Starting phenix.real_space_refine on Tue Sep 24 08:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/09_2024/7ktt_23029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/09_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_23029/09_2024/7ktt_23029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/09_2024/7ktt_23029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/09_2024/7ktt_23029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/09_2024/7ktt_23029.cif" } 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. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.81, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 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: 0.72 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: 2.09 Time building geometry restraints manager: 2.23 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: 0.00 - 2.17: 9848 2.17 - 4.34: 394 4.34 - 6.51: 56 6.51 - 8.69: 14 8.69 - 10.86: 2 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 3.040 nonbonded pdb=" O PHE A 599 " pdb=" OG1 THR A 602 " model vdw 2.259 3.040 nonbonded pdb=" O ILE A 211 " pdb=" OG1 THR A 214 " model vdw 2.262 3.040 nonbonded pdb=" O HIS A 974 " pdb=" OG1 THR A 978 " model vdw 2.281 3.040 nonbonded pdb=" OD2 ASP A 733 " pdb=" NH2 ARG A 759 " model vdw 2.295 3.120 ... (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: 0.920 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- 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 : 0.821 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: 0.2014 time to fit residues: 47.3314 Evaluate side-chains 120 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 ** 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 745 GLN A 974 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2388 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= 0.258 Angle : 0.728 7.924 10314 Z= 0.391 Chirality : 0.043 0.170 1214 Planarity : 0.006 0.054 1357 Dihedral : 6.353 21.638 1059 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.37 % Allowed : 3.70 % Favored : 95.93 % 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: -3.11 (0.23), residues: 990 helix: -1.80 (0.16), residues: 808 sheet: None (None), residues: 0 loop : -2.22 (0.43), residues: 182 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 0.014 0.002 PHE A 835 TYR 0.016 0.002 TYR A 692 ARG 0.006 0.001 ARG A 758 *********************** 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 164 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8280 (mmp) cc_final: 0.8053 (mmm) REVERT: A 196 ASN cc_start: 0.9078 (p0) cc_final: 0.8862 (p0) REVERT: A 200 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 253 TRP cc_start: 0.6535 (t-100) cc_final: 0.6155 (t-100) REVERT: A 266 MET cc_start: 0.5973 (mtt) cc_final: 0.5391 (mmt) REVERT: A 506 ASN cc_start: 0.8351 (t0) cc_final: 0.8033 (t0) REVERT: A 640 LEU cc_start: 0.8905 (mt) cc_final: 0.8670 (mt) REVERT: A 809 SER cc_start: 0.9075 (t) cc_final: 0.8788 (m) outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 0.1870 time to fit residues: 41.3351 Evaluate side-chains 117 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN A 492 HIS A 550 GLN A 554 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3226 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= 0.174 Angle : 0.626 7.025 10314 Z= 0.329 Chirality : 0.042 0.157 1214 Planarity : 0.005 0.051 1357 Dihedral : 5.678 19.570 1059 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.05 % 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: -1.76 (0.25), residues: 990 helix: -0.84 (0.17), residues: 821 sheet: None (None), residues: 0 loop : -1.96 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 394 HIS 0.003 0.001 HIS A 527 PHE 0.019 0.002 PHE A 78 TYR 0.016 0.002 TYR A 100 ARG 0.006 0.001 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 170 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8654 (mmt) cc_final: 0.8340 (mmt) REVERT: A 174 MET cc_start: 0.8230 (mmp) cc_final: 0.7968 (mmm) REVERT: A 253 TRP cc_start: 0.6436 (t-100) cc_final: 0.6020 (t-100) REVERT: A 266 MET cc_start: 0.5585 (mtt) cc_final: 0.4431 (mmt) REVERT: A 506 ASN cc_start: 0.8235 (t0) cc_final: 0.7912 (t0) REVERT: A 603 THR cc_start: 0.8669 (t) cc_final: 0.8371 (m) REVERT: A 640 LEU cc_start: 0.8894 (mt) cc_final: 0.8611 (mt) REVERT: A 666 LYS cc_start: 0.8983 (tppt) cc_final: 0.8663 (tppt) REVERT: A 698 MET cc_start: 0.8084 (mmp) cc_final: 0.7856 (mmt) REVERT: A 809 SER cc_start: 0.9099 (t) cc_final: 0.8863 (m) REVERT: A 998 MET cc_start: 0.7205 (pmm) cc_final: 0.6759 (pmm) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.1892 time to fit residues: 43.6289 Evaluate side-chains 113 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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: 8.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 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 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3541 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= 0.211 Angle : 0.646 7.436 10314 Z= 0.336 Chirality : 0.042 0.147 1214 Planarity : 0.005 0.050 1357 Dihedral : 5.480 19.133 1059 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.12 % Allowed : 2.34 % 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: -1.13 (0.26), residues: 990 helix: -0.39 (0.17), residues: 818 sheet: None (None), residues: 0 loop : -1.77 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 702 HIS 0.003 0.001 HIS A 184 PHE 0.017 0.002 PHE A 78 TYR 0.028 0.002 TYR A 107 ARG 0.007 0.001 ARG A 230 *********************** 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 160 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.9054 (m-80) cc_final: 0.8789 (m-80) REVERT: A 168 MET cc_start: 0.7662 (tpp) cc_final: 0.6421 (tpt) REVERT: A 237 MET cc_start: 0.8508 (mmt) cc_final: 0.8294 (mmt) REVERT: A 253 TRP cc_start: 0.6620 (t-100) cc_final: 0.6280 (t-100) REVERT: A 266 MET cc_start: 0.5535 (mtt) cc_final: 0.4373 (mmt) REVERT: A 506 ASN cc_start: 0.8245 (t0) cc_final: 0.7898 (t0) REVERT: A 546 ASP cc_start: 0.9360 (m-30) cc_final: 0.9148 (m-30) REVERT: A 635 ASN cc_start: 0.8924 (m110) cc_final: 0.8610 (p0) REVERT: A 640 LEU cc_start: 0.8953 (mt) cc_final: 0.8710 (mt) REVERT: A 666 LYS cc_start: 0.9020 (tppt) cc_final: 0.8568 (tppt) REVERT: A 698 MET cc_start: 0.8178 (mmp) cc_final: 0.7880 (mmp) REVERT: A 709 MET cc_start: 0.8491 (ttm) cc_final: 0.7908 (tpp) REVERT: A 809 SER cc_start: 0.9103 (t) cc_final: 0.8862 (m) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1787 time to fit residues: 39.6040 Evaluate side-chains 115 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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: 4.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7645 Z= 0.176 Angle : 0.618 7.442 10314 Z= 0.319 Chirality : 0.042 0.181 1214 Planarity : 0.004 0.056 1357 Dihedral : 5.275 19.917 1059 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -0.61 (0.26), residues: 990 helix: -0.04 (0.18), residues: 825 sheet: None (None), residues: 0 loop : -1.64 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 702 HIS 0.002 0.001 HIS A 974 PHE 0.015 0.002 PHE A 78 TYR 0.022 0.002 TYR A 107 ARG 0.005 0.000 ARG A 230 *********************** 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 167 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8894 (mt-10) REVERT: A 200 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8214 (mt-10) REVERT: A 266 MET cc_start: 0.5572 (mtt) cc_final: 0.4562 (mmt) REVERT: A 283 TRP cc_start: 0.8155 (t60) cc_final: 0.7707 (t60) REVERT: A 506 ASN cc_start: 0.8246 (t0) cc_final: 0.7917 (t0) REVERT: A 547 ARG cc_start: 0.9442 (tpp80) cc_final: 0.9232 (mmm-85) REVERT: A 603 THR cc_start: 0.8613 (t) cc_final: 0.8336 (m) REVERT: A 635 ASN cc_start: 0.8821 (m110) cc_final: 0.8586 (p0) REVERT: A 640 LEU cc_start: 0.8929 (mt) cc_final: 0.8711 (mt) REVERT: A 698 MET cc_start: 0.8125 (mmp) cc_final: 0.7880 (mmp) REVERT: A 809 SER cc_start: 0.9065 (t) cc_final: 0.8779 (m) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1862 time to fit residues: 43.3021 Evaluate side-chains 120 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 10.0000 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 187 HIS ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4219 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= 0.166 Angle : 0.610 6.961 10314 Z= 0.315 Chirality : 0.042 0.162 1214 Planarity : 0.004 0.056 1357 Dihedral : 5.165 23.755 1059 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % 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: -0.13 (0.27), residues: 990 helix: 0.30 (0.18), residues: 817 sheet: None (None), residues: 0 loop : -1.45 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 394 HIS 0.002 0.001 HIS A 492 PHE 0.008 0.001 PHE A 78 TYR 0.018 0.001 TYR A 100 ARG 0.007 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 172 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.929 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 128 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8862 (mt-10) REVERT: A 244 ILE cc_start: 0.8706 (mm) cc_final: 0.8424 (mm) REVERT: A 253 TRP cc_start: 0.6708 (t-100) cc_final: 0.6428 (t-100) REVERT: A 266 MET cc_start: 0.5399 (mtt) cc_final: 0.4148 (mmt) REVERT: A 283 TRP cc_start: 0.8173 (t60) cc_final: 0.7786 (t60) REVERT: A 506 ASN cc_start: 0.8090 (t0) cc_final: 0.7769 (t0) REVERT: A 547 ARG cc_start: 0.9423 (tpp80) cc_final: 0.9210 (mmm-85) REVERT: A 587 MET cc_start: 0.4854 (mmm) cc_final: 0.4365 (mmt) REVERT: A 603 THR cc_start: 0.8621 (t) cc_final: 0.8393 (m) REVERT: A 635 ASN cc_start: 0.8763 (m110) cc_final: 0.8534 (m110) REVERT: A 640 LEU cc_start: 0.8917 (mt) cc_final: 0.8714 (mt) REVERT: A 709 MET cc_start: 0.8390 (ttm) cc_final: 0.7971 (tpp) REVERT: A 809 SER cc_start: 0.9094 (t) cc_final: 0.8888 (m) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1759 time to fit residues: 41.8993 Evaluate side-chains 127 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7645 Z= 0.205 Angle : 0.646 7.114 10314 Z= 0.337 Chirality : 0.043 0.147 1214 Planarity : 0.004 0.052 1357 Dihedral : 5.209 25.609 1059 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % 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: -0.17 (0.27), residues: 990 helix: 0.24 (0.18), residues: 819 sheet: None (None), residues: 0 loop : -1.33 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 394 HIS 0.016 0.002 HIS A 694 PHE 0.014 0.002 PHE A 817 TYR 0.016 0.001 TYR A 100 ARG 0.006 0.000 ARG A 230 *********************** 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 162 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8879 (mt-10) REVERT: A 173 LYS cc_start: 0.9268 (pptt) cc_final: 0.8726 (tptp) REVERT: A 200 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 253 TRP cc_start: 0.6897 (t-100) cc_final: 0.6522 (t-100) REVERT: A 266 MET cc_start: 0.5523 (mtt) cc_final: 0.4609 (mmt) REVERT: A 506 ASN cc_start: 0.8125 (t0) cc_final: 0.7783 (t0) REVERT: A 587 MET cc_start: 0.5306 (mmm) cc_final: 0.4847 (mmt) REVERT: A 603 THR cc_start: 0.8706 (t) cc_final: 0.8468 (m) REVERT: A 635 ASN cc_start: 0.8783 (m110) cc_final: 0.8548 (m110) REVERT: A 698 MET cc_start: 0.8640 (mpp) cc_final: 0.8218 (mmt) REVERT: A 701 GLN cc_start: 0.8676 (mt0) cc_final: 0.8242 (mt0) REVERT: A 709 MET cc_start: 0.8379 (ttm) cc_final: 0.7852 (tpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1782 time to fit residues: 40.0914 Evaluate side-chains 119 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4547 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= 0.177 Angle : 0.629 7.243 10314 Z= 0.325 Chirality : 0.043 0.184 1214 Planarity : 0.004 0.052 1357 Dihedral : 5.068 23.582 1059 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 0.07 (0.27), residues: 990 helix: 0.46 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -1.45 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 283 HIS 0.015 0.001 HIS A 694 PHE 0.009 0.001 PHE A 817 TYR 0.022 0.002 TYR A 107 ARG 0.006 0.000 ARG A 230 *********************** 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 168 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8855 (mt-10) REVERT: A 173 LYS cc_start: 0.9282 (pptt) cc_final: 0.8778 (tptp) REVERT: A 200 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8330 (mt-10) REVERT: A 244 ILE cc_start: 0.8737 (mm) cc_final: 0.8455 (mm) REVERT: A 266 MET cc_start: 0.5398 (mtt) cc_final: 0.5093 (tpp) REVERT: A 506 ASN cc_start: 0.8004 (t0) cc_final: 0.7669 (t0) REVERT: A 547 ARG cc_start: 0.9446 (tpp80) cc_final: 0.9222 (mmm-85) REVERT: A 587 MET cc_start: 0.5159 (mmm) cc_final: 0.4709 (mmt) REVERT: A 603 THR cc_start: 0.8643 (t) cc_final: 0.8421 (m) REVERT: A 635 ASN cc_start: 0.8744 (m110) cc_final: 0.8519 (m110) REVERT: A 640 LEU cc_start: 0.8673 (mt) cc_final: 0.8199 (mt) REVERT: A 698 MET cc_start: 0.8621 (mpp) cc_final: 0.8095 (mmt) REVERT: A 701 GLN cc_start: 0.8623 (mt0) cc_final: 0.8231 (mt0) REVERT: A 709 MET cc_start: 0.8363 (ttm) cc_final: 0.7891 (tpp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1811 time to fit residues: 41.8060 Evaluate side-chains 125 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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: 5.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 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 18 GLN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** 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: 0.7748 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7645 Z= 0.248 Angle : 0.697 7.186 10314 Z= 0.361 Chirality : 0.045 0.163 1214 Planarity : 0.005 0.058 1357 Dihedral : 5.257 26.659 1059 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -0.29 (0.27), residues: 990 helix: 0.16 (0.18), residues: 813 sheet: None (None), residues: 0 loop : -1.32 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 394 HIS 0.016 0.002 HIS A 694 PHE 0.019 0.002 PHE A 817 TYR 0.026 0.002 TYR A 107 ARG 0.008 0.001 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 158 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8892 (mt-10) REVERT: A 174 MET cc_start: 0.8188 (mmp) cc_final: 0.7943 (mmm) REVERT: A 177 GLU cc_start: 0.8746 (pp20) cc_final: 0.8431 (pp20) REVERT: A 200 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 244 ILE cc_start: 0.8746 (mm) cc_final: 0.8521 (mm) REVERT: A 253 TRP cc_start: 0.7053 (t-100) cc_final: 0.6804 (t-100) REVERT: A 266 MET cc_start: 0.5653 (mtt) cc_final: 0.5432 (tpp) REVERT: A 506 ASN cc_start: 0.8096 (t0) cc_final: 0.7732 (t0) REVERT: A 547 ARG cc_start: 0.9443 (tpp80) cc_final: 0.9225 (mmm-85) REVERT: A 587 MET cc_start: 0.5472 (mmm) cc_final: 0.5098 (mmt) REVERT: A 603 THR cc_start: 0.8734 (t) cc_final: 0.8414 (m) REVERT: A 640 LEU cc_start: 0.8724 (mt) cc_final: 0.8269 (mt) REVERT: A 698 MET cc_start: 0.8710 (mpp) cc_final: 0.7965 (mmt) REVERT: A 701 GLN cc_start: 0.8654 (mt0) cc_final: 0.8185 (mt0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1878 time to fit residues: 41.2647 Evaluate side-chains 126 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** 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: 0.7655 moved from start: 0.4710 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= 0.184 Angle : 0.659 7.164 10314 Z= 0.338 Chirality : 0.043 0.170 1214 Planarity : 0.004 0.051 1357 Dihedral : 5.114 23.697 1059 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 0.12 (0.27), residues: 990 helix: 0.51 (0.18), residues: 802 sheet: None (None), residues: 0 loop : -1.44 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 283 HIS 0.015 0.001 HIS A 694 PHE 0.008 0.001 PHE A 817 TYR 0.024 0.002 TYR A 107 ARG 0.007 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 173 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.9200 (pptt) cc_final: 0.8750 (tptp) REVERT: A 177 GLU cc_start: 0.8659 (pp20) cc_final: 0.8434 (pp20) REVERT: A 200 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 244 ILE cc_start: 0.8721 (mm) cc_final: 0.8520 (mm) REVERT: A 266 MET cc_start: 0.5471 (mtt) cc_final: 0.5182 (tpp) REVERT: A 506 ASN cc_start: 0.7995 (t0) cc_final: 0.7642 (t0) REVERT: A 547 ARG cc_start: 0.9441 (tpp80) cc_final: 0.9228 (mmm-85) REVERT: A 587 MET cc_start: 0.5321 (mmm) cc_final: 0.4942 (mmt) REVERT: A 635 ASN cc_start: 0.8775 (m110) cc_final: 0.8542 (m110) REVERT: A 640 LEU cc_start: 0.8674 (mt) cc_final: 0.8215 (mt) REVERT: A 698 MET cc_start: 0.8644 (mpp) cc_final: 0.7947 (mmt) REVERT: A 701 GLN cc_start: 0.8602 (mt0) cc_final: 0.8126 (mt0) REVERT: A 709 MET cc_start: 0.8404 (ttm) cc_final: 0.8010 (tpp) REVERT: A 799 MET cc_start: 0.8431 (mmp) cc_final: 0.7965 (mmp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1858 time to fit residues: 43.9743 Evaluate side-chains 128 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.088604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.073181 restraints weight = 36225.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.074757 restraints weight = 27188.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.075928 restraints weight = 21824.783| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4899 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= 0.194 Angle : 0.654 7.275 10314 Z= 0.339 Chirality : 0.043 0.170 1214 Planarity : 0.004 0.051 1357 Dihedral : 5.090 24.092 1059 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 0.18 (0.27), residues: 990 helix: 0.57 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -1.50 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 283 HIS 0.015 0.002 HIS A 694 PHE 0.011 0.001 PHE A 817 TYR 0.024 0.002 TYR A 107 ARG 0.008 0.000 ARG A 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1666.60 seconds wall clock time: 30 minutes 32.47 seconds (1832.47 seconds total)