Starting phenix.real_space_refine on Mon Mar 11 07:24:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/03_2024/7ktt_23029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/03_2024/7ktt_23029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/03_2024/7ktt_23029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/03_2024/7ktt_23029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/03_2024/7ktt_23029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/03_2024/7ktt_23029.pdb" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4666 2.51 5 N 1372 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1055": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7568 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7568 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 35, 'TRANS': 958} Chain breaks: 1 Time building chain proxies: 4.55, per 1000 atoms: 0.60 Number of scatterers: 7568 At special positions: 0 Unit cell: (84.15, 96.525, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1487 8.00 N 1372 7.00 C 4666 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 83.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 6 through 25 Proline residue: A 15 - end of helix removed outlier: 4.726A pdb=" N GLN A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 20 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 64 removed outlier: 3.538A pdb=" N ALA A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.879A pdb=" N LYS A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.920A pdb=" N ILE A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 126 removed outlier: 3.639A pdb=" N ASP A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 151 removed outlier: 4.308A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 164 through 182 removed outlier: 4.292A pdb=" N LYS A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 218 removed outlier: 4.274A pdb=" N MET A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.571A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 249 removed outlier: 4.010A pdb=" N LEU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 241 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.796A pdb=" N MET A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.734A pdb=" N ALA A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 310 removed outlier: 3.746A pdb=" N ALA A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.519A pdb=" N ILE A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.587A pdb=" N MET A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 379 removed outlier: 3.648A pdb=" N GLN A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 362 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.660A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.631A pdb=" N LEU A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 removed outlier: 3.912A pdb=" N SER A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 455 through 478 removed outlier: 4.358A pdb=" N ALA A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.569A pdb=" N LYS A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG A 502 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.812A pdb=" N ALA A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 535 through 551 removed outlier: 4.095A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 540 " --> pdb=" O PRO A 536 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 582 removed outlier: 3.670A pdb=" N LYS A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.809A pdb=" N GLU A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 623 through 651 Processing helix chain 'A' and resid 654 through 685 Proline residue: A 673 - end of helix removed outlier: 3.546A pdb=" N ILE A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 717 removed outlier: 3.833A pdb=" N TYR A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A 693 " --> pdb=" O GLN A 689 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 743 removed outlier: 3.537A pdb=" N LEU A 723 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 729 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 743 " --> pdb=" O VAL A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 774 removed outlier: 3.515A pdb=" N LEU A 749 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 764 " --> pdb=" O ALA A 760 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 806 removed outlier: 3.674A pdb=" N SER A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Proline residue: A 796 - end of helix removed outlier: 3.548A pdb=" N GLY A 806 " --> pdb=" O LYS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 835 removed outlier: 3.864A pdb=" N ILE A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 835 " --> pdb=" O VAL A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 978 removed outlier: 4.054A pdb=" N LEU A 967 " --> pdb=" O ASN A 963 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'A' and resid 1011 through 1039 removed outlier: 3.998A pdb=" N LEU A1015 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1022 " --> pdb=" O CYS A1018 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A1030 " --> pdb=" O SER A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1054 removed outlier: 3.715A pdb=" N VAL A1052 " --> pdb=" O ASN A1048 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1073 removed outlier: 3.903A pdb=" N THR A1058 " --> pdb=" O GLU A1054 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A1059 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A1060 " --> pdb=" O ILE A1056 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1072 " --> pdb=" O THR A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1114 removed outlier: 3.608A pdb=" N SER A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1509 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: 2.41 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2547 1.34 - 1.46: 917 1.46 - 1.57: 4105 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7645 Sorted by residual: bond pdb=" C ILE A1056 " pdb=" N PRO A1057 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.56e+00 bond pdb=" CG LEU A 529 " pdb=" CD1 LEU A 529 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.12e+00 bond pdb=" C SER A 346 " pdb=" N PRO A 347 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.17e+00 bond pdb=" CA PRO A 2 " pdb=" C PRO A 2 " ideal model delta sigma weight residual 1.527 1.510 0.017 1.07e-02 8.73e+03 2.44e+00 bond pdb=" C SER A 795 " pdb=" N PRO A 796 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.10e+00 ... (remaining 7640 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.80: 167 105.80 - 113.32: 4323 113.32 - 120.83: 3800 120.83 - 128.34: 1981 128.34 - 135.86: 43 Bond angle restraints: 10314 Sorted by residual: angle pdb=" C VAL A1005 " pdb=" N ARG A1006 " pdb=" CA ARG A1006 " ideal model delta sigma weight residual 121.54 129.46 -7.92 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C THR A 6 " pdb=" N ARG A 7 " pdb=" CA ARG A 7 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N SER A 795 " pdb=" CA SER A 795 " pdb=" C SER A 795 " ideal model delta sigma weight residual 109.81 116.92 -7.11 2.21e+00 2.05e-01 1.04e+01 angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 108.88 115.69 -6.81 2.16e+00 2.14e-01 9.95e+00 angle pdb=" C ARG A1076 " pdb=" N THR A1077 " pdb=" CA THR A1077 " ideal model delta sigma weight residual 125.02 130.49 -5.47 1.76e+00 3.23e-01 9.65e+00 ... (remaining 10309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 4389 15.86 - 31.71: 332 31.71 - 47.57: 99 47.57 - 63.42: 5 63.42 - 79.28: 13 Dihedral angle restraints: 4838 sinusoidal: 1955 harmonic: 2883 Sorted by residual: dihedral pdb=" CA GLU A 707 " pdb=" C GLU A 707 " pdb=" N LYS A 708 " pdb=" CA LYS A 708 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ASN A 700 " pdb=" C ASN A 700 " pdb=" N GLN A 701 " pdb=" CA GLN A 701 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ILE A 824 " pdb=" C ILE A 824 " pdb=" N LEU A 825 " pdb=" CA LEU A 825 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 4835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 727 0.044 - 0.089: 351 0.089 - 0.133: 110 0.133 - 0.177: 21 0.177 - 0.222: 5 Chirality restraints: 1214 Sorted by residual: chirality pdb=" CG LEU A 640 " pdb=" CB LEU A 640 " pdb=" CD1 LEU A 640 " pdb=" CD2 LEU A 640 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA THR A 604 " pdb=" N THR A 604 " pdb=" C THR A 604 " pdb=" CB THR A 604 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CB THR A1011 " pdb=" CA THR A1011 " pdb=" OG1 THR A1011 " pdb=" CG2 THR A1011 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 1211 not shown) Planarity restraints: 1357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 75 " -0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 76 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 14 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO A 15 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 672 " -0.042 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 673 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 673 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 673 " -0.035 5.00e-02 4.00e+02 ... (remaining 1354 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1724 2.77 - 3.30: 8308 3.30 - 3.84: 13628 3.84 - 4.37: 16336 4.37 - 4.90: 24266 Nonbonded interactions: 64262 Sorted by model distance: nonbonded pdb=" O VAL A 57 " pdb=" OG1 THR A 61 " model vdw 2.239 2.440 nonbonded pdb=" O PHE A 599 " pdb=" OG1 THR A 602 " model vdw 2.259 2.440 nonbonded pdb=" O ILE A 211 " pdb=" OG1 THR A 214 " model vdw 2.262 2.440 nonbonded pdb=" O HIS A 974 " pdb=" OG1 THR A 978 " model vdw 2.281 2.440 nonbonded pdb=" OD2 ASP A 733 " pdb=" NH2 ARG A 759 " model vdw 2.295 2.520 ... (remaining 64257 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 3.960 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.210 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 7645 Z= 0.452 Angle : 1.037 10.857 10314 Z= 0.557 Chirality : 0.056 0.222 1214 Planarity : 0.008 0.080 1357 Dihedral : 13.234 79.278 2954 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.25 % Allowed : 4.07 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.18), residues: 990 helix: -3.53 (0.12), residues: 738 sheet: None (None), residues: 0 loop : -2.89 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP A 283 HIS 0.009 0.004 HIS A 636 PHE 0.024 0.004 PHE A 835 TYR 0.030 0.003 TYR A 107 ARG 0.011 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8818 (mt-10) REVERT: A 266 MET cc_start: 0.6440 (mtt) cc_final: 0.5200 (mmt) REVERT: A 483 ASN cc_start: 0.8626 (m-40) cc_final: 0.8330 (t0) REVERT: A 506 ASN cc_start: 0.8371 (t0) cc_final: 0.8112 (t0) REVERT: A 640 LEU cc_start: 0.8667 (mt) cc_final: 0.8431 (mt) REVERT: A 666 LYS cc_start: 0.9256 (tppt) cc_final: 0.9024 (tppt) REVERT: A 670 GLU cc_start: 0.8154 (pm20) cc_final: 0.7932 (pm20) REVERT: A 809 SER cc_start: 0.9019 (t) cc_final: 0.8799 (m) REVERT: A 1099 MET cc_start: 0.8123 (mtt) cc_final: 0.7393 (mtt) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.2107 time to fit residues: 49.4200 Evaluate side-chains 120 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 492 HIS A 516 GLN A 550 GLN A 554 GLN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A 974 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7645 Z= 0.254 Angle : 0.714 8.646 10314 Z= 0.383 Chirality : 0.042 0.164 1214 Planarity : 0.006 0.057 1357 Dihedral : 6.378 22.154 1059 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.25 % Allowed : 3.95 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.23), residues: 990 helix: -1.76 (0.16), residues: 812 sheet: None (None), residues: 0 loop : -2.27 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 394 HIS 0.004 0.002 HIS A 184 PHE 0.015 0.002 PHE A 817 TYR 0.017 0.002 TYR A 692 ARG 0.005 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8841 (mmt) cc_final: 0.8605 (mmt) REVERT: A 174 MET cc_start: 0.8290 (mmp) cc_final: 0.8080 (mmm) REVERT: A 196 ASN cc_start: 0.9109 (p0) cc_final: 0.8860 (p0) REVERT: A 200 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8643 (mt-10) REVERT: A 253 TRP cc_start: 0.6593 (t-100) cc_final: 0.6344 (t-100) REVERT: A 266 MET cc_start: 0.5980 (mtt) cc_final: 0.4557 (mmt) REVERT: A 506 ASN cc_start: 0.8338 (t0) cc_final: 0.8004 (t0) REVERT: A 640 LEU cc_start: 0.8909 (mt) cc_final: 0.8636 (mt) REVERT: A 698 MET cc_start: 0.8155 (mmp) cc_final: 0.7588 (mmp) REVERT: A 809 SER cc_start: 0.9080 (t) cc_final: 0.8774 (m) outliers start: 2 outliers final: 1 residues processed: 162 average time/residue: 0.1824 time to fit residues: 40.7185 Evaluate side-chains 113 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN A 492 HIS A 550 GLN A 554 GLN A 974 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7645 Z= 0.164 Angle : 0.614 6.755 10314 Z= 0.319 Chirality : 0.040 0.156 1214 Planarity : 0.005 0.052 1357 Dihedral : 5.665 19.379 1059 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.25 % Allowed : 3.45 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.25), residues: 990 helix: -0.75 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -2.06 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 394 HIS 0.002 0.001 HIS A 187 PHE 0.019 0.002 PHE A 78 TYR 0.026 0.002 TYR A 107 ARG 0.004 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8831 (mmt) cc_final: 0.8610 (mmt) REVERT: A 107 TYR cc_start: 0.9028 (m-80) cc_final: 0.8715 (m-80) REVERT: A 174 MET cc_start: 0.8217 (mmp) cc_final: 0.7955 (mmm) REVERT: A 253 TRP cc_start: 0.6482 (t-100) cc_final: 0.6199 (t-100) REVERT: A 266 MET cc_start: 0.5706 (mtt) cc_final: 0.5459 (mtt) REVERT: A 321 ILE cc_start: 0.8324 (mm) cc_final: 0.8083 (mm) REVERT: A 427 GLU cc_start: 0.7889 (pm20) cc_final: 0.7613 (pm20) REVERT: A 506 ASN cc_start: 0.8143 (t0) cc_final: 0.7806 (t0) REVERT: A 603 THR cc_start: 0.8684 (t) cc_final: 0.8422 (m) REVERT: A 640 LEU cc_start: 0.8852 (mt) cc_final: 0.8570 (mt) REVERT: A 666 LYS cc_start: 0.9069 (tppt) cc_final: 0.8744 (tppt) REVERT: A 698 MET cc_start: 0.8099 (mmp) cc_final: 0.7789 (mmp) REVERT: A 809 SER cc_start: 0.9084 (t) cc_final: 0.8827 (m) outliers start: 2 outliers final: 1 residues processed: 174 average time/residue: 0.2203 time to fit residues: 52.0587 Evaluate side-chains 115 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 554 GLN A 761 ASN A 974 HIS A1017 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7645 Z= 0.161 Angle : 0.605 7.334 10314 Z= 0.310 Chirality : 0.041 0.159 1214 Planarity : 0.004 0.051 1357 Dihedral : 5.303 17.813 1059 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.25 % Allowed : 3.08 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.26), residues: 990 helix: -0.13 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -1.86 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 702 HIS 0.002 0.001 HIS A 492 PHE 0.020 0.002 PHE A 78 TYR 0.021 0.002 TYR A 107 ARG 0.005 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8784 (mmt) cc_final: 0.8142 (mmt) REVERT: A 107 TYR cc_start: 0.9021 (m-80) cc_final: 0.8808 (m-80) REVERT: A 168 MET cc_start: 0.7547 (tpp) cc_final: 0.6336 (tpt) REVERT: A 253 TRP cc_start: 0.6545 (t-100) cc_final: 0.6280 (t-100) REVERT: A 264 GLU cc_start: 0.7986 (pp20) cc_final: 0.7742 (pm20) REVERT: A 266 MET cc_start: 0.5444 (mtt) cc_final: 0.4195 (mmt) REVERT: A 506 ASN cc_start: 0.8214 (t0) cc_final: 0.7836 (t0) REVERT: A 546 ASP cc_start: 0.9323 (m-30) cc_final: 0.9105 (m-30) REVERT: A 603 THR cc_start: 0.8622 (t) cc_final: 0.8279 (m) REVERT: A 635 ASN cc_start: 0.8876 (m110) cc_final: 0.8596 (p0) REVERT: A 640 LEU cc_start: 0.8901 (mt) cc_final: 0.8667 (mt) REVERT: A 666 LYS cc_start: 0.9086 (tppt) cc_final: 0.8748 (tppt) REVERT: A 697 THR cc_start: 0.8683 (m) cc_final: 0.8442 (m) REVERT: A 698 MET cc_start: 0.8099 (mmp) cc_final: 0.7852 (mmp) REVERT: A 709 MET cc_start: 0.8480 (ttm) cc_final: 0.7942 (tpp) REVERT: A 809 SER cc_start: 0.9094 (t) cc_final: 0.8885 (m) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.1834 time to fit residues: 42.8260 Evaluate side-chains 118 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 180 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 974 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7645 Z= 0.282 Angle : 0.698 8.199 10314 Z= 0.365 Chirality : 0.044 0.155 1214 Planarity : 0.005 0.053 1357 Dihedral : 5.456 22.872 1059 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 990 helix: -0.07 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 702 HIS 0.004 0.002 HIS A 184 PHE 0.021 0.003 PHE A 817 TYR 0.016 0.002 TYR A 100 ARG 0.006 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.9331 (pptt) cc_final: 0.8522 (tptp) REVERT: A 266 MET cc_start: 0.5840 (mtt) cc_final: 0.5396 (tpp) REVERT: A 506 ASN cc_start: 0.8210 (t0) cc_final: 0.7828 (t0) REVERT: A 547 ARG cc_start: 0.9484 (tpp80) cc_final: 0.9281 (mmm-85) REVERT: A 666 LYS cc_start: 0.9186 (tppt) cc_final: 0.8836 (tppt) REVERT: A 670 GLU cc_start: 0.8228 (pm20) cc_final: 0.8017 (pm20) REVERT: A 698 MET cc_start: 0.8245 (mmp) cc_final: 0.7999 (mmp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1834 time to fit residues: 39.5870 Evaluate side-chains 113 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 95 optimal weight: 0.0370 chunk 79 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN A 187 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 761 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7645 Z= 0.159 Angle : 0.611 6.956 10314 Z= 0.312 Chirality : 0.041 0.139 1214 Planarity : 0.004 0.063 1357 Dihedral : 5.157 21.978 1059 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 990 helix: 0.55 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.63 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 283 HIS 0.004 0.001 HIS A 492 PHE 0.011 0.001 PHE A 599 TYR 0.020 0.001 TYR A 100 ARG 0.009 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8992 (t70) cc_final: 0.8641 (t70) REVERT: A 128 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8818 (mt-10) REVERT: A 173 LYS cc_start: 0.9285 (pptt) cc_final: 0.8735 (tptp) REVERT: A 200 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 246 ARG cc_start: 0.8578 (mpp-170) cc_final: 0.8346 (ptp90) REVERT: A 253 TRP cc_start: 0.6415 (t-100) cc_final: 0.6039 (t-100) REVERT: A 266 MET cc_start: 0.5409 (mtt) cc_final: 0.4153 (mmt) REVERT: A 506 ASN cc_start: 0.7998 (t0) cc_final: 0.7626 (t0) REVERT: A 547 ARG cc_start: 0.9435 (tpp80) cc_final: 0.9230 (mmm-85) REVERT: A 635 ASN cc_start: 0.8772 (m110) cc_final: 0.8571 (m110) REVERT: A 640 LEU cc_start: 0.8670 (mt) cc_final: 0.8191 (mt) REVERT: A 709 MET cc_start: 0.8287 (ttm) cc_final: 0.7932 (tpp) REVERT: A 809 SER cc_start: 0.9097 (t) cc_final: 0.8893 (m) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1836 time to fit residues: 41.7408 Evaluate side-chains 116 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 554 GLN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7645 Z= 0.163 Angle : 0.620 7.108 10314 Z= 0.318 Chirality : 0.042 0.174 1214 Planarity : 0.004 0.062 1357 Dihedral : 5.028 23.285 1059 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 990 helix: 0.61 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.60 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 283 HIS 0.012 0.001 HIS A 694 PHE 0.010 0.002 PHE A 212 TYR 0.017 0.001 TYR A 100 ARG 0.005 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9514 (mt) cc_final: 0.9309 (mt) REVERT: A 128 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8833 (mt-10) REVERT: A 174 MET cc_start: 0.8112 (mmp) cc_final: 0.7822 (mmm) REVERT: A 244 ILE cc_start: 0.8649 (mm) cc_final: 0.8413 (mm) REVERT: A 253 TRP cc_start: 0.6684 (t-100) cc_final: 0.6221 (t-100) REVERT: A 266 MET cc_start: 0.5495 (mtt) cc_final: 0.4318 (mmt) REVERT: A 506 ASN cc_start: 0.7982 (t0) cc_final: 0.7614 (t0) REVERT: A 635 ASN cc_start: 0.8777 (m110) cc_final: 0.8569 (m110) REVERT: A 640 LEU cc_start: 0.8594 (mt) cc_final: 0.8109 (mt) REVERT: A 698 MET cc_start: 0.8571 (mpp) cc_final: 0.8246 (mmt) REVERT: A 701 GLN cc_start: 0.8624 (mt0) cc_final: 0.8331 (mt0) REVERT: A 709 MET cc_start: 0.8308 (ttm) cc_final: 0.7871 (tpp) REVERT: A 809 SER cc_start: 0.9093 (t) cc_final: 0.8889 (m) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.1910 time to fit residues: 41.5226 Evaluate side-chains 117 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 761 ASN A 974 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7645 Z= 0.206 Angle : 0.644 6.931 10314 Z= 0.334 Chirality : 0.043 0.159 1214 Planarity : 0.004 0.057 1357 Dihedral : 5.059 22.455 1059 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 990 helix: 0.55 (0.19), residues: 814 sheet: None (None), residues: 0 loop : -1.58 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 283 HIS 0.016 0.002 HIS A 694 PHE 0.014 0.002 PHE A 817 TYR 0.015 0.001 TYR A 100 ARG 0.004 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9536 (mt) cc_final: 0.9315 (mt) REVERT: A 128 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8861 (mt-10) REVERT: A 177 GLU cc_start: 0.8734 (pp20) cc_final: 0.8530 (pp20) REVERT: A 193 ASN cc_start: 0.8788 (m110) cc_final: 0.8575 (m110) REVERT: A 244 ILE cc_start: 0.8713 (mm) cc_final: 0.8467 (mm) REVERT: A 246 ARG cc_start: 0.8651 (mpp-170) cc_final: 0.8342 (ptp90) REVERT: A 253 TRP cc_start: 0.6932 (t-100) cc_final: 0.6493 (t-100) REVERT: A 266 MET cc_start: 0.5550 (mtt) cc_final: 0.4513 (mmt) REVERT: A 283 TRP cc_start: 0.8068 (t60) cc_final: 0.7490 (t60) REVERT: A 506 ASN cc_start: 0.8027 (t0) cc_final: 0.7635 (t0) REVERT: A 591 MET cc_start: 0.7620 (tpt) cc_final: 0.6663 (tpt) REVERT: A 635 ASN cc_start: 0.8836 (m110) cc_final: 0.8616 (m110) REVERT: A 640 LEU cc_start: 0.8659 (mt) cc_final: 0.8192 (mt) REVERT: A 670 GLU cc_start: 0.8050 (pm20) cc_final: 0.7845 (pm20) REVERT: A 698 MET cc_start: 0.8580 (mpp) cc_final: 0.8061 (mmt) REVERT: A 701 GLN cc_start: 0.8654 (mt0) cc_final: 0.8206 (mt0) REVERT: A 998 MET cc_start: 0.7453 (pmm) cc_final: 0.7057 (pmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1851 time to fit residues: 40.5706 Evaluate side-chains 116 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7645 Z= 0.186 Angle : 0.629 7.086 10314 Z= 0.323 Chirality : 0.042 0.165 1214 Planarity : 0.004 0.057 1357 Dihedral : 5.016 22.385 1059 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 990 helix: 0.67 (0.19), residues: 809 sheet: None (None), residues: 0 loop : -1.62 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 283 HIS 0.016 0.002 HIS A 694 PHE 0.011 0.001 PHE A 212 TYR 0.017 0.001 TYR A 100 ARG 0.009 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9527 (mt) cc_final: 0.9320 (mt) REVERT: A 128 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8811 (mt-10) REVERT: A 173 LYS cc_start: 0.9191 (pptt) cc_final: 0.8435 (tptp) REVERT: A 244 ILE cc_start: 0.8712 (mm) cc_final: 0.8423 (mm) REVERT: A 253 TRP cc_start: 0.6843 (t-100) cc_final: 0.6482 (t-100) REVERT: A 266 MET cc_start: 0.5586 (mtt) cc_final: 0.4501 (mmt) REVERT: A 506 ASN cc_start: 0.8011 (t0) cc_final: 0.7600 (t0) REVERT: A 587 MET cc_start: 0.5029 (mmm) cc_final: 0.4675 (mmt) REVERT: A 591 MET cc_start: 0.7675 (tpt) cc_final: 0.6644 (tpt) REVERT: A 640 LEU cc_start: 0.8680 (mt) cc_final: 0.8179 (mt) REVERT: A 646 LYS cc_start: 0.9029 (mtmm) cc_final: 0.8331 (mtmm) REVERT: A 698 MET cc_start: 0.8555 (mpp) cc_final: 0.8079 (mmt) REVERT: A 701 GLN cc_start: 0.8642 (mt0) cc_final: 0.8226 (mt0) REVERT: A 709 MET cc_start: 0.8410 (ttm) cc_final: 0.7978 (tpp) REVERT: A 779 PHE cc_start: 0.7265 (m-10) cc_final: 0.7045 (m-10) REVERT: A 998 MET cc_start: 0.7382 (pmm) cc_final: 0.7122 (pmm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1950 time to fit residues: 43.8624 Evaluate side-chains 119 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7645 Z= 0.169 Angle : 0.624 7.274 10314 Z= 0.320 Chirality : 0.041 0.177 1214 Planarity : 0.004 0.058 1357 Dihedral : 4.907 21.849 1059 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.28), residues: 990 helix: 0.89 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -1.54 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 283 HIS 0.015 0.001 HIS A 694 PHE 0.012 0.002 PHE A 126 TYR 0.019 0.001 TYR A 100 ARG 0.006 0.000 ARG A 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 HIS cc_start: 0.6688 (t-90) cc_final: 0.6397 (t-90) REVERT: A 128 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8809 (mt-10) REVERT: A 173 LYS cc_start: 0.9046 (pptt) cc_final: 0.8300 (tptp) REVERT: A 177 GLU cc_start: 0.8762 (pp20) cc_final: 0.8534 (pp20) REVERT: A 244 ILE cc_start: 0.8588 (mm) cc_final: 0.8316 (mm) REVERT: A 253 TRP cc_start: 0.6737 (t-100) cc_final: 0.6391 (t-100) REVERT: A 266 MET cc_start: 0.5426 (mtt) cc_final: 0.4443 (mmt) REVERT: A 506 ASN cc_start: 0.7888 (t0) cc_final: 0.7489 (t0) REVERT: A 587 MET cc_start: 0.4907 (mmm) cc_final: 0.3770 (mmt) REVERT: A 588 GLN cc_start: 0.7679 (pp30) cc_final: 0.7092 (pp30) REVERT: A 640 LEU cc_start: 0.8609 (mt) cc_final: 0.8077 (mt) REVERT: A 698 MET cc_start: 0.8530 (mpp) cc_final: 0.8151 (mmt) REVERT: A 701 GLN cc_start: 0.8629 (mt0) cc_final: 0.8303 (mt0) REVERT: A 709 MET cc_start: 0.8371 (ttm) cc_final: 0.7991 (tpp) REVERT: A 759 ARG cc_start: 0.7864 (mpt180) cc_final: 0.7087 (mmt90) REVERT: A 779 PHE cc_start: 0.7199 (m-10) cc_final: 0.6979 (m-10) REVERT: A 799 MET cc_start: 0.8359 (mmp) cc_final: 0.7958 (mmp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1869 time to fit residues: 43.8669 Evaluate side-chains 130 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.084243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.069155 restraints weight = 38708.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070574 restraints weight = 29300.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.071641 restraints weight = 23882.214| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7645 Z= 0.297 Angle : 0.739 8.333 10314 Z= 0.385 Chirality : 0.045 0.161 1214 Planarity : 0.005 0.052 1357 Dihedral : 5.293 24.059 1059 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 24.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 990 helix: 0.23 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -1.55 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 394 HIS 0.017 0.003 HIS A 694 PHE 0.022 0.002 PHE A 817 TYR 0.019 0.002 TYR A 100 ARG 0.006 0.001 ARG A 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.22 seconds wall clock time: 32 minutes 35.30 seconds (1955.30 seconds total)