pdb=" O ALA F 172 " ideal model delta sigma weight residual 1.237 1.298 -0.061 1.17e-02 7.31e+03 2.74e+01 bond pdb=" N MET B 392 " pdb=" CA MET B 392 " ideal model delta sigma weight residual 1.458 1.490 -0.033 7.40e-03 1.83e+04 1.96e+01 bond pdb=" C PRO C 132 " pdb=" O PRO C 132 " ideal model delta sigma weight residual 1.246 1.208 0.037 8.50e-03 1.38e+04 1.92e+01 bond pdb=" C GLU E 27 " pdb=" O GLU E 27 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" C PHE E 20 " pdb=" O PHE E 20 " ideal model delta sigma weight residual 1.237 1.283 -0.047 1.19e-02 7.06e+03 1.54e+01 ... (remaining 23673 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.26: 577 106.26 - 113.24: 12831 113.24 - 120.23: 8919 120.23 - 127.21: 9447 127.21 - 134.19: 220 Bond angle restraints: 31994 Sorted by residual: angle pdb=" C ALA B 235 " pdb=" N PRO B 236 " pdb=" CA PRO B 236 " ideal model delta sigma weight residual 119.28 126.42 -7.14 1.10e+00 8.26e-01 4.21e+01 angle pdb=" N ALA A1025 " pdb=" CA ALA A1025 " pdb=" C ALA A1025 " ideal model delta sigma weight residual 113.20 119.60 -6.40 1.21e+00 6.83e-01 2.80e+01 angle pdb=" N MET C 97 " pdb=" CA MET C 97 " pdb=" C MET C 97 " ideal model delta sigma weight residual 113.01 107.44 5.57 1.20e+00 6.94e-01 2.15e+01 angle pdb=" N ASP E 21 " pdb=" CA ASP E 21 " pdb=" C ASP E 21 " ideal model delta sigma weight residual 111.28 106.42 4.86 1.09e+00 8.42e-01 1.99e+01 angle pdb=" CA VAL A 868 " pdb=" C VAL A 868 " pdb=" O VAL A 868 " ideal model delta sigma weight residual 120.95 116.49 4.46 1.04e+00 9.25e-01 1.84e+01 ... (remaining 31989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.44: 14115 32.44 - 64.89: 334 64.89 - 97.33: 38 97.33 - 129.77: 3 129.77 - 162.22: 2 Dihedral angle restraints: 14492 sinusoidal: 5995 harmonic: 8497 Sorted by residual: dihedral pdb=" C8 GTP F 201 " pdb=" C1' GTP F 201 " pdb=" N9 GTP F 201 " pdb=" O4' GTP F 201 " ideal model delta sinusoidal sigma weight residual 104.59 -57.63 162.22 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O5' GTP F 201 " pdb=" O3A GTP F 201 " pdb=" PA GTP F 201 " pdb=" PB GTP F 201 " ideal model delta sinusoidal sigma weight residual 274.12 142.74 131.39 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" C5' GTP F 201 " pdb=" O5' GTP F 201 " pdb=" PA GTP F 201 " pdb=" O3A GTP F 201 " ideal model delta sinusoidal sigma weight residual 69.27 -54.88 124.15 1 2.00e+01 2.50e-03 3.75e+01 ... (remaining 14489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3257 0.073 - 0.147: 306 0.147 - 0.220: 39 0.220 - 0.293: 10 0.293 - 0.367: 3 Chirality restraints: 3615 Sorted by residual: chirality pdb=" CA THR E 54 " pdb=" N THR E 54 " pdb=" C THR E 54 " pdb=" CB THR E 54 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA LYS E 116 " pdb=" N LYS E 116 " pdb=" C LYS E 116 " pdb=" CB LYS E 116 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CG LEU D 47 " pdb=" CB LEU D 47 " pdb=" CD1 LEU D 47 " pdb=" CD2 LEU D 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3612 not shown) Planarity restraints: 4073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 170 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ASP F 170 " -0.082 2.00e-02 2.50e+03 pdb=" O ASP F 170 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU F 171 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 126 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ASP C 126 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP C 126 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL C 127 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1051 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C ILE B1051 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE B1051 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU B1052 " -0.016 2.00e-02 2.50e+03 ... (remaining 4070 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2524 2.75 - 3.28: 24384 3.28 - 3.82: 39065 3.82 - 4.36: 44905 4.36 - 4.90: 78889 Nonbonded interactions: 189767 Sorted by model distance: nonbonded pdb=" NE ARG A 760 " pdb=" OG1 THR C 116 " model vdw 2.207 2.520 nonbonded pdb=" O ALA F 59 " pdb=" NH1 ARG F 68 " model vdw 2.207 2.520 nonbonded pdb=" O VAL A 992 " pdb=" OD1 ASN A 996 " model vdw 2.233 3.040 nonbonded pdb=" N GLU A 61 " pdb=" OE1 GLU A 61 " model vdw 2.234 2.520 nonbonded pdb=" O SER E 40 " pdb=" NZ LYS E 43 " model vdw 2.244 2.520 ... (remaining 189762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.020 Extract box with map and model: 4.770 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 60.160 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.004 0.061 23678 Z= 0.278 Angle : 0.703 11.916 31994 Z= 0.476 Chirality : 0.046 0.367 3615 Planarity : 0.004 0.051 4073 Dihedral : 14.520 162.218 8958 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.15 % Allowed : 1.04 % Favored : 98.80 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.17), residues: 2830 helix: 3.08 (0.12), residues: 1927 sheet: -0.63 (0.60), residues: 69 loop : 0.43 (0.24), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 845 HIS 0.006 0.001 HIS C 60 PHE 0.013 0.001 PHE C 64 TYR 0.023 0.001 TYR A1138 ARG 0.013 0.001 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 550 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8080 (m-30) cc_final: 0.7848 (m-30) REVERT: A 135 ARG cc_start: 0.7239 (tpp80) cc_final: 0.6623 (ttt-90) REVERT: A 208 GLN cc_start: 0.7704 (tp40) cc_final: 0.7471 (tp40) REVERT: A 279 SER cc_start: 0.8124 (t) cc_final: 0.7806 (p) REVERT: A 333 THR cc_start: 0.8738 (p) cc_final: 0.8489 (t) REVERT: A 422 LYS cc_start: 0.8566 (pttp) cc_final: 0.8316 (pttp) REVERT: A 546 LYS cc_start: 0.7677 (tptt) cc_final: 0.7288 (pttp) REVERT: A 594 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7152 (ttmm) REVERT: A 726 ARG cc_start: 0.7405 (tpp80) cc_final: 0.7133 (tpp80) REVERT: A 988 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 1216 ASP cc_start: 0.7263 (m-30) cc_final: 0.6994 (m-30) REVERT: B 411 TYR cc_start: 0.7504 (m-80) cc_final: 0.7123 (m-80) REVERT: B 458 ILE cc_start: 0.8080 (mm) cc_final: 0.7866 (mm) REVERT: B 462 SER cc_start: 0.8418 (t) cc_final: 0.8068 (p) REVERT: B 552 MET cc_start: 0.8185 (mtt) cc_final: 0.7973 (mtm) REVERT: B 725 MET cc_start: 0.7844 (mmt) cc_final: 0.7444 (mmm) REVERT: B 940 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6778 (mt-10) REVERT: B 1057 GLU cc_start: 0.7303 (tt0) cc_final: 0.6916 (mm-30) REVERT: C 78 VAL cc_start: 0.7072 (p) cc_final: 0.6729 (m) REVERT: C 106 ILE cc_start: 0.8151 (mm) cc_final: 0.7928 (pp) REVERT: C 108 ASP cc_start: 0.8999 (m-30) cc_final: 0.8798 (m-30) REVERT: C 119 ILE cc_start: 0.8169 (mm) cc_final: 0.7464 (mm) REVERT: C 164 LYS cc_start: 0.8018 (tmmt) cc_final: 0.7685 (tmmm) REVERT: C 167 GLN cc_start: 0.6762 (tp40) cc_final: 0.6299 (pp30) REVERT: D 61 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7270 (tp) REVERT: E 49 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7134 (mp0) REVERT: F 35 THR cc_start: 0.7765 (p) cc_final: 0.7559 (p) REVERT: F 90 PHE cc_start: 0.7478 (t80) cc_final: 0.6770 (t80) REVERT: F 91 GLU cc_start: 0.8799 (tp30) cc_final: 0.8413 (tp30) REVERT: F 122 ASP cc_start: 0.8056 (t0) cc_final: 0.7632 (t0) outliers start: 4 outliers final: 5 residues processed: 554 average time/residue: 1.4686 time to fit residues: 918.7307 Evaluate side-chains 359 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 353 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 135 optimal weight: 0.0980 chunk 165 optimal weight: 7.9990 chunk 257 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 505 ASN A 756 GLN B 33 ASN B 199 HIS B 218 ASN B 274 ASN D 18 ASN D 51 ASN E 70 ASN E 71 ASN E 74 GLN F 162 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23678 Z= 0.169 Angle : 0.515 7.476 31994 Z= 0.266 Chirality : 0.038 0.272 3615 Planarity : 0.004 0.043 4073 Dihedral : 6.562 157.588 3155 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.08 % Allowed : 11.11 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.16), residues: 2830 helix: 2.67 (0.12), residues: 1922 sheet: -0.67 (0.52), residues: 77 loop : 0.26 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 698 HIS 0.007 0.001 HIS A 754 PHE 0.015 0.001 PHE B 372 TYR 0.019 0.001 TYR C 125 ARG 0.010 0.001 ARG C 538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 385 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8058 (m-30) cc_final: 0.7762 (m-30) REVERT: A 18 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 127 TYR cc_start: 0.7816 (m-10) cc_final: 0.7513 (m-10) REVERT: A 135 ARG cc_start: 0.7234 (tpp80) cc_final: 0.6711 (ttt-90) REVERT: A 142 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8511 (ttt-90) REVERT: A 150 LYS cc_start: 0.7737 (tptp) cc_final: 0.7481 (pptt) REVERT: A 274 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7353 (mmt) REVERT: A 279 SER cc_start: 0.8082 (t) cc_final: 0.7743 (p) REVERT: A 311 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7173 (ttm) REVERT: A 313 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8337 (tp) REVERT: A 422 LYS cc_start: 0.8683 (pttp) cc_final: 0.8448 (pttp) REVERT: A 546 LYS cc_start: 0.7513 (tptt) cc_final: 0.7186 (pttp) REVERT: A 594 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7293 (ttmm) REVERT: A 610 GLU cc_start: 0.7081 (mp0) cc_final: 0.6834 (mp0) REVERT: A 827 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: A 988 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 1084 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: A 1137 VAL cc_start: 0.8251 (p) cc_final: 0.7944 (m) REVERT: A 1216 ASP cc_start: 0.7362 (m-30) cc_final: 0.7041 (m-30) REVERT: B 152 GLU cc_start: 0.6924 (pp20) cc_final: 0.6547 (pp20) REVERT: B 414 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 462 SER cc_start: 0.8482 (t) cc_final: 0.8155 (p) REVERT: B 725 MET cc_start: 0.7859 (mmt) cc_final: 0.7622 (mmm) REVERT: B 865 GLU cc_start: 0.7749 (tp30) cc_final: 0.7486 (tp30) REVERT: B 940 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6824 (mt-10) REVERT: B 1093 GLN cc_start: 0.8134 (mm110) cc_final: 0.7877 (mm-40) REVERT: C 37 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6979 (mp) REVERT: C 78 VAL cc_start: 0.7150 (p) cc_final: 0.6794 (m) REVERT: C 108 ASP cc_start: 0.9056 (m-30) cc_final: 0.8824 (m-30) REVERT: C 113 ASP cc_start: 0.7746 (m-30) cc_final: 0.7444 (m-30) REVERT: C 164 LYS cc_start: 0.7573 (tmmt) cc_final: 0.7205 (tmmm) REVERT: C 167 GLN cc_start: 0.6653 (tp40) cc_final: 0.6323 (pp30) REVERT: D 65 GLU cc_start: 0.6996 (tt0) cc_final: 0.6635 (mt-10) REVERT: E 34 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7390 (tp30) REVERT: E 36 ASN cc_start: 0.8322 (t0) cc_final: 0.7699 (t160) REVERT: E 39 GLN cc_start: 0.7179 (mp10) cc_final: 0.6865 (mp10) REVERT: E 40 SER cc_start: 0.7746 (t) cc_final: 0.7202 (p) REVERT: F 45 MET cc_start: 0.7061 (tpp) cc_final: 0.6657 (tmm) REVERT: F 66 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7397 (ptt90) REVERT: F 91 GLU cc_start: 0.8793 (tp30) cc_final: 0.8517 (tp30) REVERT: F 122 ASP cc_start: 0.8116 (t0) cc_final: 0.7688 (t0) outliers start: 54 outliers final: 14 residues processed: 412 average time/residue: 1.5828 time to fit residues: 733.9970 Evaluate side-chains 358 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 337 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 155 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 258 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 256 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 505 ASN A 830 HIS A1135 GLN B1047 HIS D 18 ASN D 51 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN E 74 GLN F 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23678 Z= 0.181 Angle : 0.473 6.079 31994 Z= 0.247 Chirality : 0.037 0.143 3615 Planarity : 0.004 0.050 4073 Dihedral : 6.081 158.278 3145 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.66 % Allowed : 13.08 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.16), residues: 2830 helix: 2.61 (0.12), residues: 1918 sheet: -0.62 (0.52), residues: 77 loop : 0.14 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.006 0.001 HIS C 60 PHE 0.017 0.001 PHE A 391 TYR 0.021 0.001 TYR B 930 ARG 0.008 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 365 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 127 TYR cc_start: 0.7828 (m-10) cc_final: 0.7565 (m-10) REVERT: A 135 ARG cc_start: 0.7334 (tpp80) cc_final: 0.6740 (ttt-90) REVERT: A 142 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8501 (ttt-90) REVERT: A 150 LYS cc_start: 0.7723 (tptp) cc_final: 0.7442 (pptt) REVERT: A 274 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7437 (mmt) REVERT: A 279 SER cc_start: 0.8228 (t) cc_final: 0.7840 (p) REVERT: A 546 LYS cc_start: 0.7543 (tptt) cc_final: 0.7170 (pttp) REVERT: A 565 MET cc_start: 0.8029 (mtt) cc_final: 0.7663 (mtm) REVERT: A 594 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7311 (ttmm) REVERT: A 610 GLU cc_start: 0.7201 (mp0) cc_final: 0.6888 (mp0) REVERT: A 726 ARG cc_start: 0.7377 (tpp80) cc_final: 0.7144 (tpp80) REVERT: A 827 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 988 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 1084 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 1216 ASP cc_start: 0.7412 (m-30) cc_final: 0.7114 (m-30) REVERT: B 152 GLU cc_start: 0.6804 (pp20) cc_final: 0.6434 (pp20) REVERT: B 173 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8207 (ptt90) REVERT: B 342 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7907 (mtt-85) REVERT: B 414 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7823 (mm-30) REVERT: B 444 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7647 (pp20) REVERT: B 462 SER cc_start: 0.8543 (t) cc_final: 0.8166 (p) REVERT: B 601 MET cc_start: 0.7902 (tmm) cc_final: 0.7659 (tmt) REVERT: B 763 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6747 (ptp90) REVERT: B 865 GLU cc_start: 0.7738 (tp30) cc_final: 0.7475 (tp30) REVERT: B 940 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6916 (mt-10) REVERT: B 1057 GLU cc_start: 0.7479 (tt0) cc_final: 0.7012 (mm-30) REVERT: B 1093 GLN cc_start: 0.8185 (mm110) cc_final: 0.7936 (mm-40) REVERT: C 37 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.7023 (mp) REVERT: C 78 VAL cc_start: 0.7241 (p) cc_final: 0.6772 (m) REVERT: C 108 ASP cc_start: 0.9044 (m-30) cc_final: 0.8789 (m-30) REVERT: C 113 ASP cc_start: 0.7911 (m-30) cc_final: 0.7541 (m-30) REVERT: C 126 ASP cc_start: 0.8022 (p0) cc_final: 0.7795 (p0) REVERT: C 167 GLN cc_start: 0.6627 (tp40) cc_final: 0.6301 (tm-30) REVERT: D 65 GLU cc_start: 0.7091 (tt0) cc_final: 0.6768 (mt-10) REVERT: E 34 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: E 36 ASN cc_start: 0.8288 (t0) cc_final: 0.7633 (t0) REVERT: E 39 GLN cc_start: 0.7331 (mp10) cc_final: 0.6984 (mp10) REVERT: E 40 SER cc_start: 0.7884 (t) cc_final: 0.7360 (p) REVERT: F 66 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7479 (ptt90) REVERT: F 91 GLU cc_start: 0.8846 (tp30) cc_final: 0.8522 (tp30) REVERT: F 122 ASP cc_start: 0.8263 (t0) cc_final: 0.7929 (t0) outliers start: 69 outliers final: 16 residues processed: 404 average time/residue: 1.6014 time to fit residues: 728.4669 Evaluate side-chains 359 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 333 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 763 ARG Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 274 optimal weight: 7.9990 chunk 135 optimal weight: 0.0570 chunk 245 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 381 GLN A 505 ASN A 884 GLN B 391 ASN B 522 HIS D 51 ASN E 74 GLN F 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23678 Z= 0.284 Angle : 0.525 8.588 31994 Z= 0.272 Chirality : 0.039 0.145 3615 Planarity : 0.004 0.047 4073 Dihedral : 6.130 156.721 3145 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.01 % Allowed : 14.54 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.16), residues: 2830 helix: 2.30 (0.12), residues: 1924 sheet: -0.65 (0.51), residues: 78 loop : -0.05 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 16 HIS 0.004 0.001 HIS B 304 PHE 0.022 0.002 PHE A 391 TYR 0.021 0.001 TYR B 930 ARG 0.008 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 349 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 127 TYR cc_start: 0.7907 (m-10) cc_final: 0.7587 (m-10) REVERT: A 135 ARG cc_start: 0.7421 (tpp80) cc_final: 0.6831 (ttt-90) REVERT: A 211 SER cc_start: 0.8574 (t) cc_final: 0.8002 (m) REVERT: A 262 MET cc_start: 0.7217 (tpp) cc_final: 0.6963 (tpp) REVERT: A 279 SER cc_start: 0.8268 (t) cc_final: 0.7867 (p) REVERT: A 546 LYS cc_start: 0.7480 (tptt) cc_final: 0.7044 (pttp) REVERT: A 565 MET cc_start: 0.8091 (mtt) cc_final: 0.7745 (mtm) REVERT: A 594 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7425 (ttmm) REVERT: A 827 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: A 1084 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 1094 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: A 1216 ASP cc_start: 0.7426 (m-30) cc_final: 0.7149 (m-30) REVERT: B 152 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6820 (pp20) REVERT: B 173 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (ptt90) REVERT: B 342 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7728 (mtt-85) REVERT: B 392 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7538 (tmm) REVERT: B 414 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 462 SER cc_start: 0.8610 (t) cc_final: 0.8205 (p) REVERT: B 865 GLU cc_start: 0.7803 (tp30) cc_final: 0.7573 (tp30) REVERT: B 1057 GLU cc_start: 0.7602 (tt0) cc_final: 0.6999 (mm-30) REVERT: B 1093 GLN cc_start: 0.8220 (mm110) cc_final: 0.7987 (mm-40) REVERT: C 62 PHE cc_start: 0.7064 (t80) cc_final: 0.6840 (m-80) REVERT: C 78 VAL cc_start: 0.7506 (p) cc_final: 0.7147 (m) REVERT: C 99 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.5961 (pttm) REVERT: C 108 ASP cc_start: 0.9020 (m-30) cc_final: 0.8732 (m-30) REVERT: C 113 ASP cc_start: 0.8030 (m-30) cc_final: 0.7658 (m-30) REVERT: C 126 ASP cc_start: 0.8055 (p0) cc_final: 0.7854 (p0) REVERT: C 167 GLN cc_start: 0.6579 (tp40) cc_final: 0.6310 (tm-30) REVERT: D 65 GLU cc_start: 0.7262 (tt0) cc_final: 0.6822 (mt-10) REVERT: E 36 ASN cc_start: 0.8301 (t0) cc_final: 0.7834 (t0) REVERT: E 39 GLN cc_start: 0.7507 (mp10) cc_final: 0.7264 (mp10) REVERT: F 45 MET cc_start: 0.7295 (tpp) cc_final: 0.6627 (tmm) REVERT: F 66 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7573 (ptt90) REVERT: F 91 GLU cc_start: 0.8840 (tp30) cc_final: 0.8528 (tp30) REVERT: F 122 ASP cc_start: 0.8361 (t0) cc_final: 0.7848 (t0) REVERT: F 163 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7587 (ttm110) outliers start: 78 outliers final: 36 residues processed: 394 average time/residue: 1.5126 time to fit residues: 672.4509 Evaluate side-chains 370 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 325 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 132 ARG Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 66 HIS A 205 GLN A 216 ASN A 505 ASN F 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23678 Z= 0.218 Angle : 0.494 10.005 31994 Z= 0.256 Chirality : 0.037 0.145 3615 Planarity : 0.004 0.048 4073 Dihedral : 6.117 159.217 3145 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.93 % Allowed : 15.97 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.16), residues: 2830 helix: 2.34 (0.12), residues: 1913 sheet: -0.65 (0.51), residues: 78 loop : -0.06 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.005 0.001 HIS C 60 PHE 0.019 0.001 PHE A 391 TYR 0.022 0.001 TYR B 930 ARG 0.009 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 336 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 127 TYR cc_start: 0.7859 (m-10) cc_final: 0.7504 (m-10) REVERT: A 135 ARG cc_start: 0.7417 (tpp80) cc_final: 0.6867 (ttt-90) REVERT: A 211 SER cc_start: 0.8535 (t) cc_final: 0.8011 (m) REVERT: A 275 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7547 (t0) REVERT: A 279 SER cc_start: 0.8315 (t) cc_final: 0.7918 (p) REVERT: A 303 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: A 546 LYS cc_start: 0.7487 (tptt) cc_final: 0.7103 (pttp) REVERT: A 565 MET cc_start: 0.8070 (mtt) cc_final: 0.7754 (mtm) REVERT: A 594 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7431 (ttmm) REVERT: A 724 ASP cc_start: 0.8269 (t70) cc_final: 0.7862 (t70) REVERT: A 827 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: A 1058 HIS cc_start: 0.7599 (t-170) cc_final: 0.7293 (t-90) REVERT: A 1084 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: A 1216 ASP cc_start: 0.7411 (m-30) cc_final: 0.7080 (m-30) REVERT: B 152 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6922 (pp20) REVERT: B 173 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8251 (ptt90) REVERT: B 342 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7763 (mtt-85) REVERT: B 392 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7522 (tmm) REVERT: B 414 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 462 SER cc_start: 0.8560 (t) cc_final: 0.8159 (p) REVERT: B 665 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7219 (mmt) REVERT: B 728 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: B 865 GLU cc_start: 0.7740 (tp30) cc_final: 0.7483 (tp30) REVERT: B 1057 GLU cc_start: 0.7592 (tt0) cc_final: 0.6978 (mm-30) REVERT: B 1093 GLN cc_start: 0.8237 (mm110) cc_final: 0.8015 (mm-40) REVERT: C 62 PHE cc_start: 0.7076 (t80) cc_final: 0.6822 (m-80) REVERT: C 78 VAL cc_start: 0.7426 (p) cc_final: 0.7045 (m) REVERT: C 86 LYS cc_start: 0.7524 (mmtm) cc_final: 0.7256 (mmmt) REVERT: C 99 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.5925 (pttm) REVERT: C 108 ASP cc_start: 0.9021 (m-30) cc_final: 0.8734 (m-30) REVERT: D 61 ILE cc_start: 0.7802 (tp) cc_final: 0.7528 (tt) REVERT: D 65 GLU cc_start: 0.7270 (tt0) cc_final: 0.6896 (mt-10) REVERT: E 36 ASN cc_start: 0.8319 (t0) cc_final: 0.7885 (t0) REVERT: E 39 GLN cc_start: 0.7483 (mp10) cc_final: 0.7210 (mp10) REVERT: E 98 ASP cc_start: 0.7702 (t0) cc_final: 0.7366 (m-30) REVERT: F 45 MET cc_start: 0.7265 (tpp) cc_final: 0.6694 (tmm) REVERT: F 66 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7515 (ptt90) REVERT: F 91 GLU cc_start: 0.8836 (tp30) cc_final: 0.8490 (tp30) REVERT: F 122 ASP cc_start: 0.8405 (t0) cc_final: 0.8023 (t0) REVERT: F 163 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7613 (ttm110) outliers start: 76 outliers final: 36 residues processed: 379 average time/residue: 1.6274 time to fit residues: 694.8810 Evaluate side-chains 376 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 328 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 127 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 274 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 0.0270 chunk 144 optimal weight: 0.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 505 ASN A 884 GLN B 218 ASN F 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23678 Z= 0.163 Angle : 0.478 10.468 31994 Z= 0.246 Chirality : 0.036 0.143 3615 Planarity : 0.004 0.048 4073 Dihedral : 6.072 162.140 3145 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.58 % Allowed : 16.47 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.16), residues: 2830 helix: 2.43 (0.12), residues: 1917 sheet: -0.57 (0.52), residues: 78 loop : -0.01 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.005 0.001 HIS C 60 PHE 0.017 0.001 PHE A 391 TYR 0.022 0.001 TYR B 930 ARG 0.011 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 341 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 127 TYR cc_start: 0.7845 (m-10) cc_final: 0.7494 (m-10) REVERT: A 135 ARG cc_start: 0.7368 (tpp80) cc_final: 0.6880 (ttt-90) REVERT: A 190 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5689 (mpp80) REVERT: A 211 SER cc_start: 0.8482 (t) cc_final: 0.7989 (m) REVERT: A 279 SER cc_start: 0.8322 (t) cc_final: 0.7921 (p) REVERT: A 303 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: A 362 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7681 (tm-30) REVERT: A 546 LYS cc_start: 0.7458 (tptt) cc_final: 0.7038 (pttp) REVERT: A 565 MET cc_start: 0.8051 (mtt) cc_final: 0.7763 (mtm) REVERT: A 594 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7418 (ttmm) REVERT: A 724 ASP cc_start: 0.8201 (t70) cc_final: 0.7792 (t70) REVERT: A 726 ARG cc_start: 0.7400 (tpp80) cc_final: 0.7171 (tpp80) REVERT: A 827 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: A 876 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6411 (mt0) REVERT: A 1084 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 1216 ASP cc_start: 0.7365 (m-30) cc_final: 0.7080 (m-30) REVERT: B 152 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6978 (pp20) REVERT: B 173 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8239 (ptt90) REVERT: B 342 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7778 (mtt-85) REVERT: B 414 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7920 (mm-30) REVERT: B 462 SER cc_start: 0.8545 (t) cc_final: 0.8146 (p) REVERT: B 728 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: B 865 GLU cc_start: 0.7748 (tp30) cc_final: 0.7479 (tp30) REVERT: B 1057 GLU cc_start: 0.7611 (tt0) cc_final: 0.7033 (mm-30) REVERT: B 1093 GLN cc_start: 0.8242 (mm110) cc_final: 0.8005 (mm-40) REVERT: C 62 PHE cc_start: 0.7065 (t80) cc_final: 0.6857 (m-80) REVERT: C 78 VAL cc_start: 0.7354 (p) cc_final: 0.6945 (m) REVERT: C 86 LYS cc_start: 0.7537 (mmtm) cc_final: 0.7158 (mmmm) REVERT: C 99 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6082 (pttm) REVERT: C 108 ASP cc_start: 0.9006 (m-30) cc_final: 0.8716 (m-30) REVERT: C 538 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5428 (tpt90) REVERT: D 61 ILE cc_start: 0.7765 (tp) cc_final: 0.7506 (tt) REVERT: D 65 GLU cc_start: 0.7210 (tt0) cc_final: 0.6844 (mt-10) REVERT: E 36 ASN cc_start: 0.8313 (t0) cc_final: 0.7899 (t0) REVERT: E 39 GLN cc_start: 0.7486 (mp10) cc_final: 0.7125 (mp10) REVERT: F 45 MET cc_start: 0.7307 (tpp) cc_final: 0.6760 (tmm) REVERT: F 66 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7427 (ptt90) REVERT: F 91 GLU cc_start: 0.8819 (tp30) cc_final: 0.8500 (tp30) REVERT: F 122 ASP cc_start: 0.8379 (t0) cc_final: 0.7949 (t0) REVERT: F 163 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7591 (ttm110) outliers start: 67 outliers final: 29 residues processed: 378 average time/residue: 1.5671 time to fit residues: 669.2574 Evaluate side-chains 367 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 326 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 127 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 273 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 216 ASN A 381 GLN A 884 GLN F 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23678 Z= 0.222 Angle : 0.507 10.240 31994 Z= 0.260 Chirality : 0.037 0.141 3615 Planarity : 0.004 0.048 4073 Dihedral : 6.054 158.856 3145 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.78 % Allowed : 17.01 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.16), residues: 2830 helix: 2.35 (0.12), residues: 1916 sheet: -0.63 (0.51), residues: 78 loop : -0.06 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.004 0.001 HIS A1058 PHE 0.019 0.001 PHE A 391 TYR 0.023 0.001 TYR A 688 ARG 0.010 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 335 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7828 (m-10) cc_final: 0.7516 (m-10) REVERT: A 135 ARG cc_start: 0.7413 (tpp80) cc_final: 0.6912 (ttt-90) REVERT: A 190 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.5729 (mpp80) REVERT: A 211 SER cc_start: 0.8522 (t) cc_final: 0.8070 (m) REVERT: A 279 SER cc_start: 0.8333 (t) cc_final: 0.7921 (p) REVERT: A 297 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6844 (mttp) REVERT: A 303 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: A 362 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7694 (tm-30) REVERT: A 546 LYS cc_start: 0.7468 (tptt) cc_final: 0.7038 (pttp) REVERT: A 565 MET cc_start: 0.8102 (mtt) cc_final: 0.7805 (mtm) REVERT: A 594 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7450 (ttmm) REVERT: A 724 ASP cc_start: 0.8302 (t70) cc_final: 0.7864 (t70) REVERT: A 827 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: A 876 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6501 (mt0) REVERT: A 1058 HIS cc_start: 0.7588 (t-170) cc_final: 0.7346 (t-90) REVERT: A 1084 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 1216 ASP cc_start: 0.7385 (m-30) cc_final: 0.7134 (m-30) REVERT: B 152 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7032 (pp20) REVERT: B 173 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8244 (ptt90) REVERT: B 342 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7730 (mtt-85) REVERT: B 392 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7261 (tmm) REVERT: B 414 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7796 (mm-30) REVERT: B 462 SER cc_start: 0.8557 (t) cc_final: 0.8146 (p) REVERT: B 665 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7277 (mmt) REVERT: B 728 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: B 865 GLU cc_start: 0.7794 (tp30) cc_final: 0.7530 (tp30) REVERT: B 1057 GLU cc_start: 0.7607 (tt0) cc_final: 0.6968 (mm-30) REVERT: B 1069 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6997 (mp) REVERT: C 62 PHE cc_start: 0.7045 (t80) cc_final: 0.6840 (m-80) REVERT: C 78 VAL cc_start: 0.7452 (p) cc_final: 0.7043 (m) REVERT: C 86 LYS cc_start: 0.7530 (mmtm) cc_final: 0.7147 (mmmm) REVERT: C 99 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6042 (pttm) REVERT: C 108 ASP cc_start: 0.8992 (m-30) cc_final: 0.8709 (m-30) REVERT: C 126 ASP cc_start: 0.8035 (p0) cc_final: 0.7826 (p0) REVERT: C 538 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5464 (tpt90) REVERT: D 61 ILE cc_start: 0.7806 (tp) cc_final: 0.7535 (tt) REVERT: D 65 GLU cc_start: 0.7265 (tt0) cc_final: 0.6879 (mt-10) REVERT: E 36 ASN cc_start: 0.8289 (t0) cc_final: 0.7900 (t0) REVERT: E 39 GLN cc_start: 0.7471 (mp10) cc_final: 0.7199 (mp10) REVERT: E 98 ASP cc_start: 0.7357 (m-30) cc_final: 0.7088 (m-30) REVERT: F 66 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7411 (ptt90) REVERT: F 91 GLU cc_start: 0.8815 (tp30) cc_final: 0.8490 (tp30) REVERT: F 122 ASP cc_start: 0.8496 (t0) cc_final: 0.8168 (t0) REVERT: F 163 ARG cc_start: 0.7891 (ttp-110) cc_final: 0.7568 (ttm110) outliers start: 72 outliers final: 35 residues processed: 377 average time/residue: 1.5688 time to fit residues: 669.6710 Evaluate side-chains 375 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 324 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1227 LYS Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 127 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 884 GLN A1012 GLN F 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23678 Z= 0.179 Angle : 0.499 11.084 31994 Z= 0.254 Chirality : 0.036 0.142 3615 Planarity : 0.004 0.048 4073 Dihedral : 6.004 160.424 3141 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.62 % Allowed : 17.63 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.16), residues: 2830 helix: 2.42 (0.12), residues: 1909 sheet: -0.65 (0.52), residues: 78 loop : -0.07 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.005 0.001 HIS C 60 PHE 0.017 0.001 PHE A 391 TYR 0.024 0.001 TYR A 688 ARG 0.010 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 329 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7855 (m-10) cc_final: 0.7532 (m-10) REVERT: A 135 ARG cc_start: 0.7407 (tpp80) cc_final: 0.6862 (ttt-90) REVERT: A 142 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8525 (ttt-90) REVERT: A 211 SER cc_start: 0.8475 (t) cc_final: 0.8023 (m) REVERT: A 279 SER cc_start: 0.8336 (t) cc_final: 0.7968 (p) REVERT: A 303 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: A 362 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7774 (tm-30) REVERT: A 528 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: A 546 LYS cc_start: 0.7454 (tptt) cc_final: 0.7028 (pttp) REVERT: A 565 MET cc_start: 0.8116 (mtt) cc_final: 0.7826 (mtm) REVERT: A 594 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7430 (ttmm) REVERT: A 724 ASP cc_start: 0.8289 (t70) cc_final: 0.7874 (t70) REVERT: A 827 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: A 1058 HIS cc_start: 0.7583 (t-170) cc_final: 0.7327 (t-90) REVERT: A 1084 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 1216 ASP cc_start: 0.7378 (m-30) cc_final: 0.7116 (m-30) REVERT: B 152 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7055 (pp20) REVERT: B 173 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8225 (ptt90) REVERT: B 342 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: B 392 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7324 (tmm) REVERT: B 462 SER cc_start: 0.8554 (t) cc_final: 0.8144 (p) REVERT: B 728 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: B 865 GLU cc_start: 0.7741 (tp30) cc_final: 0.7467 (tp30) REVERT: B 1057 GLU cc_start: 0.7619 (tt0) cc_final: 0.6994 (mm-30) REVERT: B 1069 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6910 (mp) REVERT: C 62 PHE cc_start: 0.7137 (t80) cc_final: 0.6845 (m-80) REVERT: C 78 VAL cc_start: 0.7387 (p) cc_final: 0.6968 (m) REVERT: C 86 LYS cc_start: 0.7547 (mmtm) cc_final: 0.7162 (mmmm) REVERT: C 99 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6156 (pttm) REVERT: C 108 ASP cc_start: 0.8986 (m-30) cc_final: 0.8696 (m-30) REVERT: C 538 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5549 (tpt90) REVERT: D 61 ILE cc_start: 0.7793 (tp) cc_final: 0.7555 (tt) REVERT: D 65 GLU cc_start: 0.7267 (tt0) cc_final: 0.6885 (mt-10) REVERT: E 36 ASN cc_start: 0.8272 (t0) cc_final: 0.7914 (t0) REVERT: E 39 GLN cc_start: 0.7494 (mp10) cc_final: 0.7229 (mp10) REVERT: F 45 MET cc_start: 0.7375 (tpp) cc_final: 0.6752 (tmm) REVERT: F 66 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7387 (ptt90) REVERT: F 91 GLU cc_start: 0.8864 (tp30) cc_final: 0.8550 (tp30) REVERT: F 122 ASP cc_start: 0.8469 (t0) cc_final: 0.8147 (t0) REVERT: F 163 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7574 (ttm110) outliers start: 68 outliers final: 34 residues processed: 370 average time/residue: 1.5085 time to fit residues: 631.6296 Evaluate side-chains 371 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 324 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1227 LYS Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 127 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 4.9990 chunk 239 optimal weight: 0.5980 chunk 255 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 241 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 167 optimal weight: 0.0050 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 884 GLN F 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23678 Z= 0.188 Angle : 0.510 13.051 31994 Z= 0.258 Chirality : 0.036 0.141 3615 Planarity : 0.004 0.048 4073 Dihedral : 5.987 159.708 3141 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.47 % Allowed : 17.98 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.16), residues: 2830 helix: 2.39 (0.12), residues: 1913 sheet: -0.65 (0.52), residues: 78 loop : -0.05 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.005 0.001 HIS C 60 PHE 0.018 0.001 PHE A 391 TYR 0.024 0.001 TYR B 930 ARG 0.009 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 330 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7886 (m-10) cc_final: 0.7523 (m-10) REVERT: A 135 ARG cc_start: 0.7377 (tpp80) cc_final: 0.6893 (ttt-90) REVERT: A 142 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8458 (ttt-90) REVERT: A 211 SER cc_start: 0.8453 (t) cc_final: 0.8018 (m) REVERT: A 279 SER cc_start: 0.8338 (t) cc_final: 0.7974 (p) REVERT: A 303 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7285 (mt0) REVERT: A 362 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7753 (tm-30) REVERT: A 546 LYS cc_start: 0.7445 (tptt) cc_final: 0.7006 (pttp) REVERT: A 565 MET cc_start: 0.8116 (mtt) cc_final: 0.7828 (mtm) REVERT: A 594 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7439 (ttmm) REVERT: A 724 ASP cc_start: 0.8295 (t70) cc_final: 0.7888 (t70) REVERT: A 726 ARG cc_start: 0.7393 (tpp80) cc_final: 0.7170 (tpp80) REVERT: A 827 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: A 876 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6420 (mt0) REVERT: A 1058 HIS cc_start: 0.7578 (t-170) cc_final: 0.7330 (t-90) REVERT: A 1084 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: A 1216 ASP cc_start: 0.7375 (m-30) cc_final: 0.7109 (m-30) REVERT: B 152 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7004 (pp20) REVERT: B 173 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8251 (ptt90) REVERT: B 342 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7740 (mtt-85) REVERT: B 392 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7284 (tmm) REVERT: B 414 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 462 SER cc_start: 0.8530 (t) cc_final: 0.8121 (p) REVERT: B 728 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: B 824 THR cc_start: 0.8407 (p) cc_final: 0.7970 (t) REVERT: B 865 GLU cc_start: 0.7746 (tp30) cc_final: 0.7481 (tp30) REVERT: B 1057 GLU cc_start: 0.7629 (tt0) cc_final: 0.6996 (mm-30) REVERT: B 1069 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6880 (mp) REVERT: C 62 PHE cc_start: 0.7130 (t80) cc_final: 0.6840 (m-80) REVERT: C 78 VAL cc_start: 0.7373 (p) cc_final: 0.6956 (m) REVERT: C 86 LYS cc_start: 0.7522 (mmtm) cc_final: 0.7141 (mmmm) REVERT: C 99 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6091 (pttm) REVERT: C 108 ASP cc_start: 0.8985 (m-30) cc_final: 0.8694 (m-30) REVERT: C 176 LYS cc_start: 0.4728 (OUTLIER) cc_final: 0.4489 (tttm) REVERT: C 538 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5537 (tpt90) REVERT: D 61 ILE cc_start: 0.7788 (tp) cc_final: 0.7551 (tt) REVERT: D 65 GLU cc_start: 0.7264 (tt0) cc_final: 0.6872 (mt-10) REVERT: E 36 ASN cc_start: 0.8234 (t0) cc_final: 0.7893 (t0) REVERT: E 39 GLN cc_start: 0.7509 (mp10) cc_final: 0.7242 (mp10) REVERT: F 45 MET cc_start: 0.7344 (tpp) cc_final: 0.6721 (tmm) REVERT: F 66 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7385 (ptt90) REVERT: F 90 PHE cc_start: 0.7831 (t80) cc_final: 0.7050 (t80) REVERT: F 91 GLU cc_start: 0.8810 (tp30) cc_final: 0.8501 (tp30) REVERT: F 122 ASP cc_start: 0.8484 (t0) cc_final: 0.8145 (t0) REVERT: F 137 ILE cc_start: 0.8773 (mm) cc_final: 0.8296 (mm) REVERT: F 163 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.7570 (ttm110) outliers start: 64 outliers final: 35 residues processed: 370 average time/residue: 1.5447 time to fit residues: 648.3780 Evaluate side-chains 375 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 326 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 884 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 127 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 282 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN F 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23678 Z= 0.194 Angle : 0.526 12.396 31994 Z= 0.265 Chirality : 0.037 0.141 3615 Planarity : 0.004 0.048 4073 Dihedral : 5.980 159.182 3141 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.28 % Allowed : 18.29 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.16), residues: 2830 helix: 2.39 (0.12), residues: 1906 sheet: -0.65 (0.52), residues: 78 loop : -0.03 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.006 0.001 HIS C 60 PHE 0.018 0.001 PHE A 391 TYR 0.025 0.001 TYR B 930 ARG 0.010 0.000 ARG B 547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 326 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7911 (m-10) cc_final: 0.7518 (m-10) REVERT: A 135 ARG cc_start: 0.7384 (tpp80) cc_final: 0.6895 (ttt-90) REVERT: A 142 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8456 (ttt-90) REVERT: A 211 SER cc_start: 0.8460 (t) cc_final: 0.8009 (m) REVERT: A 279 SER cc_start: 0.8333 (t) cc_final: 0.7964 (p) REVERT: A 303 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7282 (mt0) REVERT: A 362 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7728 (tm-30) REVERT: A 546 LYS cc_start: 0.7443 (tptt) cc_final: 0.7005 (pttp) REVERT: A 565 MET cc_start: 0.8104 (mtt) cc_final: 0.7816 (mtm) REVERT: A 594 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7440 (ttmm) REVERT: A 724 ASP cc_start: 0.8296 (t70) cc_final: 0.7885 (t70) REVERT: A 726 ARG cc_start: 0.7394 (tpp80) cc_final: 0.7173 (tpp80) REVERT: A 827 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: A 876 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6436 (mt0) REVERT: A 1058 HIS cc_start: 0.7580 (t-170) cc_final: 0.7346 (t-90) REVERT: A 1216 ASP cc_start: 0.7365 (m-30) cc_final: 0.7114 (m-30) REVERT: B 152 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7028 (pp20) REVERT: B 173 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8245 (ptt90) REVERT: B 342 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7765 (mtt-85) REVERT: B 392 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7285 (tmm) REVERT: B 462 SER cc_start: 0.8526 (t) cc_final: 0.8118 (p) REVERT: B 525 MET cc_start: 0.8079 (tpp) cc_final: 0.7775 (mmp) REVERT: B 665 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7292 (mmt) REVERT: B 728 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: B 824 THR cc_start: 0.8408 (p) cc_final: 0.7974 (t) REVERT: B 865 GLU cc_start: 0.7750 (tp30) cc_final: 0.7485 (tp30) REVERT: B 1057 GLU cc_start: 0.7628 (tt0) cc_final: 0.6996 (mm-30) REVERT: B 1069 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6842 (mp) REVERT: C 62 PHE cc_start: 0.7159 (t80) cc_final: 0.6870 (m-80) REVERT: C 78 VAL cc_start: 0.7414 (p) cc_final: 0.7039 (m) REVERT: C 86 LYS cc_start: 0.7500 (mmtm) cc_final: 0.7209 (mmmt) REVERT: C 108 ASP cc_start: 0.8983 (m-30) cc_final: 0.8693 (m-30) REVERT: C 176 LYS cc_start: 0.4701 (OUTLIER) cc_final: 0.4454 (tttm) REVERT: C 538 ARG cc_start: 0.6148 (OUTLIER) cc_final: 0.5567 (tpt90) REVERT: D 61 ILE cc_start: 0.7784 (tp) cc_final: 0.7551 (tt) REVERT: D 65 GLU cc_start: 0.7273 (tt0) cc_final: 0.6811 (mt-10) REVERT: E 36 ASN cc_start: 0.8227 (t0) cc_final: 0.7876 (t0) REVERT: E 39 GLN cc_start: 0.7490 (mp10) cc_final: 0.7229 (mp10) REVERT: F 45 MET cc_start: 0.7369 (tpp) cc_final: 0.6740 (tmm) REVERT: F 66 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7391 (ptt90) REVERT: F 90 PHE cc_start: 0.7829 (t80) cc_final: 0.7093 (t80) REVERT: F 91 GLU cc_start: 0.8814 (tp30) cc_final: 0.8503 (tp30) REVERT: F 122 ASP cc_start: 0.8467 (t0) cc_final: 0.8115 (t0) REVERT: F 137 ILE cc_start: 0.8782 (mm) cc_final: 0.8318 (mm) REVERT: F 163 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7546 (ttm110) outliers start: 59 outliers final: 36 residues processed: 360 average time/residue: 1.5170 time to fit residues: 617.8519 Evaluate side-chains 371 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 322 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 884 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 543 TYR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 127 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 225 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN F 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.089689 restraints weight = 35581.728| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.73 r_work: 0.3067 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23678 Z= 0.182 Angle : 0.520 12.176 31994 Z= 0.262 Chirality : 0.036 0.140 3615 Planarity : 0.004 0.048 4073 Dihedral : 5.975 159.702 3141 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.12 % Allowed : 18.60 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2830 helix: 2.41 (0.12), residues: 1906 sheet: -0.62 (0.52), residues: 78 loop : -0.03 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.006 0.001 HIS C 60 PHE 0.017 0.001 PHE A 391 TYR 0.025 0.001 TYR B 930 ARG 0.010 0.000 ARG B 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10150.95 seconds wall clock time: 180 minutes 25.59 seconds (10825.59 seconds total)