Starting phenix.real_space_refine on Tue Sep 24 08:39:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/09_2024/7ktw_23032.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/09_2024/7ktw_23032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/09_2024/7ktw_23032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/09_2024/7ktw_23032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/09_2024/7ktw_23032.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/09_2024/7ktw_23032.cif" } resolution = 4.27 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= 0.032 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 4671 2.51 5 N 1373 2.21 5 O 1490 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: 7577 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7577 Classifications: {'peptide': 995} Link IDs: {'PTRANS': 35, 'TRANS': 959} Chain breaks: 1 Time building chain proxies: 4.87, per 1000 atoms: 0.64 Number of scatterers: 7577 At special positions: 0 Unit cell: (84.975, 97.35, 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 1490 8.00 N 1373 7.00 C 4671 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: 1.98 Conformation dependent library (CDL) restraints added in 1.0 seconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.622A pdb=" N GLU A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) Proline residue: A 15 - end of helix removed outlier: 3.578A pdb=" N LEU A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N MET A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 65 removed outlier: 3.783A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 98 removed outlier: 4.145A pdb=" N ASP A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.621A pdb=" N ILE A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 148 removed outlier: 4.315A pdb=" N TYR A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 removed outlier: 3.509A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.683A pdb=" N LYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 218 removed outlier: 3.629A pdb=" N MET A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.535A pdb=" N THR A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 249 removed outlier: 4.243A pdb=" N GLU A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 4.550A pdb=" N ALA A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.946A pdb=" N LYS A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 removed outlier: 3.536A pdb=" N VAL A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 342 removed outlier: 3.640A pdb=" N GLU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 389 removed outlier: 3.604A pdb=" N VAL A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.896A pdb=" N TRP A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 424 removed outlier: 3.580A pdb=" N ILE A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 451 removed outlier: 3.925A pdb=" N ARG A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 479 removed outlier: 3.746A pdb=" N LYS A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.783A pdb=" N TRP A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.634A pdb=" N GLU A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 550 removed outlier: 3.785A pdb=" N ASP A 540 " --> pdb=" O PRO A 536 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.926A pdb=" N GLN A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 599 removed outlier: 4.054A pdb=" N LEU A 572 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 586 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.870A pdb=" N ALA A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 650 removed outlier: 3.670A pdb=" N LYS A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 685 removed outlier: 3.624A pdb=" N VAL A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Proline residue: A 673 - end of helix Processing helix chain 'A' and resid 688 through 717 removed outlier: 3.810A pdb=" N ASN A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 705 " --> pdb=" O GLN A 701 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 743 removed outlier: 3.852A pdb=" N ASP A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 774 removed outlier: 3.506A pdb=" N LEU A 749 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 794 Processing helix chain 'A' and resid 794 through 805 removed outlier: 3.887A pdb=" N VAL A 798 " --> pdb=" O ILE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 836 removed outlier: 3.510A pdb=" N ILE A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 835 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 976 removed outlier: 3.808A pdb=" N LEU A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 975 " --> pdb=" O GLN A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1005 removed outlier: 3.738A pdb=" N ALA A 991 " --> pdb=" O ILE A 987 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1040 removed outlier: 3.879A pdb=" N LEU A1015 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A1026 " --> pdb=" O ILE A1022 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1054 through 1074 removed outlier: 3.868A pdb=" N THR A1058 " --> pdb=" O GLU A1054 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A1061 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1112 removed outlier: 3.806A pdb=" N SER A1084 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A1095 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A1103 " --> pdb=" O MET A1099 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1112 " --> pdb=" O GLU A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1116 removed outlier: 3.741A pdb=" N ILE A1116 " --> pdb=" O SER A1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1113 through 1116' 551 hydrogen bonds defined for protein. 1653 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: 2.16 Time building geometry restraints manager: 2.30 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: 2625 1.34 - 1.46: 1040 1.46 - 1.57: 3913 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7654 Sorted by residual: bond pdb=" C ILE A1056 " pdb=" N PRO A1057 " ideal model delta sigma weight residual 1.337 1.368 -0.031 1.24e-02 6.50e+03 6.38e+00 bond pdb=" C GLN A 964 " pdb=" N PRO A 965 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.34e+00 bond pdb=" CA THR A 710 " pdb=" C THR A 710 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.27e-02 6.20e+03 3.64e+00 bond pdb=" C VAL A 102 " pdb=" N PRO A 103 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.58e+00 bond pdb=" C GLU A 14 " pdb=" N PRO A 15 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.30e-02 5.92e+03 3.32e+00 ... (remaining 7649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 9841 2.29 - 4.57: 417 4.57 - 6.86: 47 6.86 - 9.14: 15 9.14 - 11.43: 5 Bond angle restraints: 10325 Sorted by residual: angle pdb=" C ILE A 987 " pdb=" N ILE A 988 " pdb=" CA ILE A 988 " ideal model delta sigma weight residual 120.53 130.49 -9.96 1.41e+00 5.03e-01 4.99e+01 angle pdb=" C LYS A 979 " pdb=" N TRP A 980 " pdb=" CA TRP A 980 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" N GLY A 535 " pdb=" CA GLY A 535 " pdb=" C GLY A 535 " ideal model delta sigma weight residual 112.34 120.46 -8.12 2.04e+00 2.40e-01 1.58e+01 angle pdb=" N GLY A 984 " pdb=" CA GLY A 984 " pdb=" C GLY A 984 " ideal model delta sigma weight residual 111.42 116.78 -5.36 1.42e+00 4.96e-01 1.42e+01 angle pdb=" N THR A 697 " pdb=" CA THR A 697 " pdb=" C THR A 697 " ideal model delta sigma weight residual 111.03 106.88 4.15 1.11e+00 8.12e-01 1.40e+01 ... (remaining 10320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 4418 15.12 - 30.24: 303 30.24 - 45.35: 108 45.35 - 60.47: 6 60.47 - 75.59: 9 Dihedral angle restraints: 4844 sinusoidal: 1958 harmonic: 2886 Sorted by residual: dihedral pdb=" CA ASP A 511 " pdb=" C ASP A 511 " pdb=" N ARG A 512 " pdb=" CA ARG A 512 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG A1003 " pdb=" C ARG A1003 " pdb=" N LEU A1004 " pdb=" CA LEU A1004 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ASN A 963 " pdb=" C ASN A 963 " pdb=" N GLN A 964 " pdb=" CA GLN A 964 " ideal model delta harmonic sigma weight residual 180.00 157.09 22.91 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 4841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 844 0.051 - 0.102: 294 0.102 - 0.153: 63 0.153 - 0.204: 11 0.204 - 0.255: 3 Chirality restraints: 1215 Sorted by residual: chirality pdb=" CG LEU A 250 " pdb=" CB LEU A 250 " pdb=" CD1 LEU A 250 " pdb=" CD2 LEU A 250 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CG LEU A 322 " pdb=" CB LEU A 322 " pdb=" CD1 LEU A 322 " pdb=" CD2 LEU A 322 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL A 3 " pdb=" CA VAL A 3 " pdb=" CG1 VAL A 3 " pdb=" CG2 VAL A 3 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1212 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 346 " -0.054 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 347 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 964 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 965 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 965 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 965 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 42 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 43 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.033 5.00e-02 4.00e+02 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1348 2.75 - 3.29: 8626 3.29 - 3.83: 13765 3.83 - 4.36: 16773 4.36 - 4.90: 24654 Nonbonded interactions: 65166 Sorted by model distance: nonbonded pdb=" O ASP A 121 " pdb=" OG1 THR A 125 " model vdw 2.214 3.040 nonbonded pdb=" O HIS A 694 " pdb=" OG1 THR A 697 " model vdw 2.222 3.040 nonbonded pdb=" O GLU A 143 " pdb=" OG1 THR A 146 " model vdw 2.248 3.040 nonbonded pdb=" O LEU A 191 " pdb=" OG SER A 194 " model vdw 2.275 3.040 nonbonded pdb=" O VAL A1069 " pdb=" OG1 THR A1072 " model vdw 2.277 3.040 ... (remaining 65161 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: 0.010 Normalize map: mean=0, sd=1: 0.800 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.500 Find NCS groups from input model: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 0.071 7654 Z= 0.457 Angle : 1.121 11.429 10325 Z= 0.644 Chirality : 0.054 0.255 1215 Planarity : 0.007 0.080 1358 Dihedral : 12.461 75.590 2958 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.18 % 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: -4.61 (0.20), residues: 991 helix: -2.98 (0.13), residues: 745 sheet: None (None), residues: 0 loop : -2.47 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 702 HIS 0.018 0.004 HIS A 27 PHE 0.029 0.004 PHE A 4 TYR 0.022 0.003 TYR A 107 ARG 0.020 0.002 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 0.867 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: 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 72 ARG cc_start: 0.8532 (tpm170) cc_final: 0.8268 (tpm170) REVERT: A 113 ARG cc_start: 0.9219 (ptm160) cc_final: 0.8717 (ptp-170) REVERT: A 137 VAL cc_start: 0.9530 (t) cc_final: 0.9222 (t) REVERT: A 174 MET cc_start: 0.8746 (mmm) cc_final: 0.8395 (mmm) REVERT: A 181 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 190 MET cc_start: 0.9301 (mtt) cc_final: 0.9003 (mtt) REVERT: A 199 LYS cc_start: 0.8947 (tptp) cc_final: 0.8717 (tptp) REVERT: A 201 LEU cc_start: 0.9649 (tp) cc_final: 0.9361 (tp) REVERT: A 205 LEU cc_start: 0.9770 (tt) cc_final: 0.9504 (tp) REVERT: A 237 MET cc_start: 0.9499 (mtm) cc_final: 0.8901 (ttm) REVERT: A 245 ILE cc_start: 0.9249 (mt) cc_final: 0.8923 (mt) REVERT: A 416 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7365 (mtp180) REVERT: A 471 GLN cc_start: 0.8739 (pt0) cc_final: 0.8012 (pt0) REVERT: A 498 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9037 (mm-30) REVERT: A 502 ARG cc_start: 0.9104 (ttp80) cc_final: 0.8692 (ttt-90) REVERT: A 533 MET cc_start: 0.9493 (mtm) cc_final: 0.8977 (mtp) REVERT: A 591 MET cc_start: 0.9096 (tpt) cc_final: 0.8728 (tpt) REVERT: A 635 ASN cc_start: 0.9219 (m-40) cc_final: 0.8952 (m110) REVERT: A 646 LYS cc_start: 0.9313 (mtmm) cc_final: 0.8910 (mtmm) REVERT: A 701 GLN cc_start: 0.9372 (tp-100) cc_final: 0.9132 (tp-100) REVERT: A 707 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8967 (tp30) REVERT: A 748 MET cc_start: 0.9247 (mmp) cc_final: 0.9019 (mmm) REVERT: A 784 LYS cc_start: 0.9666 (ttmm) cc_final: 0.9439 (tppt) REVERT: A 797 MET cc_start: 0.9275 (mmm) cc_final: 0.9028 (mmp) REVERT: A 799 MET cc_start: 0.9476 (mtt) cc_final: 0.9006 (tpt) REVERT: A 823 ARG cc_start: 0.9272 (mpp80) cc_final: 0.8851 (mtt180) REVERT: A 836 GLN cc_start: 0.8696 (mm110) cc_final: 0.8410 (mp10) REVERT: A 1028 GLU cc_start: 0.9667 (tt0) cc_final: 0.9402 (tm-30) REVERT: A 1046 ARG cc_start: 0.9239 (ttm110) cc_final: 0.8709 (mtm110) REVERT: A 1073 MET cc_start: 0.9216 (mmt) cc_final: 0.8959 (mmm) REVERT: A 1083 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8429 (mm-30) REVERT: A 1090 MET cc_start: 0.9116 (mmt) cc_final: 0.8799 (mmm) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.2700 time to fit residues: 77.0885 Evaluate side-chains 167 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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: 0.4980 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 471 GLN A 575 GLN A 814 GLN A1086 GLN A1093 HIS A1094 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7654 Z= 0.218 Angle : 0.722 7.331 10325 Z= 0.384 Chirality : 0.041 0.142 1215 Planarity : 0.006 0.050 1358 Dihedral : 5.763 19.872 1060 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.49 % Allowed : 3.08 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.23), residues: 991 helix: -1.40 (0.15), residues: 812 sheet: None (None), residues: 0 loop : -2.43 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 258 HIS 0.009 0.002 HIS A 694 PHE 0.018 0.003 PHE A 126 TYR 0.020 0.002 TYR A 107 ARG 0.010 0.001 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 229 time to evaluate : 1.048 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 THR cc_start: 0.9596 (p) cc_final: 0.9384 (t) REVERT: A 113 ARG cc_start: 0.9055 (ptm160) cc_final: 0.8193 (ptm160) REVERT: A 174 MET cc_start: 0.8823 (mmm) cc_final: 0.8181 (mmm) REVERT: A 176 ASP cc_start: 0.9473 (t0) cc_final: 0.8729 (t0) REVERT: A 180 GLN cc_start: 0.9267 (mt0) cc_final: 0.8973 (mm-40) REVERT: A 205 LEU cc_start: 0.9672 (tt) cc_final: 0.9412 (tt) REVERT: A 237 MET cc_start: 0.9467 (mtm) cc_final: 0.8959 (mtm) REVERT: A 252 SER cc_start: 0.9061 (t) cc_final: 0.8832 (t) REVERT: A 253 TRP cc_start: 0.4398 (m100) cc_final: 0.3710 (m100) REVERT: A 331 MET cc_start: 0.8817 (ttt) cc_final: 0.8464 (ttt) REVERT: A 424 ASP cc_start: 0.8904 (t0) cc_final: 0.8620 (m-30) REVERT: A 431 ILE cc_start: 0.8577 (mm) cc_final: 0.8335 (mm) REVERT: A 471 GLN cc_start: 0.8855 (pt0) cc_final: 0.8392 (pt0) REVERT: A 533 MET cc_start: 0.9445 (mtm) cc_final: 0.9201 (mtp) REVERT: A 662 GLN cc_start: 0.9450 (mt0) cc_final: 0.9037 (mp10) REVERT: A 748 MET cc_start: 0.9312 (mmp) cc_final: 0.9076 (mpp) REVERT: A 749 LEU cc_start: 0.8823 (mt) cc_final: 0.8441 (mt) REVERT: A 792 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9364 (mmmm) REVERT: A 799 MET cc_start: 0.9554 (mtt) cc_final: 0.9189 (tpt) REVERT: A 823 ARG cc_start: 0.9227 (mpp80) cc_final: 0.8773 (mtt180) REVERT: A 998 MET cc_start: 0.8411 (tpp) cc_final: 0.8047 (tpp) REVERT: A 1029 VAL cc_start: 0.9572 (t) cc_final: 0.9337 (t) REVERT: A 1046 ARG cc_start: 0.9366 (ttm110) cc_final: 0.8758 (mtm110) REVERT: A 1083 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8234 (mm-30) REVERT: A 1090 MET cc_start: 0.9083 (mmt) cc_final: 0.8754 (mmm) outliers start: 4 outliers final: 0 residues processed: 230 average time/residue: 0.2574 time to fit residues: 74.3790 Evaluate side-chains 177 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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: 3.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 179 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN A 814 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7654 Z= 0.195 Angle : 0.664 7.113 10325 Z= 0.343 Chirality : 0.040 0.120 1215 Planarity : 0.005 0.044 1358 Dihedral : 5.324 18.635 1060 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.37 % Allowed : 4.19 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.25), residues: 991 helix: -0.55 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -2.03 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 253 HIS 0.009 0.001 HIS A 187 PHE 0.018 0.002 PHE A 78 TYR 0.023 0.001 TYR A 107 ARG 0.022 0.001 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 0.841 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: 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: 0.9024 (mmm) cc_final: 0.8325 (mmm) REVERT: A 176 ASP cc_start: 0.9503 (t0) cc_final: 0.9167 (t0) REVERT: A 180 GLN cc_start: 0.9277 (mt0) cc_final: 0.8917 (mm-40) REVERT: A 187 HIS cc_start: 0.8339 (t70) cc_final: 0.8017 (t70) REVERT: A 201 LEU cc_start: 0.9570 (tp) cc_final: 0.9152 (tp) REVERT: A 205 LEU cc_start: 0.9636 (tt) cc_final: 0.9288 (tt) REVERT: A 216 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8996 (tmtt) REVERT: A 224 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9238 (mt-10) REVERT: A 227 LEU cc_start: 0.9694 (tp) cc_final: 0.9390 (pp) REVERT: A 237 MET cc_start: 0.9537 (mtm) cc_final: 0.9015 (mtm) REVERT: A 252 SER cc_start: 0.9154 (t) cc_final: 0.8895 (t) REVERT: A 253 TRP cc_start: 0.4413 (m100) cc_final: 0.3845 (m100) REVERT: A 416 ARG cc_start: 0.7730 (mtp180) cc_final: 0.7079 (mtp180) REVERT: A 496 LYS cc_start: 0.9282 (mtmm) cc_final: 0.9029 (mttt) REVERT: A 533 MET cc_start: 0.9454 (mtm) cc_final: 0.9227 (mtp) REVERT: A 591 MET cc_start: 0.9380 (mmm) cc_final: 0.9148 (mmm) REVERT: A 633 PHE cc_start: 0.9189 (t80) cc_final: 0.8852 (t80) REVERT: A 635 ASN cc_start: 0.9161 (m110) cc_final: 0.8901 (m110) REVERT: A 662 GLN cc_start: 0.9466 (mt0) cc_final: 0.9047 (mp10) REVERT: A 792 LYS cc_start: 0.9570 (mmtm) cc_final: 0.9362 (mmmm) REVERT: A 799 MET cc_start: 0.9542 (mtt) cc_final: 0.9167 (tpt) REVERT: A 832 ARG cc_start: 0.8791 (tpm170) cc_final: 0.8166 (tpp-160) REVERT: A 1046 ARG cc_start: 0.9355 (ttm110) cc_final: 0.8953 (ttm110) REVERT: A 1083 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8135 (mm-30) REVERT: A 1090 MET cc_start: 0.9019 (mmt) cc_final: 0.8708 (mmm) REVERT: A 1110 GLU cc_start: 0.9328 (mp0) cc_final: 0.9087 (mp0) outliers start: 3 outliers final: 0 residues processed: 229 average time/residue: 0.2372 time to fit residues: 68.8174 Evaluate side-chains 168 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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: 9.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 193 ASN A 279 GLN A 379 ASN A 492 HIS ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7654 Z= 0.186 Angle : 0.658 6.989 10325 Z= 0.339 Chirality : 0.040 0.162 1215 Planarity : 0.004 0.060 1358 Dihedral : 4.998 18.359 1060 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.25 % Allowed : 3.82 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.26), residues: 991 helix: -0.02 (0.17), residues: 803 sheet: None (None), residues: 0 loop : -1.61 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 702 HIS 0.008 0.001 HIS A 187 PHE 0.019 0.002 PHE A 78 TYR 0.020 0.001 TYR A 107 ARG 0.008 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 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: 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: symmetry clash REVERT: A 138 CYS cc_start: 0.8841 (m) cc_final: 0.8559 (m) REVERT: A 174 MET cc_start: 0.8852 (mmm) cc_final: 0.8610 (mmm) REVERT: A 176 ASP cc_start: 0.9493 (t0) cc_final: 0.8884 (t0) REVERT: A 180 GLN cc_start: 0.9202 (mt0) cc_final: 0.8882 (mm-40) REVERT: A 205 LEU cc_start: 0.9631 (tt) cc_final: 0.9255 (tt) REVERT: A 216 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8942 (tmtt) REVERT: A 224 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9240 (mt-10) REVERT: A 227 LEU cc_start: 0.9697 (tp) cc_final: 0.9400 (pp) REVERT: A 237 MET cc_start: 0.9472 (mtm) cc_final: 0.9235 (mtt) REVERT: A 245 ILE cc_start: 0.9401 (mt) cc_final: 0.8749 (mt) REVERT: A 253 TRP cc_start: 0.4488 (m100) cc_final: 0.4244 (m100) REVERT: A 416 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7041 (mtp180) REVERT: A 496 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9000 (mttt) REVERT: A 533 MET cc_start: 0.9439 (mtm) cc_final: 0.9177 (mtp) REVERT: A 633 PHE cc_start: 0.9125 (t80) cc_final: 0.8894 (t80) REVERT: A 635 ASN cc_start: 0.9158 (m110) cc_final: 0.8857 (m110) REVERT: A 662 GLN cc_start: 0.9433 (mt0) cc_final: 0.9229 (mp10) REVERT: A 709 MET cc_start: 0.8911 (mmt) cc_final: 0.8708 (mmt) REVERT: A 799 MET cc_start: 0.9544 (mtt) cc_final: 0.9181 (tpt) REVERT: A 832 ARG cc_start: 0.8724 (tpm170) cc_final: 0.8140 (tpp-160) REVERT: A 1046 ARG cc_start: 0.9336 (ttm110) cc_final: 0.8899 (ttm110) REVERT: A 1090 MET cc_start: 0.8951 (mmt) cc_final: 0.8630 (mmm) REVERT: A 1099 MET cc_start: 0.8442 (mmp) cc_final: 0.8132 (mmp) outliers start: 2 outliers final: 1 residues processed: 221 average time/residue: 0.2482 time to fit residues: 69.5784 Evaluate side-chains 171 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 492 HIS A 593 GLN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7654 Z= 0.213 Angle : 0.691 7.159 10325 Z= 0.359 Chirality : 0.041 0.169 1215 Planarity : 0.004 0.050 1358 Dihedral : 4.941 22.914 1060 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -0.25 (0.26), residues: 991 helix: 0.22 (0.18), residues: 806 sheet: None (None), residues: 0 loop : -1.39 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 394 HIS 0.005 0.001 HIS A 187 PHE 0.016 0.002 PHE A 78 TYR 0.016 0.002 TYR A 107 ARG 0.007 0.001 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9293 (mmm) cc_final: 0.8926 (mmm) REVERT: A 86 THR cc_start: 0.9593 (p) cc_final: 0.9387 (p) REVERT: A 113 ARG cc_start: 0.9175 (ptm-80) cc_final: 0.8206 (ptp-110) REVERT: A 128 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8873 (mt-10) REVERT: A 174 MET cc_start: 0.9037 (mmm) cc_final: 0.8782 (mmm) REVERT: A 205 LEU cc_start: 0.9653 (tt) cc_final: 0.9394 (tt) REVERT: A 227 LEU cc_start: 0.9699 (tp) cc_final: 0.9414 (pp) REVERT: A 237 MET cc_start: 0.9510 (mtm) cc_final: 0.9113 (mtp) REVERT: A 245 ILE cc_start: 0.9403 (mt) cc_final: 0.8898 (mt) REVERT: A 252 SER cc_start: 0.9097 (m) cc_final: 0.8892 (t) REVERT: A 416 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7007 (mtp180) REVERT: A 525 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8998 (mm-30) REVERT: A 533 MET cc_start: 0.9369 (mtm) cc_final: 0.9044 (mtt) REVERT: A 633 PHE cc_start: 0.9184 (t80) cc_final: 0.8907 (t80) REVERT: A 635 ASN cc_start: 0.9166 (m110) cc_final: 0.8912 (m110) REVERT: A 646 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8914 (mttm) REVERT: A 662 GLN cc_start: 0.9449 (mt0) cc_final: 0.8992 (mp10) REVERT: A 707 GLU cc_start: 0.9347 (mp0) cc_final: 0.9110 (mp0) REVERT: A 799 MET cc_start: 0.9579 (mtt) cc_final: 0.9183 (tpt) REVERT: A 832 ARG cc_start: 0.8775 (tpm170) cc_final: 0.8239 (tpp-160) REVERT: A 994 MET cc_start: 0.9211 (ppp) cc_final: 0.8975 (ppp) REVERT: A 1046 ARG cc_start: 0.9316 (ttm110) cc_final: 0.8843 (ttm110) REVERT: A 1090 MET cc_start: 0.8962 (mmt) cc_final: 0.8633 (mmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2527 time to fit residues: 64.4933 Evaluate side-chains 160 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.0030 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 279 GLN ** A 694 HIS ** 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: 0.8088 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7654 Z= 0.204 Angle : 0.689 7.958 10325 Z= 0.352 Chirality : 0.041 0.152 1215 Planarity : 0.004 0.048 1358 Dihedral : 4.866 20.624 1060 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.49 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: -0.14 (0.26), residues: 991 helix: 0.31 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -1.42 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 253 HIS 0.004 0.001 HIS A 187 PHE 0.018 0.002 PHE A 78 TYR 0.016 0.001 TYR A 107 ARG 0.005 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.892 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: 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 74 MET cc_start: 0.9317 (mmm) cc_final: 0.8731 (mmm) REVERT: A 163 ASN cc_start: 0.9137 (m110) cc_final: 0.8932 (m-40) REVERT: A 174 MET cc_start: 0.9039 (mmm) cc_final: 0.8797 (mmm) REVERT: A 176 ASP cc_start: 0.9277 (m-30) cc_final: 0.8959 (m-30) REVERT: A 227 LEU cc_start: 0.9708 (tp) cc_final: 0.9423 (pp) REVERT: A 237 MET cc_start: 0.9489 (mtm) cc_final: 0.9249 (mtt) REVERT: A 245 ILE cc_start: 0.9426 (mt) cc_final: 0.8808 (mt) REVERT: A 407 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8569 (tm-30) REVERT: A 416 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7278 (mtp180) REVERT: A 479 ARG cc_start: 0.8911 (mmp80) cc_final: 0.8523 (mmm160) REVERT: A 525 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9041 (mm-30) REVERT: A 533 MET cc_start: 0.9340 (mtm) cc_final: 0.8905 (mtm) REVERT: A 633 PHE cc_start: 0.9154 (t80) cc_final: 0.8878 (t80) REVERT: A 635 ASN cc_start: 0.9132 (m110) cc_final: 0.8875 (m110) REVERT: A 645 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8578 (mt-10) REVERT: A 646 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8892 (mttm) REVERT: A 662 GLN cc_start: 0.9427 (mt0) cc_final: 0.9199 (mp10) REVERT: A 702 TRP cc_start: 0.9048 (t60) cc_final: 0.8574 (t60) REVERT: A 799 MET cc_start: 0.9546 (mtt) cc_final: 0.9173 (tpt) REVERT: A 832 ARG cc_start: 0.8756 (tpm170) cc_final: 0.8235 (tpp-160) REVERT: A 994 MET cc_start: 0.9154 (ppp) cc_final: 0.8913 (ppp) REVERT: A 1011 THR cc_start: 0.8838 (m) cc_final: 0.8498 (p) REVERT: A 1046 ARG cc_start: 0.9337 (ttm110) cc_final: 0.8906 (ttm110) REVERT: A 1081 ASP cc_start: 0.8767 (t0) cc_final: 0.8196 (p0) REVERT: A 1090 MET cc_start: 0.8908 (mmt) cc_final: 0.8597 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2531 time to fit residues: 66.6156 Evaluate side-chains 161 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7654 Z= 0.195 Angle : 0.711 7.395 10325 Z= 0.369 Chirality : 0.042 0.149 1215 Planarity : 0.004 0.046 1358 Dihedral : 4.835 20.335 1060 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 (0.26), residues: 991 helix: 0.30 (0.18), residues: 811 sheet: None (None), residues: 0 loop : -1.52 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 253 HIS 0.007 0.001 HIS A 187 PHE 0.020 0.002 PHE A 78 TYR 0.015 0.001 TYR A 107 ARG 0.003 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.987 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: 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: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9360 (mmm) cc_final: 0.8951 (mmm) REVERT: A 132 ARG cc_start: 0.9228 (mmm160) cc_final: 0.8912 (mmm-85) REVERT: A 174 MET cc_start: 0.8909 (mmm) cc_final: 0.8621 (mmm) REVERT: A 190 MET cc_start: 0.9393 (pmm) cc_final: 0.9140 (pmm) REVERT: A 227 LEU cc_start: 0.9694 (tp) cc_final: 0.9214 (pp) REVERT: A 237 MET cc_start: 0.9489 (mtm) cc_final: 0.9253 (mtt) REVERT: A 245 ILE cc_start: 0.9452 (mt) cc_final: 0.8926 (mt) REVERT: A 407 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 416 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7288 (mtp180) REVERT: A 479 ARG cc_start: 0.8905 (mmp80) cc_final: 0.8527 (mmm160) REVERT: A 525 GLU cc_start: 0.9245 (mm-30) cc_final: 0.9035 (mm-30) REVERT: A 533 MET cc_start: 0.9400 (mtm) cc_final: 0.8960 (mtm) REVERT: A 633 PHE cc_start: 0.9129 (t80) cc_final: 0.8878 (t80) REVERT: A 635 ASN cc_start: 0.9097 (m110) cc_final: 0.8839 (m110) REVERT: A 645 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8566 (mt-10) REVERT: A 662 GLN cc_start: 0.9398 (mt0) cc_final: 0.9153 (mp10) REVERT: A 702 TRP cc_start: 0.9058 (t60) cc_final: 0.8697 (t60) REVERT: A 707 GLU cc_start: 0.9323 (mp0) cc_final: 0.9098 (mp0) REVERT: A 759 ARG cc_start: 0.8941 (mmt90) cc_final: 0.8411 (mmt90) REVERT: A 799 MET cc_start: 0.9542 (mtt) cc_final: 0.9180 (tpt) REVERT: A 832 ARG cc_start: 0.8700 (tpm170) cc_final: 0.8182 (tpp-160) REVERT: A 1011 THR cc_start: 0.8789 (m) cc_final: 0.8447 (p) REVERT: A 1046 ARG cc_start: 0.9328 (ttm110) cc_final: 0.8891 (ttm110) REVERT: A 1081 ASP cc_start: 0.8729 (t0) cc_final: 0.8291 (p0) REVERT: A 1090 MET cc_start: 0.8864 (mmt) cc_final: 0.8522 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2494 time to fit residues: 65.3225 Evaluate side-chains 166 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 492 HIS ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7654 Z= 0.193 Angle : 0.695 7.600 10325 Z= 0.358 Chirality : 0.041 0.129 1215 Planarity : 0.004 0.056 1358 Dihedral : 4.743 19.858 1060 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -0.08 (0.27), residues: 991 helix: 0.38 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.63 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 253 HIS 0.007 0.002 HIS A 187 PHE 0.020 0.002 PHE A 78 TYR 0.020 0.002 TYR A 107 ARG 0.004 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.926 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: 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 74 MET cc_start: 0.9371 (mmm) cc_final: 0.8937 (mmm) REVERT: A 132 ARG cc_start: 0.9201 (mmm160) cc_final: 0.8922 (mmm-85) REVERT: A 174 MET cc_start: 0.8868 (mmm) cc_final: 0.8599 (mmm) REVERT: A 190 MET cc_start: 0.9302 (pmm) cc_final: 0.9093 (pmm) REVERT: A 237 MET cc_start: 0.9475 (mtm) cc_final: 0.9233 (mtt) REVERT: A 245 ILE cc_start: 0.9463 (mt) cc_final: 0.8943 (mt) REVERT: A 479 ARG cc_start: 0.8956 (mmp80) cc_final: 0.8585 (mmm160) REVERT: A 525 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8946 (mm-30) REVERT: A 533 MET cc_start: 0.9393 (mtm) cc_final: 0.8976 (mtm) REVERT: A 587 MET cc_start: 0.6564 (mmm) cc_final: 0.6023 (mmt) REVERT: A 633 PHE cc_start: 0.9125 (t80) cc_final: 0.8867 (t80) REVERT: A 635 ASN cc_start: 0.9089 (m110) cc_final: 0.8835 (m110) REVERT: A 645 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 662 GLN cc_start: 0.9381 (mt0) cc_final: 0.9122 (mp10) REVERT: A 701 GLN cc_start: 0.9168 (tp40) cc_final: 0.8919 (tp-100) REVERT: A 702 TRP cc_start: 0.9065 (t60) cc_final: 0.8682 (t60) REVERT: A 759 ARG cc_start: 0.8909 (mmt90) cc_final: 0.8276 (mmt90) REVERT: A 799 MET cc_start: 0.9551 (mtt) cc_final: 0.9170 (tpt) REVERT: A 1001 MET cc_start: 0.8668 (ppp) cc_final: 0.8422 (ppp) REVERT: A 1011 THR cc_start: 0.8770 (m) cc_final: 0.8494 (p) REVERT: A 1046 ARG cc_start: 0.9324 (ttm110) cc_final: 0.8894 (ttm110) REVERT: A 1081 ASP cc_start: 0.8784 (t0) cc_final: 0.8344 (p0) REVERT: A 1083 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7587 (mm-30) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2513 time to fit residues: 64.5812 Evaluate side-chains 163 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 0.0980 chunk 53 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 773 ASN ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7654 Z= 0.205 Angle : 0.702 7.324 10325 Z= 0.366 Chirality : 0.042 0.136 1215 Planarity : 0.004 0.045 1358 Dihedral : 4.722 19.879 1060 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.12 % Allowed : 0.99 % Favored : 98.89 % 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: 0.06 (0.27), residues: 991 helix: 0.46 (0.18), residues: 806 sheet: None (None), residues: 0 loop : -1.43 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 253 HIS 0.007 0.002 HIS A 187 PHE 0.025 0.002 PHE A 779 TYR 0.019 0.001 TYR A 107 ARG 0.006 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 0.936 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: 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 74 MET cc_start: 0.9337 (mmm) cc_final: 0.8958 (mmm) REVERT: A 132 ARG cc_start: 0.9184 (mmm160) cc_final: 0.8909 (mmm-85) REVERT: A 174 MET cc_start: 0.8926 (mmm) cc_final: 0.8302 (mmm) REVERT: A 176 ASP cc_start: 0.9479 (t0) cc_final: 0.9261 (t70) REVERT: A 181 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8423 (mm-30) REVERT: A 237 MET cc_start: 0.9483 (mtm) cc_final: 0.9183 (mtt) REVERT: A 479 ARG cc_start: 0.9009 (mmp80) cc_final: 0.8626 (mmm160) REVERT: A 525 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8965 (mm-30) REVERT: A 533 MET cc_start: 0.9427 (mtm) cc_final: 0.8988 (mtm) REVERT: A 587 MET cc_start: 0.6594 (mmm) cc_final: 0.6082 (mmt) REVERT: A 633 PHE cc_start: 0.9132 (t80) cc_final: 0.8847 (t80) REVERT: A 635 ASN cc_start: 0.9107 (m110) cc_final: 0.8849 (m110) REVERT: A 645 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 662 GLN cc_start: 0.9393 (mt0) cc_final: 0.9129 (mp10) REVERT: A 701 GLN cc_start: 0.9191 (tp40) cc_final: 0.8944 (tp-100) REVERT: A 702 TRP cc_start: 0.9067 (t60) cc_final: 0.8649 (t60) REVERT: A 707 GLU cc_start: 0.9316 (mp0) cc_final: 0.9064 (mp0) REVERT: A 709 MET cc_start: 0.8964 (mmt) cc_final: 0.8683 (mmm) REVERT: A 759 ARG cc_start: 0.8918 (mmt90) cc_final: 0.8401 (mmt90) REVERT: A 799 MET cc_start: 0.9539 (mtt) cc_final: 0.9164 (tpt) REVERT: A 1001 MET cc_start: 0.8658 (ppp) cc_final: 0.8446 (ppp) REVERT: A 1011 THR cc_start: 0.8818 (m) cc_final: 0.8529 (p) REVERT: A 1046 ARG cc_start: 0.9319 (ttm110) cc_final: 0.8885 (ttm110) REVERT: A 1073 MET cc_start: 0.9166 (mmp) cc_final: 0.8936 (mmp) REVERT: A 1081 ASP cc_start: 0.8795 (t0) cc_final: 0.8357 (p0) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2398 time to fit residues: 60.3594 Evaluate side-chains 151 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 0.8980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.0000 chunk 48 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 974 HIS ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7654 Z= 0.194 Angle : 0.724 7.641 10325 Z= 0.378 Chirality : 0.042 0.145 1215 Planarity : 0.004 0.047 1358 Dihedral : 4.716 19.625 1060 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 0.10 (0.27), residues: 991 helix: 0.48 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -1.28 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 980 HIS 0.006 0.001 HIS A 187 PHE 0.022 0.003 PHE A 779 TYR 0.019 0.002 TYR A 107 ARG 0.006 0.000 ARG A 433 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.885 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: 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: symmetry clash REVERT: A 74 MET cc_start: 0.9326 (mmm) cc_final: 0.8950 (mmm) REVERT: A 132 ARG cc_start: 0.9194 (mmm160) cc_final: 0.8952 (mmm-85) REVERT: A 136 ARG cc_start: 0.9236 (mtm-85) cc_final: 0.9021 (ttm110) REVERT: A 237 MET cc_start: 0.9477 (mtm) cc_final: 0.9162 (mtt) REVERT: A 245 ILE cc_start: 0.9463 (mm) cc_final: 0.8909 (mt) REVERT: A 479 ARG cc_start: 0.9047 (mmp80) cc_final: 0.8687 (mmm160) REVERT: A 533 MET cc_start: 0.9405 (mtm) cc_final: 0.8937 (mtm) REVERT: A 633 PHE cc_start: 0.9132 (t80) cc_final: 0.8892 (t80) REVERT: A 635 ASN cc_start: 0.9017 (m110) cc_final: 0.8718 (m110) REVERT: A 645 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8679 (mt-10) REVERT: A 662 GLN cc_start: 0.9363 (mt0) cc_final: 0.9054 (mp10) REVERT: A 694 HIS cc_start: 0.9261 (t-170) cc_final: 0.9027 (t-90) REVERT: A 698 MET cc_start: 0.8960 (mmm) cc_final: 0.8686 (mmm) REVERT: A 701 GLN cc_start: 0.9141 (tp40) cc_final: 0.8909 (tp-100) REVERT: A 702 TRP cc_start: 0.9054 (t60) cc_final: 0.8629 (t60) REVERT: A 707 GLU cc_start: 0.9272 (mp0) cc_final: 0.9018 (mp0) REVERT: A 735 ASP cc_start: 0.9337 (m-30) cc_final: 0.9131 (m-30) REVERT: A 759 ARG cc_start: 0.8875 (mmt90) cc_final: 0.8302 (mmt90) REVERT: A 799 MET cc_start: 0.9533 (mtt) cc_final: 0.9166 (tpt) REVERT: A 1011 THR cc_start: 0.8769 (m) cc_final: 0.8511 (p) REVERT: A 1046 ARG cc_start: 0.9274 (ttm110) cc_final: 0.8862 (ttm110) REVERT: A 1081 ASP cc_start: 0.8784 (t0) cc_final: 0.8353 (p0) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2307 time to fit residues: 59.9324 Evaluate side-chains 173 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.087431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.068843 restraints weight = 35347.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.070743 restraints weight = 26229.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.072179 restraints weight = 20810.918| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7654 Z= 0.219 Angle : 0.724 7.353 10325 Z= 0.381 Chirality : 0.042 0.156 1215 Planarity : 0.004 0.052 1358 Dihedral : 4.680 20.327 1060 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.32 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: 0.08 (0.27), residues: 991 helix: 0.47 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -1.36 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 980 HIS 0.008 0.002 HIS A 187 PHE 0.023 0.003 PHE A 779 TYR 0.018 0.001 TYR A 107 ARG 0.006 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.55 seconds wall clock time: 36 minutes 55.05 seconds (2215.05 seconds total)