Starting phenix.real_space_refine on Thu Jan 18 03:04:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/01_2024/7ktw_23032.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/01_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_23032/01_2024/7ktw_23032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/01_2024/7ktw_23032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/01_2024/7ktw_23032.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktw_23032/01_2024/7ktw_23032.pdb" } 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 Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1055": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 4.39, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 4.3 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: 0.69 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: 2.17 Time building geometry restraints manager: 3.17 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: 96.39 - 103.92: 102 103.92 - 111.44: 3359 111.44 - 118.96: 3072 118.96 - 126.48: 3719 126.48 - 134.01: 73 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 2.440 nonbonded pdb=" O HIS A 694 " pdb=" OG1 THR A 697 " model vdw 2.222 2.440 nonbonded pdb=" O GLU A 143 " pdb=" OG1 THR A 146 " model vdw 2.248 2.440 nonbonded pdb=" O LEU A 191 " pdb=" OG SER A 194 " model vdw 2.275 2.440 nonbonded pdb=" O VAL A1069 " pdb=" OG1 THR A1072 " model vdw 2.277 2.440 ... (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: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.940 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.950 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- 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 : 0.887 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: 0.2682 time to fit residues: 77.1194 Evaluate side-chains 167 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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: 0.0980 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 40 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 179 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 471 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN A1093 HIS A1094 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7654 Z= 0.196 Angle : 0.686 7.111 10325 Z= 0.362 Chirality : 0.039 0.147 1215 Planarity : 0.005 0.052 1358 Dihedral : 5.736 19.961 1060 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.62 % Allowed : 3.20 % 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: -2.53 (0.23), residues: 991 helix: -1.32 (0.16), residues: 809 sheet: None (None), residues: 0 loop : -2.42 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 394 HIS 0.010 0.002 HIS A 694 PHE 0.019 0.003 PHE A 78 TYR 0.019 0.002 TYR A 107 ARG 0.005 0.001 ARG A 132 *********************** 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 234 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 0.667 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: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.9107 (ptm160) cc_final: 0.8092 (ptm160) REVERT: A 174 MET cc_start: 0.8815 (mmm) cc_final: 0.7953 (mmm) REVERT: A 176 ASP cc_start: 0.9468 (t0) cc_final: 0.9029 (t0) REVERT: A 180 GLN cc_start: 0.9257 (mt0) cc_final: 0.8929 (mm-40) REVERT: A 190 MET cc_start: 0.9457 (mtt) cc_final: 0.9231 (mtm) REVERT: A 205 LEU cc_start: 0.9677 (tt) cc_final: 0.9444 (tt) REVERT: A 424 ASP cc_start: 0.8882 (t0) cc_final: 0.8591 (m-30) REVERT: A 431 ILE cc_start: 0.8553 (mm) cc_final: 0.8307 (mm) REVERT: A 471 GLN cc_start: 0.8834 (pt0) cc_final: 0.8252 (pt0) REVERT: A 533 MET cc_start: 0.9438 (mtm) cc_final: 0.9200 (mtp) REVERT: A 633 PHE cc_start: 0.9153 (t80) cc_final: 0.8770 (t80) REVERT: A 662 GLN cc_start: 0.9431 (mt0) cc_final: 0.9034 (mp10) REVERT: A 745 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8258 (mm110) REVERT: A 748 MET cc_start: 0.9280 (mmp) cc_final: 0.9043 (mpp) REVERT: A 799 MET cc_start: 0.9552 (mtt) cc_final: 0.9184 (tpt) REVERT: A 823 ARG cc_start: 0.9197 (mpp80) cc_final: 0.8794 (mtt180) REVERT: A 998 MET cc_start: 0.8366 (tpp) cc_final: 0.8069 (tpp) REVERT: A 1029 VAL cc_start: 0.9572 (t) cc_final: 0.9344 (t) REVERT: A 1046 ARG cc_start: 0.9273 (ttm110) cc_final: 0.8658 (mtm110) REVERT: A 1083 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8200 (mm-30) REVERT: A 1090 MET cc_start: 0.9087 (mmt) cc_final: 0.8755 (mmm) outliers start: 5 outliers final: 0 residues processed: 229 average time/residue: 0.2070 time to fit residues: 60.0900 Evaluate side-chains 180 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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: 5.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 382 GLN A 575 GLN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7654 Z= 0.211 Angle : 0.653 6.638 10325 Z= 0.345 Chirality : 0.039 0.119 1215 Planarity : 0.004 0.048 1358 Dihedral : 5.342 17.790 1060 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.49 % Allowed : 2.96 % Favored : 96.55 % 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: -1.15 (0.25), residues: 991 helix: -0.35 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.08 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 394 HIS 0.007 0.002 HIS A 694 PHE 0.015 0.003 PHE A 78 TYR 0.026 0.002 TYR A 107 ARG 0.005 0.000 ARG A 769 *********************** 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 217 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 0.925 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 113 ARG cc_start: 0.9068 (ptm160) cc_final: 0.8006 (ptm160) REVERT: A 174 MET cc_start: 0.9006 (mmm) cc_final: 0.8353 (mmm) REVERT: A 181 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8349 (mm-30) REVERT: A 201 LEU cc_start: 0.9587 (tp) cc_final: 0.9375 (tp) REVERT: A 205 LEU cc_start: 0.9670 (tt) cc_final: 0.9364 (tt) REVERT: A 224 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9254 (mt-10) REVERT: A 227 LEU cc_start: 0.9710 (tp) cc_final: 0.9411 (pp) REVERT: A 237 MET cc_start: 0.9560 (mtp) cc_final: 0.9267 (ttm) REVERT: A 533 MET cc_start: 0.9437 (mtm) cc_final: 0.9233 (mtp) REVERT: A 591 MET cc_start: 0.9368 (mmm) cc_final: 0.9043 (mmm) REVERT: A 633 PHE cc_start: 0.9202 (t80) cc_final: 0.8797 (t80) REVERT: A 635 ASN cc_start: 0.9200 (m110) cc_final: 0.8963 (m110) REVERT: A 662 GLN cc_start: 0.9468 (mt0) cc_final: 0.9074 (mp10) REVERT: A 799 MET cc_start: 0.9562 (mtt) cc_final: 0.9152 (tpt) REVERT: A 832 ARG cc_start: 0.8877 (tpm170) cc_final: 0.8252 (tpp-160) REVERT: A 1046 ARG cc_start: 0.9194 (ttm110) cc_final: 0.8703 (ttm110) REVERT: A 1083 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8118 (mm-30) REVERT: A 1090 MET cc_start: 0.9106 (mmt) cc_final: 0.8785 (mmm) REVERT: A 1110 GLU cc_start: 0.9379 (mp0) cc_final: 0.9149 (mp0) outliers start: 4 outliers final: 0 residues processed: 214 average time/residue: 0.2352 time to fit residues: 63.6604 Evaluate side-chains 170 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 379 ASN A 382 GLN A 701 GLN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7654 Z= 0.210 Angle : 0.639 6.295 10325 Z= 0.334 Chirality : 0.039 0.188 1215 Planarity : 0.004 0.045 1358 Dihedral : 5.110 18.162 1060 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.12 % Allowed : 3.20 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.26), residues: 991 helix: 0.19 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 394 HIS 0.008 0.002 HIS A 187 PHE 0.017 0.002 PHE A 78 TYR 0.024 0.002 TYR A 107 ARG 0.005 0.000 ARG A 512 *********************** 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 212 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 0.669 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 174 MET cc_start: 0.9092 (mmm) cc_final: 0.8131 (mmm) REVERT: A 176 ASP cc_start: 0.9334 (t0) cc_final: 0.8624 (t70) REVERT: A 177 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9088 (mt-10) REVERT: A 180 GLN cc_start: 0.9202 (mt0) cc_final: 0.8948 (mm-40) REVERT: A 181 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8333 (mm-30) REVERT: A 201 LEU cc_start: 0.9588 (tp) cc_final: 0.9169 (tp) REVERT: A 205 LEU cc_start: 0.9671 (tt) cc_final: 0.9391 (tt) REVERT: A 227 LEU cc_start: 0.9707 (tp) cc_final: 0.9436 (pp) REVERT: A 237 MET cc_start: 0.9558 (mtp) cc_final: 0.9184 (mtp) REVERT: A 245 ILE cc_start: 0.9359 (mt) cc_final: 0.8796 (mt) REVERT: A 331 MET cc_start: 0.8892 (ttp) cc_final: 0.8602 (ptm) REVERT: A 525 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8932 (mm-30) REVERT: A 533 MET cc_start: 0.9445 (mtm) cc_final: 0.9238 (mtp) REVERT: A 618 ASP cc_start: 0.8930 (t0) cc_final: 0.8521 (m-30) REVERT: A 633 PHE cc_start: 0.9187 (t80) cc_final: 0.8852 (t80) REVERT: A 635 ASN cc_start: 0.9235 (m110) cc_final: 0.8983 (m110) REVERT: A 646 LYS cc_start: 0.9298 (mttt) cc_final: 0.8963 (mttt) REVERT: A 662 GLN cc_start: 0.9466 (mt0) cc_final: 0.8979 (mp10) REVERT: A 694 HIS cc_start: 0.9075 (t-170) cc_final: 0.8695 (t-90) REVERT: A 702 TRP cc_start: 0.9161 (t60) cc_final: 0.8678 (t60) REVERT: A 759 ARG cc_start: 0.9156 (mpt180) cc_final: 0.8753 (mmt90) REVERT: A 799 MET cc_start: 0.9585 (mtt) cc_final: 0.9201 (tpt) REVERT: A 832 ARG cc_start: 0.8797 (tpm170) cc_final: 0.8017 (tpp-160) REVERT: A 1046 ARG cc_start: 0.9154 (ttm110) cc_final: 0.8621 (ttm110) REVERT: A 1083 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7849 (mp0) REVERT: A 1090 MET cc_start: 0.9077 (mmt) cc_final: 0.8716 (mmm) REVERT: A 1099 MET cc_start: 0.8058 (mmp) cc_final: 0.7697 (mmp) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1804 time to fit residues: 48.3237 Evaluate side-chains 155 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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: 3.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 71 optimal weight: 0.0870 chunk 39 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 382 GLN A 701 GLN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4309 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= 0.195 Angle : 0.652 6.899 10325 Z= 0.338 Chirality : 0.039 0.172 1215 Planarity : 0.004 0.059 1358 Dihedral : 4.950 17.273 1060 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 991 helix: 0.43 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -1.61 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 394 HIS 0.002 0.001 HIS A1093 PHE 0.016 0.002 PHE A 78 TYR 0.025 0.002 TYR A 107 ARG 0.004 0.000 ARG A 132 *********************** 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 208 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 0.976 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 113 ARG cc_start: 0.9208 (ptm-80) cc_final: 0.8295 (ptp-110) REVERT: A 174 MET cc_start: 0.8973 (mmm) cc_final: 0.8221 (mmm) REVERT: A 176 ASP cc_start: 0.9332 (t0) cc_final: 0.8655 (t70) REVERT: A 180 GLN cc_start: 0.9177 (mt0) cc_final: 0.8936 (mm-40) REVERT: A 201 LEU cc_start: 0.9615 (tp) cc_final: 0.9175 (tp) REVERT: A 205 LEU cc_start: 0.9665 (tt) cc_final: 0.9353 (tt) REVERT: A 227 LEU cc_start: 0.9710 (tp) cc_final: 0.9451 (pp) REVERT: A 237 MET cc_start: 0.9555 (mtp) cc_final: 0.9158 (mtp) REVERT: A 245 ILE cc_start: 0.9383 (mt) cc_final: 0.8898 (mm) REVERT: A 531 ASN cc_start: 0.9286 (p0) cc_final: 0.9033 (p0) REVERT: A 533 MET cc_start: 0.9440 (mtm) cc_final: 0.9229 (mtp) REVERT: A 591 MET cc_start: 0.9206 (mmm) cc_final: 0.8849 (mmm) REVERT: A 618 ASP cc_start: 0.8928 (t0) cc_final: 0.8535 (m-30) REVERT: A 633 PHE cc_start: 0.9211 (t80) cc_final: 0.8944 (t80) REVERT: A 635 ASN cc_start: 0.9215 (m110) cc_final: 0.8912 (m110) REVERT: A 694 HIS cc_start: 0.9090 (t-170) cc_final: 0.8678 (t-90) REVERT: A 702 TRP cc_start: 0.9142 (t60) cc_final: 0.8720 (t60) REVERT: A 759 ARG cc_start: 0.9170 (mpt180) cc_final: 0.8658 (mmt90) REVERT: A 799 MET cc_start: 0.9569 (mtt) cc_final: 0.9163 (tpt) REVERT: A 998 MET cc_start: 0.8893 (ttm) cc_final: 0.8497 (ttt) REVERT: A 1046 ARG cc_start: 0.9181 (ttm110) cc_final: 0.8566 (mtm110) REVERT: A 1090 MET cc_start: 0.9069 (mmt) cc_final: 0.8708 (mmm) REVERT: A 1110 GLU cc_start: 0.9380 (mp0) cc_final: 0.9138 (mp0) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.2327 time to fit residues: 61.6060 Evaluate side-chains 160 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 50 optimal weight: 0.2980 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 382 GLN A 701 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4645 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= 0.193 Angle : 0.665 7.806 10325 Z= 0.347 Chirality : 0.040 0.156 1215 Planarity : 0.005 0.066 1358 Dihedral : 4.915 18.281 1060 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.25 % Allowed : 2.83 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 991 helix: 0.40 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -1.55 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 394 HIS 0.009 0.001 HIS A 187 PHE 0.018 0.002 PHE A 78 TYR 0.022 0.002 TYR A 107 ARG 0.008 0.001 ARG A 339 *********************** 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 211 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 0.901 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: symmetry clash REVERT: A 132 ARG cc_start: 0.9122 (mtt90) cc_final: 0.8780 (mmm160) REVERT: A 135 ILE cc_start: 0.8993 (mp) cc_final: 0.8687 (mp) REVERT: A 174 MET cc_start: 0.8948 (mmm) cc_final: 0.8676 (mmm) REVERT: A 176 ASP cc_start: 0.9461 (t0) cc_final: 0.8889 (t70) REVERT: A 205 LEU cc_start: 0.9649 (tt) cc_final: 0.9256 (tt) REVERT: A 227 LEU cc_start: 0.9720 (tp) cc_final: 0.9397 (pp) REVERT: A 245 ILE cc_start: 0.9374 (mt) cc_final: 0.8853 (mt) REVERT: A 331 MET cc_start: 0.8875 (ttp) cc_final: 0.8553 (ptm) REVERT: A 407 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8633 (tm-30) REVERT: A 416 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7529 (mtp180) REVERT: A 618 ASP cc_start: 0.8941 (t0) cc_final: 0.8560 (m-30) REVERT: A 633 PHE cc_start: 0.9228 (t80) cc_final: 0.8942 (t80) REVERT: A 635 ASN cc_start: 0.9130 (m110) cc_final: 0.8904 (m110) REVERT: A 694 HIS cc_start: 0.9106 (t-170) cc_final: 0.8805 (t70) REVERT: A 702 TRP cc_start: 0.9142 (t60) cc_final: 0.8755 (t60) REVERT: A 759 ARG cc_start: 0.9109 (mpt180) cc_final: 0.8585 (mmt90) REVERT: A 799 MET cc_start: 0.9565 (mtt) cc_final: 0.9158 (tpt) REVERT: A 998 MET cc_start: 0.8970 (ttm) cc_final: 0.8593 (ttt) REVERT: A 1046 ARG cc_start: 0.9254 (ttm110) cc_final: 0.8729 (ttm110) REVERT: A 1073 MET cc_start: 0.9272 (mmm) cc_final: 0.9047 (mmm) REVERT: A 1090 MET cc_start: 0.9033 (mmt) cc_final: 0.8672 (mmm) outliers start: 2 outliers final: 1 residues processed: 210 average time/residue: 0.2459 time to fit residues: 64.6763 Evaluate side-chains 161 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 279 GLN A 382 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4966 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= 0.201 Angle : 0.677 8.179 10325 Z= 0.351 Chirality : 0.040 0.147 1215 Planarity : 0.004 0.046 1358 Dihedral : 4.870 18.228 1060 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.12 % Allowed : 1.85 % 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: 0.15 (0.27), residues: 991 helix: 0.56 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -1.42 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 394 HIS 0.007 0.001 HIS A 187 PHE 0.018 0.002 PHE A 78 TYR 0.022 0.002 TYR A 107 ARG 0.006 0.001 ARG A 230 *********************** 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 203 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 0.691 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 22 HIS cc_start: 0.8786 (t70) cc_final: 0.8549 (t-90) REVERT: A 113 ARG cc_start: 0.9239 (ptm160) cc_final: 0.8261 (ptp-110) REVERT: A 135 ILE cc_start: 0.9008 (mp) cc_final: 0.8760 (mp) REVERT: A 174 MET cc_start: 0.8994 (mmm) cc_final: 0.8699 (mmm) REVERT: A 205 LEU cc_start: 0.9625 (tt) cc_final: 0.9409 (tt) REVERT: A 245 ILE cc_start: 0.9381 (mt) cc_final: 0.8887 (mt) REVERT: A 331 MET cc_start: 0.8801 (ttp) cc_final: 0.8505 (ptm) REVERT: A 407 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8639 (tm-30) REVERT: A 416 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7648 (mtp180) REVERT: A 479 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8579 (mmm160) REVERT: A 633 PHE cc_start: 0.9206 (t80) cc_final: 0.8917 (t80) REVERT: A 635 ASN cc_start: 0.9094 (m110) cc_final: 0.8873 (m110) REVERT: A 701 GLN cc_start: 0.9076 (tp40) cc_final: 0.8825 (tp-100) REVERT: A 702 TRP cc_start: 0.9098 (t60) cc_final: 0.8656 (t60) REVERT: A 759 ARG cc_start: 0.9107 (mpt180) cc_final: 0.8586 (mmt90) REVERT: A 799 MET cc_start: 0.9581 (mtt) cc_final: 0.9181 (tpt) REVERT: A 998 MET cc_start: 0.9001 (ttm) cc_final: 0.8569 (ttm) REVERT: A 1046 ARG cc_start: 0.9198 (ttm110) cc_final: 0.8721 (ttm110) REVERT: A 1073 MET cc_start: 0.9013 (mmm) cc_final: 0.8658 (mmm) REVERT: A 1090 MET cc_start: 0.9042 (mmt) cc_final: 0.8670 (mmm) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.2527 time to fit residues: 64.8201 Evaluate side-chains 159 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 0.0070 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 279 GLN A 382 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7654 Z= 0.191 Angle : 0.678 8.537 10325 Z= 0.349 Chirality : 0.040 0.135 1215 Planarity : 0.004 0.045 1358 Dihedral : 4.789 18.637 1060 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.12 % Allowed : 1.11 % Favored : 98.77 % 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: 0.28 (0.27), residues: 991 helix: 0.66 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -1.48 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 394 HIS 0.008 0.001 HIS A 187 PHE 0.020 0.003 PHE A 779 TYR 0.021 0.001 TYR A 107 ARG 0.006 0.000 ARG A 512 *********************** 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: 1 poor density : 201 time to evaluate : 0.907 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: 0.9210 (tpp) cc_final: 0.8770 (mmm) REVERT: A 113 ARG cc_start: 0.8530 (ttt-90) cc_final: 0.8148 (ptp-110) REVERT: A 164 LEU cc_start: 0.9086 (pp) cc_final: 0.8638 (pp) REVERT: A 174 MET cc_start: 0.8835 (mmm) cc_final: 0.8399 (mmm) REVERT: A 176 ASP cc_start: 0.8984 (t70) cc_final: 0.8773 (t70) REVERT: A 177 GLU cc_start: 0.8915 (mp0) cc_final: 0.8577 (mp0) REVERT: A 195 MET cc_start: 0.9215 (mmm) cc_final: 0.8878 (tpt) REVERT: A 245 ILE cc_start: 0.9419 (mt) cc_final: 0.9052 (mm) REVERT: A 331 MET cc_start: 0.8765 (ttp) cc_final: 0.8531 (ptm) REVERT: A 407 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 479 ARG cc_start: 0.9043 (mmp80) cc_final: 0.8683 (mmm160) REVERT: A 533 MET cc_start: 0.9435 (mtm) cc_final: 0.9120 (mtm) REVERT: A 633 PHE cc_start: 0.9200 (t80) cc_final: 0.8908 (t80) REVERT: A 635 ASN cc_start: 0.9071 (m110) cc_final: 0.8829 (m110) REVERT: A 701 GLN cc_start: 0.9080 (tp40) cc_final: 0.8842 (tp-100) REVERT: A 702 TRP cc_start: 0.9092 (t60) cc_final: 0.8734 (t60) REVERT: A 712 LEU cc_start: 0.9446 (tp) cc_final: 0.9220 (pp) REVERT: A 799 MET cc_start: 0.9580 (mtt) cc_final: 0.9190 (tpt) REVERT: A 998 MET cc_start: 0.9044 (ttm) cc_final: 0.8596 (ttm) REVERT: A 1046 ARG cc_start: 0.9318 (ttm110) cc_final: 0.8862 (ttm110) REVERT: A 1081 ASP cc_start: 0.8644 (t0) cc_final: 0.8029 (p0) REVERT: A 1090 MET cc_start: 0.9053 (mmt) cc_final: 0.8656 (mmm) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2362 time to fit residues: 60.5060 Evaluate side-chains 154 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 6.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 382 GLN A 516 GLN A 685 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7654 Z= 0.202 Angle : 0.688 7.679 10325 Z= 0.353 Chirality : 0.040 0.139 1215 Planarity : 0.004 0.044 1358 Dihedral : 4.813 18.057 1060 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % 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: 0.29 (0.27), residues: 991 helix: 0.64 (0.18), residues: 795 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 394 HIS 0.007 0.002 HIS A 187 PHE 0.024 0.002 PHE A 779 TYR 0.022 0.001 TYR A 107 ARG 0.005 0.001 ARG A 512 *********************** 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 197 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.980 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 74 MET cc_start: 0.9294 (tpp) cc_final: 0.8882 (mmm) REVERT: A 78 PHE cc_start: 0.9305 (p90) cc_final: 0.9010 (p90) REVERT: A 113 ARG cc_start: 0.8977 (ttt-90) cc_final: 0.8230 (ttm110) REVERT: A 164 LEU cc_start: 0.9057 (pp) cc_final: 0.8717 (pp) REVERT: A 174 MET cc_start: 0.8788 (mmm) cc_final: 0.8312 (mmm) REVERT: A 176 ASP cc_start: 0.9006 (t70) cc_final: 0.8776 (t70) REVERT: A 177 GLU cc_start: 0.8910 (mp0) cc_final: 0.8574 (mp0) REVERT: A 195 MET cc_start: 0.9284 (mmm) cc_final: 0.9019 (tpt) REVERT: A 245 ILE cc_start: 0.9441 (mt) cc_final: 0.9076 (mm) REVERT: A 331 MET cc_start: 0.8759 (ttp) cc_final: 0.8525 (ptm) REVERT: A 407 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8616 (tm-30) REVERT: A 479 ARG cc_start: 0.9091 (mmp80) cc_final: 0.8721 (mmm160) REVERT: A 533 MET cc_start: 0.9432 (mtm) cc_final: 0.9030 (mtp) REVERT: A 633 PHE cc_start: 0.9203 (t80) cc_final: 0.8905 (t80) REVERT: A 635 ASN cc_start: 0.9067 (m110) cc_final: 0.8837 (m110) REVERT: A 701 GLN cc_start: 0.9111 (tp40) cc_final: 0.8856 (tp-100) REVERT: A 702 TRP cc_start: 0.9130 (t60) cc_final: 0.8764 (t60) REVERT: A 707 GLU cc_start: 0.9353 (mp0) cc_final: 0.9031 (mp0) REVERT: A 799 MET cc_start: 0.9569 (mtt) cc_final: 0.9196 (tpt) REVERT: A 998 MET cc_start: 0.9044 (ttm) cc_final: 0.8639 (ttm) REVERT: A 1046 ARG cc_start: 0.9314 (ttm110) cc_final: 0.8862 (ttm110) REVERT: A 1090 MET cc_start: 0.9082 (mmt) cc_final: 0.8825 (mmm) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2429 time to fit residues: 61.1006 Evaluate side-chains 157 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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: 0.0000 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 382 GLN A 694 HIS ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7654 Z= 0.201 Angle : 0.707 8.252 10325 Z= 0.362 Chirality : 0.040 0.158 1215 Planarity : 0.004 0.045 1358 Dihedral : 4.817 18.030 1060 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.12 % Allowed : 0.74 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 991 helix: 0.59 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 394 HIS 0.011 0.002 HIS A 974 PHE 0.045 0.003 PHE A 212 TYR 0.021 0.001 TYR A 107 ARG 0.005 0.000 ARG A 512 ********************** 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 197 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.955 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 78 PHE cc_start: 0.9280 (p90) cc_final: 0.9013 (p90) REVERT: A 113 ARG cc_start: 0.8938 (ttt-90) cc_final: 0.8228 (ttm110) REVERT: A 164 LEU cc_start: 0.9084 (pp) cc_final: 0.8681 (pp) REVERT: A 174 MET cc_start: 0.8714 (mmm) cc_final: 0.8211 (mmm) REVERT: A 176 ASP cc_start: 0.9012 (t70) cc_final: 0.8764 (t70) REVERT: A 177 GLU cc_start: 0.8867 (mp0) cc_final: 0.8467 (mp0) REVERT: A 181 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8386 (mm-30) REVERT: A 195 MET cc_start: 0.9249 (mmm) cc_final: 0.9023 (tpt) REVERT: A 245 ILE cc_start: 0.9439 (mt) cc_final: 0.9068 (mm) REVERT: A 331 MET cc_start: 0.8746 (ttp) cc_final: 0.8512 (ptm) REVERT: A 407 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 479 ARG cc_start: 0.9106 (mmp80) cc_final: 0.8736 (mmm160) REVERT: A 496 LYS cc_start: 0.9343 (mtmm) cc_final: 0.9035 (mttt) REVERT: A 533 MET cc_start: 0.9425 (mtm) cc_final: 0.9029 (mtp) REVERT: A 633 PHE cc_start: 0.9191 (t80) cc_final: 0.8920 (t80) REVERT: A 635 ASN cc_start: 0.9027 (m110) cc_final: 0.8802 (m110) REVERT: A 645 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 701 GLN cc_start: 0.9097 (tp40) cc_final: 0.8838 (tp-100) REVERT: A 702 TRP cc_start: 0.9125 (t60) cc_final: 0.8679 (t60) REVERT: A 707 GLU cc_start: 0.9349 (mp0) cc_final: 0.9031 (mp0) REVERT: A 799 MET cc_start: 0.9563 (mtt) cc_final: 0.9194 (tpt) REVERT: A 998 MET cc_start: 0.9062 (ttm) cc_final: 0.8763 (ttm) REVERT: A 1046 ARG cc_start: 0.9335 (ttm110) cc_final: 0.8888 (ttm110) REVERT: A 1081 ASP cc_start: 0.8789 (t0) cc_final: 0.8323 (p0) REVERT: A 1090 MET cc_start: 0.9034 (mmt) cc_final: 0.8652 (mmm) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2540 time to fit residues: 63.6363 Evaluate side-chains 159 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 382 GLN ** A 814 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.087799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.069791 restraints weight = 35031.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.071725 restraints weight = 25944.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.073218 restraints weight = 20494.998| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7654 Z= 0.192 Angle : 0.709 10.120 10325 Z= 0.356 Chirality : 0.040 0.141 1215 Planarity : 0.004 0.045 1358 Dihedral : 4.704 17.785 1060 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.12 % Allowed : 0.86 % Favored : 99.01 % 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: 0.31 (0.27), residues: 991 helix: 0.68 (0.18), residues: 803 sheet: None (None), residues: 0 loop : -1.57 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 394 HIS 0.011 0.002 HIS A 974 PHE 0.042 0.003 PHE A 212 TYR 0.019 0.001 TYR A 107 ARG 0.005 0.000 ARG A 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.45 seconds wall clock time: 44 minutes 12.63 seconds (2652.63 seconds total)