Starting phenix.real_space_refine on Mon Mar 11 07:28:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/03_2024/7ktu_23030.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/03_2024/7ktu_23030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/03_2024/7ktu_23030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/03_2024/7ktu_23030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/03_2024/7ktu_23030.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/03_2024/7ktu_23030.pdb" } resolution = 4.15 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= 0.031 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 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 PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" 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-dev-5265/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: 4.78, per 1000 atoms: 0.63 Number of scatterers: 7577 At special positions: 0 Unit cell: (82.5, 98.175, 127.875, 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: 3.40 Conformation dependent library (CDL) restraints added in 1.5 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: 47 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Proline residue: A 15 - end of helix removed outlier: 3.601A pdb=" N HIS A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 64 removed outlier: 3.603A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 98 removed outlier: 4.084A pdb=" N ASP A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.771A pdb=" N ILE A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 108 through 151 removed outlier: 3.610A pdb=" N ILE A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 removed outlier: 3.855A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.759A pdb=" N LYS A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.847A pdb=" N MET A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 224 through 250 removed outlier: 4.290A pdb=" N LYS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 286 removed outlier: 4.270A pdb=" N SER A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.867A pdb=" N GLN A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.785A pdb=" N ARG A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 359 through 390 removed outlier: 3.814A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.128A pdb=" N TRP A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.902A pdb=" N ARG A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 removed outlier: 4.441A pdb=" N GLU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.673A pdb=" N ARG A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 484 removed outlier: 3.593A pdb=" N ARG A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 514 through 532 removed outlier: 3.588A pdb=" N ILE A 519 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 removed outlier: 3.926A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP A 540 " --> pdb=" O PRO A 536 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 573 through 596 removed outlier: 4.105A pdb=" N GLN A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.674A pdb=" N LEU A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 651 Processing helix chain 'A' and resid 654 through 683 Proline residue: A 673 - end of helix removed outlier: 3.518A pdb=" N VAL A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 717 removed outlier: 3.632A pdb=" N GLU A 693 " --> pdb=" O GLN A 689 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 743 removed outlier: 3.567A pdb=" N ALA A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 774 removed outlier: 3.638A pdb=" N GLY A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 786 through 807 removed outlier: 3.666A pdb=" N LEU A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Proline residue: A 796 - end of helix Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.610A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 836 removed outlier: 3.602A pdb=" N ALA A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 979 removed outlier: 3.814A pdb=" N SER A 972 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1005 removed outlier: 3.568A pdb=" N ALA A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1007 No H-bonds generated for 'chain 'A' and resid 1006 through 1007' Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1011 through 1038 removed outlier: 3.594A pdb=" N ILE A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A1038 " --> pdb=" O LYS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1053 removed outlier: 3.611A pdb=" N ARG A1046 " --> pdb=" O ASP A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1074 removed outlier: 3.845A pdb=" N THR A1058 " --> pdb=" O GLU A1054 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A1060 " --> pdb=" O ILE A1056 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A1061 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1114 removed outlier: 3.534A pdb=" N SER A1084 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET A1090 " --> pdb=" O GLN A1086 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A1107 " --> pdb=" O LYS A1103 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1602 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: 2.30 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1736 1.33 - 1.45: 1313 1.45 - 1.57: 4529 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7654 Sorted by residual: bond pdb=" C SER A 456 " pdb=" N PRO A 457 " ideal model delta sigma weight residual 1.336 1.387 -0.052 1.23e-02 6.61e+03 1.77e+01 bond pdb=" C ASP A 424 " pdb=" N PRO A 425 " ideal model delta sigma weight residual 1.337 1.382 -0.046 1.11e-02 8.12e+03 1.68e+01 bond pdb=" CA THR A 215 " pdb=" C THR A 215 " ideal model delta sigma weight residual 1.523 1.470 0.052 1.41e-02 5.03e+03 1.38e+01 bond pdb=" C THR A 215 " pdb=" O THR A 215 " ideal model delta sigma weight residual 1.236 1.207 0.028 1.35e-02 5.49e+03 4.40e+00 bond pdb=" C ASP A 505 " pdb=" N ASN A 506 " ideal model delta sigma weight residual 1.332 1.316 0.016 8.60e-03 1.35e+04 3.58e+00 ... (remaining 7649 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.90: 160 105.90 - 112.95: 4206 112.95 - 120.01: 2807 120.01 - 127.06: 3094 127.06 - 134.12: 58 Bond angle restraints: 10325 Sorted by residual: angle pdb=" C LYS A 639 " pdb=" N LEU A 640 " pdb=" CA LEU A 640 " ideal model delta sigma weight residual 120.54 127.14 -6.60 1.35e+00 5.49e-01 2.39e+01 angle pdb=" N VAL A 713 " pdb=" CA VAL A 713 " pdb=" C VAL A 713 " ideal model delta sigma weight residual 110.72 106.66 4.06 1.01e+00 9.80e-01 1.62e+01 angle pdb=" N GLY A 401 " pdb=" CA GLY A 401 " pdb=" C GLY A 401 " ideal model delta sigma weight residual 112.34 119.70 -7.36 2.04e+00 2.40e-01 1.30e+01 angle pdb=" C THR A 710 " pdb=" N GLY A 711 " pdb=" CA GLY A 711 " ideal model delta sigma weight residual 120.13 124.50 -4.37 1.26e+00 6.30e-01 1.20e+01 angle pdb=" N GLN A 964 " pdb=" CA GLN A 964 " pdb=" C GLN A 964 " ideal model delta sigma weight residual 109.81 117.43 -7.62 2.21e+00 2.05e-01 1.19e+01 ... (remaining 10320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 4449 15.88 - 31.75: 300 31.75 - 47.63: 81 47.63 - 63.50: 3 63.50 - 79.38: 11 Dihedral angle restraints: 4844 sinusoidal: 1958 harmonic: 2886 Sorted by residual: dihedral pdb=" CA ASN A1094 " pdb=" C ASN A1094 " pdb=" N ALA A1095 " pdb=" CA ALA A1095 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ALA A 615 " pdb=" C ALA A 615 " pdb=" N PRO A 616 " pdb=" CA PRO A 616 " ideal model delta harmonic sigma weight residual 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ASP A 106 " pdb=" C ASP A 106 " pdb=" N TYR A 107 " pdb=" CA TYR A 107 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 4841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 769 0.043 - 0.085: 321 0.085 - 0.128: 101 0.128 - 0.171: 15 0.171 - 0.213: 9 Chirality restraints: 1215 Sorted by residual: chirality pdb=" CB ILE A 808 " pdb=" CA ILE A 808 " pdb=" CG1 ILE A 808 " pdb=" CG2 ILE A 808 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 519 " pdb=" CA ILE A 519 " pdb=" CG1 ILE A 519 " pdb=" CG2 ILE A 519 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE A 730 " pdb=" CA ILE A 730 " pdb=" CG1 ILE A 730 " pdb=" CG2 ILE A 730 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1212 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 42 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 43 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 75 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 76 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 615 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.85e+00 pdb=" N PRO A 616 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 616 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 616 " 0.036 5.00e-02 4.00e+02 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2010 2.79 - 3.32: 8345 3.32 - 3.84: 13479 3.84 - 4.37: 16454 4.37 - 4.90: 24124 Nonbonded interactions: 64412 Sorted by model distance: nonbonded pdb=" O ILE A 661 " pdb=" OG SER A 664 " model vdw 2.259 2.440 nonbonded pdb=" O ILE A 211 " pdb=" OG1 THR A 214 " model vdw 2.259 2.440 nonbonded pdb=" O HIS A 694 " pdb=" OG1 THR A 697 " model vdw 2.263 2.440 nonbonded pdb=" O ILE A1065 " pdb=" OG1 THR A1068 " model vdw 2.269 2.440 nonbonded pdb=" O ALA A 440 " pdb=" OG SER A 443 " model vdw 2.289 2.440 ... (remaining 64407 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.950 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.070 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.006 0.058 7654 Z= 0.397 Angle : 1.047 9.532 10325 Z= 0.603 Chirality : 0.052 0.213 1215 Planarity : 0.007 0.076 1358 Dihedral : 12.608 79.380 2958 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.37 % Allowed : 4.06 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.18), residues: 991 helix: -3.49 (0.12), residues: 745 sheet: None (None), residues: 0 loop : -2.82 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP A 980 HIS 0.008 0.003 HIS A 187 PHE 0.025 0.004 PHE A 78 TYR 0.021 0.003 TYR A 160 ARG 0.014 0.001 ARG A 780 *********************** 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 209 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7824 (mmm) cc_final: 0.7318 (mmm) REVERT: A 195 MET cc_start: 0.8341 (tmt) cc_final: 0.8107 (tmt) REVERT: A 209 MET cc_start: 0.9218 (mmt) cc_final: 0.8928 (mmm) REVERT: A 246 ARG cc_start: 0.9182 (mpt-90) cc_final: 0.8851 (mmt90) REVERT: A 305 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 377 MET cc_start: 0.7705 (ttt) cc_final: 0.6987 (tpp) REVERT: A 498 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8873 (mp0) REVERT: A 550 GLN cc_start: 0.9096 (pt0) cc_final: 0.8896 (pt0) REVERT: A 578 ASP cc_start: 0.8660 (m-30) cc_final: 0.8345 (t0) REVERT: A 640 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8926 (mm) REVERT: A 655 LYS cc_start: 0.8997 (tptp) cc_final: 0.8670 (pttp) REVERT: A 666 LYS cc_start: 0.9524 (mtmt) cc_final: 0.9177 (mtpt) REVERT: A 669 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8396 (ttp-110) REVERT: A 799 MET cc_start: 0.9133 (mmt) cc_final: 0.8779 (mmp) REVERT: A 1090 MET cc_start: 0.8415 (mmt) cc_final: 0.8022 (mmt) REVERT: A 1103 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8600 (mttt) outliers start: 3 outliers final: 0 residues processed: 209 average time/residue: 0.2241 time to fit residues: 60.4357 Evaluate side-chains 137 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS A 550 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A1086 GLN A1093 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7654 Z= 0.223 Angle : 0.712 10.391 10325 Z= 0.377 Chirality : 0.039 0.149 1215 Planarity : 0.005 0.048 1358 Dihedral : 6.138 24.270 1060 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.37 % Allowed : 3.33 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.23), residues: 991 helix: -1.78 (0.16), residues: 809 sheet: None (None), residues: 0 loop : -3.29 (0.38), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 258 HIS 0.005 0.001 HIS A1093 PHE 0.020 0.002 PHE A 232 TYR 0.014 0.002 TYR A 822 ARG 0.004 0.000 ARG A 832 *********************** 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 194 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 0.831 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: A 174 MET cc_start: 0.7973 (mmm) cc_final: 0.7537 (mmm) REVERT: A 241 ILE cc_start: 0.9348 (mt) cc_final: 0.9012 (tt) REVERT: A 246 ARG cc_start: 0.9271 (mpt-90) cc_final: 0.8897 (mpt180) REVERT: A 247 VAL cc_start: 0.8941 (t) cc_final: 0.8734 (p) REVERT: A 462 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7258 (pt) REVERT: A 578 ASP cc_start: 0.8854 (m-30) cc_final: 0.8420 (t0) REVERT: A 618 ASP cc_start: 0.7831 (m-30) cc_final: 0.7586 (m-30) REVERT: A 666 LYS cc_start: 0.9400 (mtmt) cc_final: 0.8957 (mtmt) REVERT: A 667 THR cc_start: 0.9211 (p) cc_final: 0.8228 (p) REVERT: A 669 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8218 (ttp-110) REVERT: A 709 MET cc_start: 0.8791 (ttm) cc_final: 0.8491 (ttm) REVERT: A 799 MET cc_start: 0.9128 (mmt) cc_final: 0.8832 (mmt) REVERT: A 975 ARG cc_start: 0.7972 (mpt180) cc_final: 0.7107 (mmt180) REVERT: A 979 LYS cc_start: 0.9413 (ptmm) cc_final: 0.9109 (mmtp) REVERT: A 1004 LEU cc_start: 0.9642 (mp) cc_final: 0.9321 (mt) REVERT: A 1083 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8253 (mp0) REVERT: A 1099 MET cc_start: 0.8838 (mmm) cc_final: 0.8621 (mmt) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.2079 time to fit residues: 52.2770 Evaluate side-chains 137 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 89 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS A 550 GLN A 974 HIS A1078 ASN A1096 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7654 Z= 0.208 Angle : 0.667 7.882 10325 Z= 0.350 Chirality : 0.040 0.131 1215 Planarity : 0.004 0.043 1358 Dihedral : 5.643 24.916 1060 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.12 % Allowed : 2.83 % 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: -2.06 (0.25), residues: 991 helix: -0.90 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -2.83 (0.41), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 980 HIS 0.005 0.001 HIS A 492 PHE 0.022 0.002 PHE A 232 TYR 0.010 0.001 TYR A 822 ARG 0.006 0.000 ARG A 409 *********************** 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 180 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.9688 (tttm) cc_final: 0.9406 (mttt) REVERT: A 174 MET cc_start: 0.8004 (mmm) cc_final: 0.7565 (mmm) REVERT: A 241 ILE cc_start: 0.9298 (mt) cc_final: 0.8938 (tt) REVERT: A 246 ARG cc_start: 0.9253 (mpt-90) cc_final: 0.8943 (mpt180) REVERT: A 254 ASP cc_start: 0.8015 (p0) cc_final: 0.7783 (p0) REVERT: A 451 GLN cc_start: 0.7751 (tp40) cc_final: 0.6391 (mm110) REVERT: A 578 ASP cc_start: 0.8861 (m-30) cc_final: 0.8490 (t0) REVERT: A 618 ASP cc_start: 0.7742 (m-30) cc_final: 0.7492 (m-30) REVERT: A 634 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8656 (mp0) REVERT: A 667 THR cc_start: 0.9276 (p) cc_final: 0.8970 (p) REVERT: A 709 MET cc_start: 0.8782 (ttm) cc_final: 0.8563 (ttm) REVERT: A 975 ARG cc_start: 0.7956 (mpt180) cc_final: 0.7241 (mmt180) REVERT: A 1004 LEU cc_start: 0.9638 (mp) cc_final: 0.9154 (mt) REVERT: A 1083 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8223 (mp0) REVERT: A 1090 MET cc_start: 0.7865 (mmt) cc_final: 0.7613 (mmt) REVERT: A 1099 MET cc_start: 0.8868 (mmm) cc_final: 0.8658 (mmt) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2166 time to fit residues: 51.0888 Evaluate side-chains 131 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.0030 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 overall best weight: 0.9632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS A 705 ASN A 974 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4163 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= 0.179 Angle : 0.648 8.981 10325 Z= 0.331 Chirality : 0.040 0.136 1215 Planarity : 0.004 0.041 1358 Dihedral : 5.429 25.022 1060 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.12 % Allowed : 3.57 % Favored : 96.31 % 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: -1.32 (0.25), residues: 991 helix: -0.37 (0.17), residues: 811 sheet: None (None), residues: 0 loop : -2.65 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 980 HIS 0.006 0.001 HIS A 492 PHE 0.018 0.002 PHE A 232 TYR 0.010 0.002 TYR A 822 ARG 0.003 0.000 ARG A 409 *********************** 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 176 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 0.913 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: A 11 SER cc_start: 0.8989 (p) cc_final: 0.8677 (p) REVERT: A 174 MET cc_start: 0.7991 (mmm) cc_final: 0.7549 (mmm) REVERT: A 241 ILE cc_start: 0.9335 (mt) cc_final: 0.8909 (tt) REVERT: A 246 ARG cc_start: 0.9253 (mpt-90) cc_final: 0.8886 (mmt-90) REVERT: A 254 ASP cc_start: 0.8043 (p0) cc_final: 0.7705 (p0) REVERT: A 578 ASP cc_start: 0.8841 (m-30) cc_final: 0.8449 (t0) REVERT: A 618 ASP cc_start: 0.7828 (m-30) cc_final: 0.7580 (m-30) REVERT: A 659 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8694 (pt0) REVERT: A 662 GLN cc_start: 0.8548 (pp30) cc_final: 0.8334 (tm-30) REVERT: A 667 THR cc_start: 0.9190 (p) cc_final: 0.8870 (p) REVERT: A 669 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: A 709 MET cc_start: 0.8731 (ttm) cc_final: 0.8481 (ttm) REVERT: A 799 MET cc_start: 0.8980 (mmt) cc_final: 0.8697 (mmt) REVERT: A 1004 LEU cc_start: 0.9623 (mp) cc_final: 0.9158 (mt) REVERT: A 1083 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8117 (mp0) REVERT: A 1090 MET cc_start: 0.7584 (mmt) cc_final: 0.7318 (mmt) REVERT: A 1103 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8748 (mtmt) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.2049 time to fit residues: 48.3903 Evaluate side-chains 135 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 0.0770 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS A 550 GLN A 705 ASN A 974 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7654 Z= 0.163 Angle : 0.644 7.743 10325 Z= 0.327 Chirality : 0.039 0.155 1215 Planarity : 0.004 0.050 1358 Dihedral : 5.236 24.451 1060 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.78 % 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: -0.77 (0.26), residues: 991 helix: 0.03 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.50 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 980 HIS 0.006 0.001 HIS A 492 PHE 0.016 0.001 PHE A 232 TYR 0.007 0.001 TYR A 692 ARG 0.004 0.000 ARG A 7 *********************** 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 169 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 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: A 174 MET cc_start: 0.7938 (mmm) cc_final: 0.7524 (mmm) REVERT: A 241 ILE cc_start: 0.9274 (mt) cc_final: 0.8831 (tt) REVERT: A 246 ARG cc_start: 0.9247 (mpt-90) cc_final: 0.8910 (mmt-90) REVERT: A 254 ASP cc_start: 0.8078 (p0) cc_final: 0.7711 (p0) REVERT: A 266 MET cc_start: 0.7313 (mmt) cc_final: 0.7006 (mmt) REVERT: A 451 GLN cc_start: 0.7667 (tp40) cc_final: 0.6292 (mm110) REVERT: A 498 GLU cc_start: 0.9298 (mp0) cc_final: 0.9023 (mp0) REVERT: A 578 ASP cc_start: 0.8833 (m-30) cc_final: 0.8441 (t0) REVERT: A 587 MET cc_start: 0.2652 (mmm) cc_final: 0.2283 (mmt) REVERT: A 618 ASP cc_start: 0.7900 (m-30) cc_final: 0.7670 (m-30) REVERT: A 659 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8637 (pt0) REVERT: A 667 THR cc_start: 0.9187 (p) cc_final: 0.8875 (p) REVERT: A 697 THR cc_start: 0.8597 (p) cc_final: 0.8346 (p) REVERT: A 698 MET cc_start: 0.8729 (mmm) cc_final: 0.8208 (mmm) REVERT: A 709 MET cc_start: 0.8717 (ttm) cc_final: 0.8438 (ttm) REVERT: A 748 MET cc_start: 0.8307 (mmt) cc_final: 0.8005 (mmp) REVERT: A 1073 MET cc_start: 0.8304 (mmm) cc_final: 0.7942 (tpt) REVERT: A 1083 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8111 (mp0) REVERT: A 1103 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8626 (ttmm) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2013 time to fit residues: 45.4096 Evaluate side-chains 131 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 0.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7654 Z= 0.188 Angle : 0.655 8.805 10325 Z= 0.336 Chirality : 0.039 0.133 1215 Planarity : 0.004 0.047 1358 Dihedral : 5.136 24.421 1060 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 991 helix: 0.26 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -2.40 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 503 HIS 0.005 0.001 HIS A 492 PHE 0.018 0.002 PHE A 599 TYR 0.030 0.002 TYR A 692 ARG 0.004 0.000 ARG A 669 *********************** 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 164 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7947 (mmm) cc_final: 0.7536 (mmm) REVERT: A 241 ILE cc_start: 0.9311 (mt) cc_final: 0.8862 (tt) REVERT: A 246 ARG cc_start: 0.9285 (mpt-90) cc_final: 0.8966 (mmt-90) REVERT: A 254 ASP cc_start: 0.8043 (p0) cc_final: 0.7605 (p0) REVERT: A 305 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8600 (mm-30) REVERT: A 451 GLN cc_start: 0.7756 (tp40) cc_final: 0.6343 (mm110) REVERT: A 578 ASP cc_start: 0.8830 (m-30) cc_final: 0.8452 (t0) REVERT: A 587 MET cc_start: 0.2745 (mmm) cc_final: 0.2468 (mmt) REVERT: A 659 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8734 (pt0) REVERT: A 666 LYS cc_start: 0.9255 (mtmt) cc_final: 0.9009 (mtpt) REVERT: A 667 THR cc_start: 0.9277 (p) cc_final: 0.8766 (p) REVERT: A 709 MET cc_start: 0.8709 (ttm) cc_final: 0.8370 (ttm) REVERT: A 748 MET cc_start: 0.8292 (mmt) cc_final: 0.7985 (mmp) REVERT: A 799 MET cc_start: 0.8927 (mmt) cc_final: 0.8682 (mmt) REVERT: A 1073 MET cc_start: 0.8347 (mmm) cc_final: 0.8033 (tpt) REVERT: A 1083 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8139 (mp0) REVERT: A 1103 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8563 (ttmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2082 time to fit residues: 45.7544 Evaluate side-chains 134 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5041 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= 0.185 Angle : 0.663 9.458 10325 Z= 0.339 Chirality : 0.040 0.157 1215 Planarity : 0.004 0.038 1358 Dihedral : 5.095 24.307 1060 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 0.41 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -2.53 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 503 HIS 0.006 0.001 HIS A 492 PHE 0.020 0.002 PHE A 599 TYR 0.028 0.002 TYR A 692 ARG 0.004 0.000 ARG A 669 *********************** 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 169 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7904 (mmm) cc_final: 0.7498 (mmm) REVERT: A 241 ILE cc_start: 0.9304 (mt) cc_final: 0.8860 (tt) REVERT: A 246 ARG cc_start: 0.9280 (mpt-90) cc_final: 0.8948 (mmt-90) REVERT: A 254 ASP cc_start: 0.7955 (p0) cc_final: 0.7477 (p0) REVERT: A 266 MET cc_start: 0.7337 (mmt) cc_final: 0.7056 (mmt) REVERT: A 498 GLU cc_start: 0.9344 (mp0) cc_final: 0.9065 (mp0) REVERT: A 578 ASP cc_start: 0.8825 (m-30) cc_final: 0.8462 (t0) REVERT: A 587 MET cc_start: 0.2777 (mmm) cc_final: 0.2360 (mmt) REVERT: A 659 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8724 (pt0) REVERT: A 666 LYS cc_start: 0.9254 (mtmt) cc_final: 0.9004 (mtpt) REVERT: A 667 THR cc_start: 0.9273 (p) cc_final: 0.8497 (p) REVERT: A 748 MET cc_start: 0.8341 (mmt) cc_final: 0.8035 (mmp) REVERT: A 799 MET cc_start: 0.8936 (mmt) cc_final: 0.8679 (mmt) REVERT: A 832 ARG cc_start: 0.8416 (tpt90) cc_final: 0.8198 (tpt90) REVERT: A 1083 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8145 (mp0) REVERT: A 1103 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8545 (ttmm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2030 time to fit residues: 45.7551 Evaluate side-chains 130 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 83 optimal weight: 0.0470 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS A 632 ASN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7654 Z= 0.229 Angle : 0.696 9.246 10325 Z= 0.362 Chirality : 0.042 0.159 1215 Planarity : 0.004 0.036 1358 Dihedral : 5.184 23.629 1060 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 991 helix: 0.45 (0.18), residues: 813 sheet: None (None), residues: 0 loop : -2.44 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 503 HIS 0.008 0.002 HIS A 187 PHE 0.019 0.003 PHE A 599 TYR 0.028 0.002 TYR A 692 ARG 0.004 0.001 ARG A 416 *********************** 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 160 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8173 (tt0) cc_final: 0.7407 (pp20) REVERT: A 174 MET cc_start: 0.7941 (mmm) cc_final: 0.7535 (mmm) REVERT: A 195 MET cc_start: 0.8597 (ttp) cc_final: 0.8223 (tmm) REVERT: A 241 ILE cc_start: 0.9287 (mt) cc_final: 0.8843 (tt) REVERT: A 246 ARG cc_start: 0.9279 (mpt-90) cc_final: 0.8956 (mmt-90) REVERT: A 254 ASP cc_start: 0.7892 (p0) cc_final: 0.7401 (p0) REVERT: A 451 GLN cc_start: 0.7808 (tp40) cc_final: 0.6214 (mm110) REVERT: A 498 GLU cc_start: 0.9361 (mp0) cc_final: 0.9120 (mp0) REVERT: A 578 ASP cc_start: 0.8843 (m-30) cc_final: 0.8501 (t0) REVERT: A 587 MET cc_start: 0.2839 (mmm) cc_final: 0.2386 (mmt) REVERT: A 666 LYS cc_start: 0.9283 (mtmt) cc_final: 0.8902 (mtpt) REVERT: A 667 THR cc_start: 0.9338 (p) cc_final: 0.8733 (p) REVERT: A 748 MET cc_start: 0.8344 (mmt) cc_final: 0.8022 (mmp) REVERT: A 799 MET cc_start: 0.8910 (mmt) cc_final: 0.8682 (mmt) REVERT: A 832 ARG cc_start: 0.8376 (tpt90) cc_final: 0.8171 (tpt90) REVERT: A 1083 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8166 (mp0) REVERT: A 1103 LYS cc_start: 0.9085 (mtpt) cc_final: 0.8563 (ttmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2074 time to fit residues: 44.3108 Evaluate side-chains 128 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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: 20.0000 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5335 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= 0.210 Angle : 0.684 10.694 10325 Z= 0.353 Chirality : 0.041 0.151 1215 Planarity : 0.004 0.035 1358 Dihedral : 5.163 23.704 1060 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 991 helix: 0.55 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -2.32 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 503 HIS 0.006 0.001 HIS A 492 PHE 0.020 0.002 PHE A 232 TYR 0.024 0.002 TYR A 692 ARG 0.005 0.000 ARG A 502 *********************** 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 163 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8143 (tt0) cc_final: 0.7383 (pp20) REVERT: A 195 MET cc_start: 0.8578 (ttp) cc_final: 0.8204 (tmm) REVERT: A 241 ILE cc_start: 0.9311 (mt) cc_final: 0.8905 (tt) REVERT: A 246 ARG cc_start: 0.9276 (mpt-90) cc_final: 0.8954 (mmt-90) REVERT: A 254 ASP cc_start: 0.7864 (p0) cc_final: 0.7311 (p0) REVERT: A 354 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 377 MET cc_start: 0.7354 (ttt) cc_final: 0.6434 (tpp) REVERT: A 451 GLN cc_start: 0.7736 (tp40) cc_final: 0.6040 (mm-40) REVERT: A 498 GLU cc_start: 0.9345 (mp0) cc_final: 0.9095 (mp0) REVERT: A 578 ASP cc_start: 0.8819 (m-30) cc_final: 0.8496 (t0) REVERT: A 587 MET cc_start: 0.2642 (mmm) cc_final: 0.2374 (mmt) REVERT: A 591 MET cc_start: 0.8576 (tpt) cc_final: 0.8230 (tpt) REVERT: A 659 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8775 (pt0) REVERT: A 666 LYS cc_start: 0.9255 (mtmt) cc_final: 0.9050 (mtpt) REVERT: A 667 THR cc_start: 0.9308 (p) cc_final: 0.8952 (p) REVERT: A 748 MET cc_start: 0.8375 (mmt) cc_final: 0.8047 (mmp) REVERT: A 799 MET cc_start: 0.8917 (mmt) cc_final: 0.8675 (mmt) REVERT: A 1083 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8204 (mp0) REVERT: A 1103 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8555 (ttmm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2076 time to fit residues: 45.0400 Evaluate side-chains 129 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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: 5.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7654 Z= 0.174 Angle : 0.678 10.888 10325 Z= 0.341 Chirality : 0.040 0.133 1215 Planarity : 0.004 0.037 1358 Dihedral : 5.072 24.029 1060 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 991 helix: 0.68 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -2.19 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 503 HIS 0.007 0.001 HIS A 492 PHE 0.015 0.002 PHE A 232 TYR 0.022 0.001 TYR A 692 ARG 0.004 0.000 ARG A1107 ********************** 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 176 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.968 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: A 28 GLU cc_start: 0.8034 (tt0) cc_final: 0.7473 (tm-30) REVERT: A 170 LYS cc_start: 0.9051 (tptt) cc_final: 0.8842 (tptt) REVERT: A 174 MET cc_start: 0.7778 (mmm) cc_final: 0.7405 (mmm) REVERT: A 241 ILE cc_start: 0.9316 (mt) cc_final: 0.8883 (tt) REVERT: A 246 ARG cc_start: 0.9251 (mpt-90) cc_final: 0.8915 (mmt-90) REVERT: A 254 ASP cc_start: 0.7812 (p0) cc_final: 0.7211 (p0) REVERT: A 305 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8530 (mm-30) REVERT: A 354 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 377 MET cc_start: 0.7275 (ttt) cc_final: 0.6577 (tpp) REVERT: A 386 LYS cc_start: 0.9017 (pttt) cc_final: 0.8811 (tttt) REVERT: A 451 GLN cc_start: 0.7704 (tp40) cc_final: 0.6068 (mm-40) REVERT: A 498 GLU cc_start: 0.9343 (mp0) cc_final: 0.9077 (mp0) REVERT: A 578 ASP cc_start: 0.8848 (m-30) cc_final: 0.8508 (t0) REVERT: A 591 MET cc_start: 0.8512 (tpt) cc_final: 0.8225 (tpt) REVERT: A 659 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8746 (pt0) REVERT: A 667 THR cc_start: 0.9224 (p) cc_final: 0.8971 (p) REVERT: A 698 MET cc_start: 0.8604 (mmm) cc_final: 0.8019 (mmm) REVERT: A 748 MET cc_start: 0.8343 (mmt) cc_final: 0.8016 (mmp) REVERT: A 799 MET cc_start: 0.8922 (mmt) cc_final: 0.8658 (mmt) REVERT: A 1083 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8183 (mp0) REVERT: A 1099 MET cc_start: 0.8939 (mmt) cc_final: 0.8666 (mmt) REVERT: A 1103 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8595 (ttmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2132 time to fit residues: 49.5171 Evaluate side-chains 136 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.090741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.072814 restraints weight = 35472.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.074708 restraints weight = 26238.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.076124 restraints weight = 20630.042| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7654 Z= 0.186 Angle : 0.685 10.360 10325 Z= 0.346 Chirality : 0.041 0.223 1215 Planarity : 0.004 0.053 1358 Dihedral : 5.087 23.849 1060 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: 0.22 (0.27), residues: 991 helix: 0.72 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -2.15 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP A 980 HIS 0.005 0.001 HIS A 492 PHE 0.029 0.002 PHE A 599 TYR 0.021 0.001 TYR A 692 ARG 0.003 0.000 ARG A 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1785.52 seconds wall clock time: 33 minutes 14.03 seconds (1994.03 seconds total)