Starting phenix.real_space_refine on Mon Apr 8 13:44:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ty8_20581/04_2024/6ty8_20581_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= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 53 5.16 5 C 8653 2.51 5 N 2323 2.21 5 O 2575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 147": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "A ARG 1175": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13607 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9571 Classifications: {'peptide': 1196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 1155} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3985 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 479} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.49, per 1000 atoms: 0.55 Number of scatterers: 13607 At special positions: 0 Unit cell: (105.138, 147.618, 88.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 3 15.00 O 2575 8.00 N 2323 7.00 C 8653 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: 5.33 Conformation dependent library (CDL) restraints added in 2.0 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 15 sheets defined 44.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 20 through 33 removed outlier: 3.637A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 145 through 160 removed outlier: 3.540A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.857A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.728A pdb=" N GLN A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.366A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 321 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.836A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 removed outlier: 4.092A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 501 through 512 removed outlier: 4.407A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.691A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.959A pdb=" N ALA A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 666 removed outlier: 3.749A pdb=" N HIS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.546A pdb=" N LEU A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 753 through 766 Processing helix chain 'A' and resid 774 through 787 Processing helix chain 'A' and resid 798 through 810 removed outlier: 3.669A pdb=" N TYR A 801 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 802 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 803 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 808 " --> pdb=" O TYR A 805 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A 809 " --> pdb=" O ASN A 806 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 810 " --> pdb=" O ASN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.544A pdb=" N LEU A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 878 removed outlier: 3.557A pdb=" N LYS A 871 " --> pdb=" O GLY A 868 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 874 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 878 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 887 removed outlier: 3.918A pdb=" N GLN A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 902 through 910 Processing helix chain 'A' and resid 919 through 923 Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 943 through 958 Processing helix chain 'A' and resid 971 through 979 removed outlier: 3.775A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1006 Processing helix chain 'A' and resid 1015 through 1020 removed outlier: 3.750A pdb=" N ALA A1018 " --> pdb=" O PRO A1015 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1019 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1037 No H-bonds generated for 'chain 'A' and resid 1035 through 1037' Processing helix chain 'A' and resid 1039 through 1041 No H-bonds generated for 'chain 'A' and resid 1039 through 1041' Processing helix chain 'A' and resid 1054 through 1061 Processing helix chain 'A' and resid 1067 through 1080 removed outlier: 3.599A pdb=" N LEU A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 4.667A pdb=" N ASN A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1134 removed outlier: 3.709A pdb=" N GLY A1122 " --> pdb=" O PRO A1118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1161 removed outlier: 3.518A pdb=" N ALA A1158 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG A1160 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1161 " --> pdb=" O ALA A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1171 No H-bonds generated for 'chain 'A' and resid 1168 through 1171' Processing helix chain 'A' and resid 1175 through 1188 Processing helix chain 'A' and resid 1204 through 1212 removed outlier: 3.889A pdb=" N GLY A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1218 No H-bonds generated for 'chain 'A' and resid 1215 through 1218' Processing helix chain 'B' and resid 10 through 13 No H-bonds generated for 'chain 'B' and resid 10 through 13' Processing helix chain 'B' and resid 44 through 62 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 162 through 165 No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.773A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.854A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 374 removed outlier: 4.154A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 4.068A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 417 through 428 Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 442 through 460 removed outlier: 3.631A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.733A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.700A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 54 through 58 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.571A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 477 through 479 removed outlier: 3.775A pdb=" N VAL A 477 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 541 through 547 removed outlier: 3.916A pdb=" N THR A 674 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN A 687 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 672 " --> pdb=" O GLN A 687 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 585 through 590 Processing sheet with id= F, first strand: chain 'A' and resid 622 through 624 Processing sheet with id= G, first strand: chain 'A' and resid 719 through 721 Processing sheet with id= H, first strand: chain 'A' and resid 992 through 994 removed outlier: 3.993A pdb=" N LYS A 992 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 797 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 831 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1022 through 1026 Processing sheet with id= J, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.707A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.450A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 157 through 159 removed outlier: 5.955A pdb=" N HIS B 182 " --> pdb=" O ILE B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 204 through 208 Processing sheet with id= N, first strand: chain 'B' and resid 297 through 299 removed outlier: 6.035A pdb=" N THR B 261 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 313 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 543 through 546 removed outlier: 4.333A pdb=" N THR B 543 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 485 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL B 351 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 487 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1314 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: 4.32 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2227 1.31 - 1.43: 3836 1.43 - 1.56: 7737 1.56 - 1.68: 9 1.68 - 1.81: 94 Bond restraints: 13903 Sorted by residual: bond pdb=" C1A GTA A1301 " pdb=" O4A GTA A1301 " ideal model delta sigma weight residual 1.591 1.293 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C3B GTA A1301 " pdb=" C4B GTA A1301 " ideal model delta sigma weight residual 1.275 1.545 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C1A GTA A1301 " pdb=" C2A GTA A1301 " ideal model delta sigma weight residual 1.325 1.574 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C4B GTA A1301 " pdb=" O4B GTA A1301 " ideal model delta sigma weight residual 1.556 1.309 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C3B GTA A1301 " pdb=" O3B GTA A1301 " ideal model delta sigma weight residual 1.482 1.358 0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 13898 not shown) Histogram of bond angle deviations from ideal: 97.84 - 106.69: 353 106.69 - 115.54: 8378 115.54 - 124.39: 9884 124.39 - 133.24: 208 133.24 - 142.09: 19 Bond angle restraints: 18842 Sorted by residual: angle pdb=" N GLU A1138 " pdb=" CA GLU A1138 " pdb=" C GLU A1138 " ideal model delta sigma weight residual 110.24 120.83 -10.59 1.41e+00 5.03e-01 5.64e+01 angle pdb=" N ILE B 498 " pdb=" CA ILE B 498 " pdb=" C ILE B 498 " ideal model delta sigma weight residual 106.88 117.60 -10.72 1.52e+00 4.33e-01 4.97e+01 angle pdb=" N THR B 497 " pdb=" CA THR B 497 " pdb=" C THR B 497 " ideal model delta sigma weight residual 111.36 118.76 -7.40 1.09e+00 8.42e-01 4.61e+01 angle pdb=" C1B GTA A1301 " pdb=" N9C GTA A1301 " pdb=" C4C GTA A1301 " ideal model delta sigma weight residual 121.43 140.70 -19.27 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C1A GTA A1301 " pdb=" N9 GTA A1301 " pdb=" C4 GTA A1301 " ideal model delta sigma weight residual 114.98 133.36 -18.38 3.00e+00 1.11e-01 3.76e+01 ... (remaining 18837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8014 17.95 - 35.90: 254 35.90 - 53.84: 48 53.84 - 71.79: 5 71.79 - 89.74: 3 Dihedral angle restraints: 8324 sinusoidal: 3334 harmonic: 4990 Sorted by residual: dihedral pdb=" CA THR A 347 " pdb=" C THR A 347 " pdb=" N LEU A 348 " pdb=" CA LEU A 348 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA LEU A 767 " pdb=" C LEU A 767 " pdb=" N LEU A 768 " pdb=" CA LEU A 768 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ILE A 249 " pdb=" C ILE A 249 " pdb=" N LYS A 250 " pdb=" CA LYS A 250 " ideal model delta harmonic sigma weight residual 180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 8321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1872 0.083 - 0.165: 210 0.165 - 0.248: 13 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CA ASP A 483 " pdb=" N ASP A 483 " pdb=" C ASP A 483 " pdb=" CB ASP A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB VAL A 548 " pdb=" CA VAL A 548 " pdb=" CG1 VAL A 548 " pdb=" CG2 VAL A 548 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 2098 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " -0.025 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP A 606 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 363 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C GLN A 363 " 0.054 2.00e-02 2.50e+03 pdb=" O GLN A 363 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 364 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 769 " -0.012 2.00e-02 2.50e+03 1.88e-02 6.20e+00 pdb=" CG PHE A 769 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 769 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 769 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 769 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 769 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 769 " 0.001 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1519 2.75 - 3.29: 12682 3.29 - 3.82: 22077 3.82 - 4.36: 27350 4.36 - 4.90: 46302 Nonbonded interactions: 109930 Sorted by model distance: nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.210 2.440 nonbonded pdb=" OH TYR B 16 " pdb=" OD2 ASP B 161 " model vdw 2.319 2.440 nonbonded pdb=" O SER A1152 " pdb=" OH TYR A1183 " model vdw 2.322 2.440 nonbonded pdb=" O ILE A 202 " pdb=" OG1 THR A 205 " model vdw 2.324 2.440 nonbonded pdb=" O CYS A 574 " pdb=" ND2 ASN A 603 " model vdw 2.326 2.520 ... (remaining 109925 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: 0.850 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: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 37.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.008 0.298 13903 Z= 0.568 Angle : 0.986 19.268 18842 Z= 0.555 Chirality : 0.056 0.414 2101 Planarity : 0.006 0.059 2400 Dihedral : 9.803 89.739 5116 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.91 % Rotamer: Outliers : 0.75 % Allowed : 1.90 % Favored : 97.35 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % 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: -3.24 (0.16), residues: 1684 helix: -2.34 (0.13), residues: 820 sheet: -1.47 (0.39), residues: 150 loop : -1.86 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP A 606 HIS 0.018 0.003 HIS B 490 PHE 0.042 0.004 PHE A 769 TYR 0.030 0.003 TYR A 900 ARG 0.013 0.001 ARG A1175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 424 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ASP cc_start: 0.7298 (p0) cc_final: 0.6961 (p0) REVERT: A 551 MET cc_start: 0.8024 (ttp) cc_final: 0.7783 (ttt) REVERT: A 809 SER cc_start: 0.8327 (t) cc_final: 0.8105 (p) REVERT: A 877 ASP cc_start: 0.8426 (t0) cc_final: 0.8224 (t0) REVERT: A 926 SER cc_start: 0.3976 (OUTLIER) cc_final: 0.3366 (p) outliers start: 11 outliers final: 3 residues processed: 430 average time/residue: 1.6714 time to fit residues: 772.1912 Evaluate side-chains 235 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain B residue 497 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 0.0040 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 126 HIS A 164 ASN A 274 GLN A 486 GLN A 514 ASN A 617 GLN A 648 HIS A 807 ASN A 880 ASN A 887 GLN A1136 ASN A1193 ASN B 9 HIS B 212 ASN B 459 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13903 Z= 0.234 Angle : 0.541 8.719 18842 Z= 0.284 Chirality : 0.041 0.156 2101 Planarity : 0.004 0.047 2400 Dihedral : 6.057 81.603 1901 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.41 % Allowed : 14.52 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 1684 helix: -0.67 (0.17), residues: 802 sheet: -1.25 (0.39), residues: 153 loop : -1.15 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 606 HIS 0.008 0.001 HIS A1039 PHE 0.016 0.002 PHE A 45 TYR 0.018 0.002 TYR A 308 ARG 0.004 0.001 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 364 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7300 (mtm-85) REVERT: A 877 ASP cc_start: 0.8647 (t0) cc_final: 0.8439 (t70) REVERT: A 926 SER cc_start: 0.4262 (OUTLIER) cc_final: 0.3516 (p) REVERT: A 978 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: A 1028 ASP cc_start: 0.7261 (t0) cc_final: 0.7013 (t0) REVERT: A 1080 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7841 (mtt180) REVERT: B 43 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7384 (mp) outliers start: 65 outliers final: 23 residues processed: 278 average time/residue: 1.5252 time to fit residues: 458.2652 Evaluate side-chains 239 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 497 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 0.1980 chunk 165 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 114 ASN A 274 GLN A 514 ASN A1084 HIS B 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13903 Z= 0.286 Angle : 0.539 8.312 18842 Z= 0.282 Chirality : 0.042 0.156 2101 Planarity : 0.004 0.040 2400 Dihedral : 5.649 77.195 1898 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.50 % Allowed : 14.59 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1684 helix: -0.05 (0.18), residues: 803 sheet: -0.93 (0.39), residues: 146 loop : -0.90 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 606 HIS 0.008 0.001 HIS A1036 PHE 0.015 0.002 PHE A 206 TYR 0.023 0.002 TYR B 13 ARG 0.008 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 214 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: A 131 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8372 (ttmt) REVERT: A 319 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8422 (mm) REVERT: A 859 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: A 957 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8730 (ptmm) REVERT: A 978 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: A 1028 ASP cc_start: 0.7257 (t0) cc_final: 0.6992 (t0) REVERT: A 1080 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7762 (mtt180) REVERT: B 43 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7531 (mp) REVERT: B 443 ARG cc_start: 0.5570 (mpt180) cc_final: 0.4927 (mpt180) outliers start: 81 outliers final: 34 residues processed: 263 average time/residue: 1.5716 time to fit residues: 445.1181 Evaluate side-chains 247 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.0970 chunk 16 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 164 ASN A 486 GLN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13903 Z= 0.311 Angle : 0.543 9.003 18842 Z= 0.281 Chirality : 0.043 0.159 2101 Planarity : 0.004 0.038 2400 Dihedral : 5.526 74.325 1896 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.95 % Allowed : 15.60 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1684 helix: 0.21 (0.18), residues: 801 sheet: -0.81 (0.39), residues: 146 loop : -0.68 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 606 HIS 0.007 0.001 HIS A1036 PHE 0.014 0.002 PHE A 206 TYR 0.024 0.002 TYR B 13 ARG 0.006 0.001 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 204 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: A 319 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8427 (mm) REVERT: A 859 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: A 957 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8797 (ptmm) REVERT: A 978 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: A 1028 ASP cc_start: 0.7281 (t0) cc_final: 0.7036 (t0) REVERT: A 1080 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7846 (mtt180) REVERT: B 14 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: B 43 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7705 (mp) REVERT: B 199 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7003 (ttp-110) REVERT: B 413 ASP cc_start: 0.7683 (p0) cc_final: 0.7433 (p0) REVERT: B 443 ARG cc_start: 0.5868 (mpt180) cc_final: 0.4922 (mpt180) REVERT: B 444 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7577 (mtpt) outliers start: 73 outliers final: 42 residues processed: 251 average time/residue: 1.6129 time to fit residues: 436.5383 Evaluate side-chains 244 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 0.0170 chunk 40 optimal weight: 9.9990 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN A 887 GLN A1095 GLN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13903 Z= 0.308 Angle : 0.535 8.754 18842 Z= 0.276 Chirality : 0.042 0.157 2101 Planarity : 0.004 0.035 2400 Dihedral : 5.455 72.148 1896 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.36 % Allowed : 15.47 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1684 helix: 0.33 (0.18), residues: 803 sheet: -0.74 (0.39), residues: 146 loop : -0.58 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 606 HIS 0.006 0.001 HIS A1036 PHE 0.014 0.002 PHE A 206 TYR 0.019 0.002 TYR B 13 ARG 0.007 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 198 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: A 317 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8397 (ptm-80) REVERT: A 319 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 859 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: A 899 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: A 957 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8778 (ptmm) REVERT: A 978 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: A 1028 ASP cc_start: 0.7317 (t0) cc_final: 0.7081 (t0) REVERT: B 14 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: B 43 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 199 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7010 (ttp-110) REVERT: B 413 ASP cc_start: 0.7668 (p0) cc_final: 0.7433 (p0) REVERT: B 443 ARG cc_start: 0.5931 (mpt180) cc_final: 0.4998 (mpt180) REVERT: B 444 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7584 (mtpt) outliers start: 79 outliers final: 46 residues processed: 243 average time/residue: 1.6391 time to fit residues: 428.4031 Evaluate side-chains 247 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 486 GLN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13903 Z= 0.260 Angle : 0.508 9.388 18842 Z= 0.264 Chirality : 0.041 0.155 2101 Planarity : 0.004 0.034 2400 Dihedral : 5.300 69.071 1896 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.43 % Allowed : 15.20 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1684 helix: 0.49 (0.18), residues: 803 sheet: -0.71 (0.38), residues: 154 loop : -0.52 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 260 HIS 0.005 0.001 HIS A1036 PHE 0.013 0.001 PHE A 206 TYR 0.015 0.001 TYR B 13 ARG 0.008 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 199 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: A 317 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8367 (ptm-80) REVERT: A 319 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 532 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: A 899 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: A 957 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8769 (ptmm) REVERT: A 978 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: A 1028 ASP cc_start: 0.7267 (t0) cc_final: 0.7023 (t0) REVERT: B 43 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7776 (mp) REVERT: B 199 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7050 (ttp-110) REVERT: B 443 ARG cc_start: 0.5901 (mpt180) cc_final: 0.4985 (mpt180) REVERT: B 444 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7556 (mtpt) outliers start: 80 outliers final: 43 residues processed: 247 average time/residue: 1.5763 time to fit residues: 419.3532 Evaluate side-chains 248 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 195 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 514 ASN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13903 Z= 0.290 Angle : 0.524 9.157 18842 Z= 0.272 Chirality : 0.042 0.156 2101 Planarity : 0.004 0.034 2400 Dihedral : 5.286 66.646 1896 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.88 % Allowed : 15.94 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1684 helix: 0.52 (0.18), residues: 802 sheet: -0.69 (0.39), residues: 149 loop : -0.50 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 PHE 0.014 0.001 PHE A 206 TYR 0.015 0.002 TYR B 13 ARG 0.008 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 200 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: A 317 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8368 (ptm-80) REVERT: A 319 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (mm) REVERT: A 532 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8408 (mtm) REVERT: A 957 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8757 (ptmm) REVERT: A 978 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: A 1028 ASP cc_start: 0.7265 (t0) cc_final: 0.7022 (t0) REVERT: B 43 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7812 (mp) REVERT: B 199 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7067 (ttp-110) REVERT: B 413 ASP cc_start: 0.7778 (p0) cc_final: 0.7567 (p0) REVERT: B 443 ARG cc_start: 0.6007 (mpt180) cc_final: 0.5100 (mpt180) REVERT: B 444 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7562 (mtpt) outliers start: 72 outliers final: 46 residues processed: 245 average time/residue: 1.6273 time to fit residues: 430.3537 Evaluate side-chains 248 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 134 HIS A 137 GLN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13903 Z= 0.171 Angle : 0.488 9.883 18842 Z= 0.255 Chirality : 0.040 0.163 2101 Planarity : 0.003 0.037 2400 Dihedral : 5.084 64.279 1896 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.73 % Allowed : 17.44 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1684 helix: 0.74 (0.19), residues: 803 sheet: -0.62 (0.39), residues: 149 loop : -0.44 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 260 HIS 0.004 0.001 HIS A1036 PHE 0.011 0.001 PHE A 206 TYR 0.011 0.001 TYR A1183 ARG 0.009 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7096 (pt0) REVERT: A 317 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8335 (ptm-80) REVERT: A 319 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 859 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: A 957 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8729 (ptmm) REVERT: A 978 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6858 (mp10) REVERT: A 1028 ASP cc_start: 0.7229 (t0) cc_final: 0.7000 (t0) REVERT: B 43 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 443 ARG cc_start: 0.5855 (mpt180) cc_final: 0.5238 (mtt180) outliers start: 55 outliers final: 30 residues processed: 230 average time/residue: 1.6129 time to fit residues: 399.0045 Evaluate side-chains 225 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 0.0070 chunk 136 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13903 Z= 0.275 Angle : 0.531 9.282 18842 Z= 0.273 Chirality : 0.042 0.190 2101 Planarity : 0.004 0.042 2400 Dihedral : 5.138 62.866 1896 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.60 % Allowed : 18.18 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1684 helix: 0.71 (0.19), residues: 802 sheet: -0.60 (0.39), residues: 149 loop : -0.48 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 PHE 0.014 0.001 PHE A 206 TYR 0.015 0.001 TYR A1183 ARG 0.010 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7127 (pt0) REVERT: A 133 MET cc_start: 0.8985 (ttp) cc_final: 0.8773 (ttt) REVERT: A 317 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8347 (ptm-80) REVERT: A 319 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 859 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: A 957 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8736 (ptmm) REVERT: A 978 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6847 (mp10) REVERT: A 1028 ASP cc_start: 0.7263 (t0) cc_final: 0.6989 (t0) REVERT: B 43 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7729 (mp) REVERT: B 199 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7066 (ttp-110) REVERT: B 443 ARG cc_start: 0.6013 (mpt180) cc_final: 0.5079 (mpt180) outliers start: 53 outliers final: 35 residues processed: 222 average time/residue: 1.6206 time to fit residues: 387.1458 Evaluate side-chains 235 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 550 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 110 optimal weight: 0.0670 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 overall best weight: 5.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 137 GLN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13903 Z= 0.308 Angle : 0.547 9.354 18842 Z= 0.281 Chirality : 0.042 0.167 2101 Planarity : 0.004 0.044 2400 Dihedral : 5.205 61.047 1896 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.19 % Allowed : 19.06 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1684 helix: 0.69 (0.19), residues: 802 sheet: -0.54 (0.39), residues: 154 loop : -0.49 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 606 HIS 0.006 0.001 HIS A1036 PHE 0.014 0.001 PHE A 206 TYR 0.015 0.002 TYR A1183 ARG 0.010 0.000 ARG A 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: A 317 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8335 (ptm-80) REVERT: A 319 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 859 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: A 957 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8734 (ptmm) REVERT: A 978 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: A 1028 ASP cc_start: 0.7266 (t0) cc_final: 0.6993 (t0) REVERT: B 43 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 75 ASP cc_start: 0.8015 (m-30) cc_final: 0.7754 (m-30) REVERT: B 199 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7067 (ttp-110) REVERT: B 443 ARG cc_start: 0.6052 (mpt180) cc_final: 0.5177 (mpt180) outliers start: 47 outliers final: 34 residues processed: 218 average time/residue: 1.7053 time to fit residues: 400.6649 Evaluate side-chains 231 residues out of total 1475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 55 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.084886 restraints weight = 18409.881| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.62 r_work: 0.2734 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13903 Z= 0.121 Angle : 0.455 10.074 18842 Z= 0.236 Chirality : 0.038 0.147 2101 Planarity : 0.003 0.049 2400 Dihedral : 4.822 57.921 1896 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.04 % Allowed : 20.28 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1684 helix: 1.01 (0.19), residues: 802 sheet: -0.52 (0.39), residues: 149 loop : -0.36 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 260 HIS 0.003 0.001 HIS A1039 PHE 0.010 0.001 PHE B 491 TYR 0.010 0.001 TYR A1100 ARG 0.011 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6546.76 seconds wall clock time: 117 minutes 33.64 seconds (7053.64 seconds total)