Starting phenix.real_space_refine on Wed Mar 12 07:57:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ktt_23029/03_2025/7ktt_23029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ktt_23029/03_2025/7ktt_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/cci-nas-00/data/ceres_data/7ktt_23029/03_2025/7ktt_23029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ktt_23029/03_2025/7ktt_23029.map" model { file = "/net/cci-nas-00/data/ceres_data/7ktt_23029/03_2025/7ktt_23029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ktt_23029/03_2025/7ktt_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-5624/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: 4.62, per 1000 atoms: 0.61 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: 1.69 Conformation dependent library (CDL) restraints added in 1.0 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: 0.68 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: 2.14 Time building geometry restraints manager: 2.05 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: 1.640 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.070 Find NCS groups from input model: 0.100 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.806 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: 0.2066 time to fit residues: 48.1684 Evaluate side-chains 120 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.084338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.068733 restraints weight = 37418.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.070266 restraints weight = 28133.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.071382 restraints weight = 22612.723| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.832 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: 0.8293 (mmp) cc_final: 0.8059 (mmm) REVERT: A 200 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8636 (mt-10) REVERT: A 253 TRP cc_start: 0.6572 (t-100) cc_final: 0.6133 (t-100) REVERT: A 266 MET cc_start: 0.6097 (mtt) cc_final: 0.5515 (mmt) REVERT: A 506 ASN cc_start: 0.8388 (t0) cc_final: 0.8040 (t0) REVERT: A 640 LEU cc_start: 0.9010 (mt) cc_final: 0.8764 (mt) REVERT: A 809 SER cc_start: 0.8990 (t) cc_final: 0.8723 (m) outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 0.1845 time to fit residues: 40.9004 Evaluate side-chains 117 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 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 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS A 550 GLN A 554 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.087698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.072163 restraints weight = 37105.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.073663 restraints weight = 28152.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.074789 restraints weight = 22809.863| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7645 Z= 0.170 Angle : 0.627 7.060 10314 Z= 0.329 Chirality : 0.042 0.175 1214 Planarity : 0.005 0.052 1357 Dihedral : 5.683 19.491 1059 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.12 % Allowed : 3.45 % Favored : 96.42 % 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: -1.79 (0.25), residues: 990 helix: -0.85 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -1.99 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 394 HIS 0.002 0.001 HIS A 527 PHE 0.018 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 174 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8513 (mmt) cc_final: 0.8242 (mmt) REVERT: A 174 MET cc_start: 0.8219 (mmp) cc_final: 0.7930 (mmm) REVERT: A 253 TRP cc_start: 0.6372 (t-100) cc_final: 0.5937 (t-100) REVERT: A 266 MET cc_start: 0.5617 (mtt) cc_final: 0.4575 (mmt) REVERT: A 506 ASN cc_start: 0.8242 (t0) cc_final: 0.7888 (t0) REVERT: A 546 ASP cc_start: 0.9342 (m-30) cc_final: 0.9134 (m-30) REVERT: A 603 THR cc_start: 0.8660 (t) cc_final: 0.8372 (m) REVERT: A 635 ASN cc_start: 0.8926 (m110) cc_final: 0.8680 (m110) REVERT: A 640 LEU cc_start: 0.8971 (mt) cc_final: 0.8669 (mt) REVERT: A 666 LYS cc_start: 0.8992 (tppt) cc_final: 0.8636 (tppt) REVERT: A 698 MET cc_start: 0.8038 (mmp) cc_final: 0.7809 (mmp) REVERT: A 998 MET cc_start: 0.7266 (pmm) cc_final: 0.6777 (pmm) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1866 time to fit residues: 44.6809 Evaluate side-chains 113 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.085819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.070512 restraints weight = 37679.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.071967 restraints weight = 28705.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073019 restraints weight = 23341.967| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3590 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 : 0.644 7.758 10314 Z= 0.336 Chirality : 0.042 0.148 1214 Planarity : 0.005 0.050 1357 Dihedral : 5.479 19.170 1059 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % 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: -1.17 (0.25), residues: 990 helix: -0.41 (0.17), residues: 817 sheet: None (None), residues: 0 loop : -1.89 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 702 HIS 0.004 0.001 HIS A 27 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 159 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.9001 (m-80) cc_final: 0.8730 (m-80) REVERT: A 168 MET cc_start: 0.7817 (tpp) cc_final: 0.6551 (tpt) REVERT: A 174 MET cc_start: 0.8407 (mmp) cc_final: 0.8192 (mmm) REVERT: A 237 MET cc_start: 0.8496 (mmt) cc_final: 0.8143 (mmt) REVERT: A 266 MET cc_start: 0.5494 (mtt) cc_final: 0.4400 (mmt) REVERT: A 506 ASN cc_start: 0.8276 (t0) cc_final: 0.7907 (t0) REVERT: A 635 ASN cc_start: 0.8961 (m110) cc_final: 0.8725 (m110) REVERT: A 640 LEU cc_start: 0.9061 (mt) cc_final: 0.8810 (mt) REVERT: A 666 LYS cc_start: 0.9077 (tppt) cc_final: 0.8605 (tppt) REVERT: A 698 MET cc_start: 0.8170 (mmp) cc_final: 0.7873 (mmp) REVERT: A 709 MET cc_start: 0.8483 (ttm) cc_final: 0.7871 (tpp) REVERT: A 998 MET cc_start: 0.7620 (pmm) cc_final: 0.7143 (pmm) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2068 time to fit residues: 45.1464 Evaluate side-chains 112 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 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 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 187 HIS ** 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 701 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.084426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069131 restraints weight = 38032.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.070631 restraints weight = 28823.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.071656 restraints weight = 23271.294| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3767 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= 0.238 Angle : 0.665 7.458 10314 Z= 0.347 Chirality : 0.043 0.173 1214 Planarity : 0.005 0.056 1357 Dihedral : 5.425 19.076 1059 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -0.90 (0.26), residues: 990 helix: -0.23 (0.17), residues: 819 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 702 HIS 0.004 0.001 HIS A 974 PHE 0.017 0.003 PHE A 817 TYR 0.022 0.002 TYR A 107 ARG 0.006 0.001 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 153 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8464 (mmp) cc_final: 0.8197 (mmm) REVERT: A 253 TRP cc_start: 0.6830 (t-100) cc_final: 0.6400 (t-100) REVERT: A 266 MET cc_start: 0.5777 (mtt) cc_final: 0.4894 (mmt) REVERT: A 283 TRP cc_start: 0.8204 (t60) cc_final: 0.7726 (t60) REVERT: A 506 ASN cc_start: 0.8224 (t0) cc_final: 0.7862 (t0) REVERT: A 640 LEU cc_start: 0.9075 (mt) cc_final: 0.8866 (mt) REVERT: A 998 MET cc_start: 0.7804 (pmm) cc_final: 0.7593 (pmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1678 time to fit residues: 36.1195 Evaluate side-chains 118 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 59 optimal weight: 0.0050 chunk 22 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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 369 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** A 701 GLN A 974 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.085615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070376 restraints weight = 37762.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.071851 restraints weight = 28510.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.072961 restraints weight = 22959.698| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7645 Z= 0.217 Angle : 0.649 6.854 10314 Z= 0.339 Chirality : 0.043 0.169 1214 Planarity : 0.005 0.056 1357 Dihedral : 5.363 26.310 1059 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: -0.63 (0.26), residues: 990 helix: -0.07 (0.18), residues: 823 sheet: None (None), residues: 0 loop : -1.51 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 394 HIS 0.017 0.002 HIS A 694 PHE 0.016 0.002 PHE A 78 TYR 0.018 0.001 TYR A 100 ARG 0.007 0.001 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 166 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8964 (mt-10) REVERT: A 174 MET cc_start: 0.8545 (mmp) cc_final: 0.8223 (mmm) REVERT: A 193 ASN cc_start: 0.8791 (m110) cc_final: 0.8499 (m110) REVERT: A 266 MET cc_start: 0.5706 (mtt) cc_final: 0.4765 (mmt) REVERT: A 506 ASN cc_start: 0.8217 (t0) cc_final: 0.7855 (t0) REVERT: A 603 THR cc_start: 0.8697 (t) cc_final: 0.8410 (m) REVERT: A 698 MET cc_start: 0.8611 (mpp) cc_final: 0.8142 (mmt) REVERT: A 701 GLN cc_start: 0.8583 (mt0) cc_final: 0.8107 (mt0) REVERT: A 709 MET cc_start: 0.8445 (ttm) cc_final: 0.7878 (tpp) REVERT: A 998 MET cc_start: 0.7926 (pmm) cc_final: 0.7563 (pmm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1924 time to fit residues: 43.8801 Evaluate side-chains 117 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 A 369 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.087679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072403 restraints weight = 36307.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.073906 restraints weight = 27615.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.075080 restraints weight = 22343.764| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4325 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= 0.183 Angle : 0.646 7.203 10314 Z= 0.334 Chirality : 0.043 0.160 1214 Planarity : 0.004 0.056 1357 Dihedral : 5.302 24.535 1059 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -0.33 (0.26), residues: 990 helix: 0.19 (0.18), residues: 815 sheet: None (None), residues: 0 loop : -1.65 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 283 HIS 0.015 0.002 HIS A 694 PHE 0.014 0.002 PHE A 626 TYR 0.019 0.001 TYR A 100 ARG 0.007 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 168 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8956 (t70) cc_final: 0.8646 (t70) REVERT: A 128 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8907 (mt-10) REVERT: A 173 LYS cc_start: 0.9355 (pptt) cc_final: 0.8758 (tptp) REVERT: A 233 THR cc_start: 0.9033 (m) cc_final: 0.8790 (p) REVERT: A 253 TRP cc_start: 0.6869 (t-100) cc_final: 0.6542 (t-100) REVERT: A 266 MET cc_start: 0.5651 (mtt) cc_final: 0.4503 (mmt) REVERT: A 506 ASN cc_start: 0.8179 (t0) cc_final: 0.7804 (t0) REVERT: A 603 THR cc_start: 0.8693 (t) cc_final: 0.8405 (m) REVERT: A 635 ASN cc_start: 0.8905 (m110) cc_final: 0.8705 (m110) REVERT: A 640 LEU cc_start: 0.8869 (mt) cc_final: 0.8408 (mt) REVERT: A 698 MET cc_start: 0.8669 (mpp) cc_final: 0.8303 (mmt) REVERT: A 701 GLN cc_start: 0.8656 (mt0) cc_final: 0.8253 (mt0) REVERT: A 709 MET cc_start: 0.8434 (ttm) cc_final: 0.7900 (tpp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1684 time to fit residues: 39.5857 Evaluate side-chains 123 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 369 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.085322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.069977 restraints weight = 38445.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.071479 restraints weight = 29056.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.072595 restraints weight = 23477.344| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4357 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= 0.251 Angle : 0.703 11.096 10314 Z= 0.365 Chirality : 0.045 0.178 1214 Planarity : 0.005 0.051 1357 Dihedral : 5.337 25.531 1059 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.55 (0.26), residues: 990 helix: 0.01 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.60 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 394 HIS 0.015 0.002 HIS A 694 PHE 0.019 0.002 PHE A 817 TYR 0.017 0.002 TYR A 100 ARG 0.006 0.001 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 160 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8917 (t70) cc_final: 0.8611 (t70) REVERT: A 128 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8936 (mt-10) REVERT: A 200 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 253 TRP cc_start: 0.7204 (t-100) cc_final: 0.6849 (t-100) REVERT: A 266 MET cc_start: 0.5906 (mtt) cc_final: 0.5648 (tpp) REVERT: A 283 TRP cc_start: 0.8270 (t60) cc_final: 0.7736 (t60) REVERT: A 506 ASN cc_start: 0.8216 (t0) cc_final: 0.7823 (t0) REVERT: A 591 MET cc_start: 0.8066 (tpt) cc_final: 0.7735 (tpt) REVERT: A 640 LEU cc_start: 0.8909 (mt) cc_final: 0.8572 (mt) REVERT: A 698 MET cc_start: 0.8677 (mpp) cc_final: 0.8064 (mmt) REVERT: A 701 GLN cc_start: 0.8641 (mt0) cc_final: 0.8129 (mt0) REVERT: A 709 MET cc_start: 0.8420 (ttm) cc_final: 0.7899 (tpp) REVERT: A 998 MET cc_start: 0.7754 (pmm) cc_final: 0.7499 (pmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1684 time to fit residues: 38.2650 Evaluate side-chains 118 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 180 GLN A 369 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** A 701 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.084718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.069408 restraints weight = 38462.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.070910 restraints weight = 28851.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.072038 restraints weight = 23102.880| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7645 Z= 0.256 Angle : 0.704 11.667 10314 Z= 0.366 Chirality : 0.045 0.153 1214 Planarity : 0.005 0.049 1357 Dihedral : 5.366 24.979 1059 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 990 helix: -0.01 (0.18), residues: 815 sheet: None (None), residues: 0 loop : -1.55 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 394 HIS 0.014 0.002 HIS A 694 PHE 0.019 0.002 PHE A 817 TYR 0.018 0.002 TYR A 100 ARG 0.006 0.001 ARG A 230 *********************** 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 155 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8338 (mmp) cc_final: 0.8088 (mmm) REVERT: A 177 GLU cc_start: 0.8866 (pp20) cc_final: 0.8663 (pp20) REVERT: A 244 ILE cc_start: 0.8897 (mm) cc_final: 0.8683 (mm) REVERT: A 253 TRP cc_start: 0.7211 (t-100) cc_final: 0.6900 (t-100) REVERT: A 266 MET cc_start: 0.5825 (mtt) cc_final: 0.5607 (tpp) REVERT: A 283 TRP cc_start: 0.8251 (t60) cc_final: 0.7783 (t60) REVERT: A 506 ASN cc_start: 0.8204 (t0) cc_final: 0.7791 (t0) REVERT: A 640 LEU cc_start: 0.8919 (mt) cc_final: 0.8473 (mt) REVERT: A 698 MET cc_start: 0.8618 (mpp) cc_final: 0.8030 (mmt) REVERT: A 701 GLN cc_start: 0.8512 (mt0) cc_final: 0.8030 (mt0) REVERT: A 709 MET cc_start: 0.8329 (ttm) cc_final: 0.7868 (tpp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1852 time to fit residues: 40.5994 Evaluate side-chains 124 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 369 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.087994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072503 restraints weight = 36664.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.074035 restraints weight = 27516.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.075206 restraints weight = 22120.652| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7645 Z= 0.188 Angle : 0.683 10.110 10314 Z= 0.350 Chirality : 0.044 0.185 1214 Planarity : 0.005 0.054 1357 Dihedral : 5.259 26.896 1059 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 0.30 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -1.50 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 283 HIS 0.014 0.001 HIS A 694 PHE 0.008 0.001 PHE A 817 TYR 0.018 0.001 TYR A 100 ARG 0.009 0.001 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 167 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.9205 (pptt) cc_final: 0.8703 (tptp) REVERT: A 233 THR cc_start: 0.8922 (m) cc_final: 0.8695 (p) REVERT: A 244 ILE cc_start: 0.8839 (mm) cc_final: 0.8635 (mm) REVERT: A 266 MET cc_start: 0.5546 (mtt) cc_final: 0.4744 (mmt) REVERT: A 506 ASN cc_start: 0.8080 (t0) cc_final: 0.7671 (t0) REVERT: A 635 ASN cc_start: 0.8853 (m110) cc_final: 0.8637 (m-40) REVERT: A 640 LEU cc_start: 0.8826 (mt) cc_final: 0.8377 (mt) REVERT: A 698 MET cc_start: 0.8643 (mpp) cc_final: 0.7877 (mmt) REVERT: A 701 GLN cc_start: 0.8493 (mt0) cc_final: 0.8027 (mt0) REVERT: A 709 MET cc_start: 0.8352 (ttm) cc_final: 0.8022 (tpp) REVERT: A 799 MET cc_start: 0.8256 (mmp) cc_final: 0.7853 (mmp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1854 time to fit residues: 43.9815 Evaluate side-chains 122 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 369 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.085988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.070678 restraints weight = 37306.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.072188 restraints weight = 28038.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073186 restraints weight = 22571.736| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7645 Z= 0.236 Angle : 0.707 11.515 10314 Z= 0.364 Chirality : 0.045 0.160 1214 Planarity : 0.005 0.051 1357 Dihedral : 5.285 23.258 1059 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.29 (0.27), residues: 990 helix: 0.20 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.51 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 253 HIS 0.014 0.002 HIS A 694 PHE 0.016 0.002 PHE A 817 TYR 0.016 0.001 TYR A 100 ARG 0.008 0.001 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.31 seconds wall clock time: 42 minutes 7.09 seconds (2527.09 seconds total)