Starting phenix.real_space_refine on Tue May 27 22:50:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soc_40653/05_2025/8soc_40653_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soc_40653/05_2025/8soc_40653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8soc_40653/05_2025/8soc_40653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soc_40653/05_2025/8soc_40653.map" model { file = "/net/cci-nas-00/data/ceres_data/8soc_40653/05_2025/8soc_40653_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soc_40653/05_2025/8soc_40653_neut_trim.cif" } resolution = 3.5 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= 0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 85 5.16 5 C 9472 2.51 5 N 2564 2.21 5 O 2747 1.98 5 H 14881 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29751 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 15717 Classifications: {'peptide': 965} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 919} Chain breaks: 9 Chain: "B" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7877 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 466} Chain breaks: 8 Chain: "C" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.30, per 1000 atoms: 0.45 Number of scatterers: 29751 At special positions: 0 Unit cell: (98.28, 136.08, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 2 15.00 O 2747 8.00 N 2564 7.00 C 9472 6.00 H 14881 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 18 sheets defined 43.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.767A pdb=" N LYS A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.624A pdb=" N TYR A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 removed outlier: 3.566A pdb=" N ARG A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.603A pdb=" N LYS A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) 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 240 through 252 removed outlier: 3.585A pdb=" N THR A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.790A pdb=" N LYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.741A pdb=" N LEU A 502 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.583A pdb=" N VAL A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.537A pdb=" N ILE A 558 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 584 through 587 removed outlier: 6.434A pdb=" N LYS A 587 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.816A pdb=" N GLN A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.596A pdb=" N MET A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.644A pdb=" N ALA A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 4.749A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 removed outlier: 3.970A pdb=" N PHE A 669 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 670 " --> pdb=" O VAL A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 670' Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.636A pdb=" N ARG A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.501A pdb=" N GLY A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 701 " --> pdb=" O TRP A 697 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 removed outlier: 3.626A pdb=" N ILE A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 751 removed outlier: 3.557A pdb=" N LEU A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 838 through 858 removed outlier: 3.579A pdb=" N GLU A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 853 " --> pdb=" O ARG A 849 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 894 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 917 through 943 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.686A pdb=" N LEU A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1021 removed outlier: 3.542A pdb=" N ARG A1021 " --> pdb=" O TYR A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1038 removed outlier: 3.681A pdb=" N ILE A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1054 removed outlier: 4.082A pdb=" N ARG A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1054 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1077 removed outlier: 3.673A pdb=" N VAL A1074 " --> pdb=" O ASP A1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 22 Processing helix chain 'B' and resid 39 through 50 removed outlier: 3.659A pdb=" N ARG B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 73 removed outlier: 4.275A pdb=" N PHE B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.562A pdb=" N ARG B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.850A pdb=" N CYS B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.596A pdb=" N ALA B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.773A pdb=" N LEU B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 206 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.599A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 Processing helix chain 'B' and resid 247 through 265 removed outlier: 3.865A pdb=" N GLN B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.702A pdb=" N GLN B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 543 removed outlier: 4.168A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 removed outlier: 4.071A pdb=" N PHE B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 550' Processing helix chain 'B' and resid 606 through 613 Processing helix chain 'B' and resid 613 through 620 Processing helix chain 'B' and resid 650 through 663 removed outlier: 3.505A pdb=" N TYR B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.512A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'G' and resid 5 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.597A pdb=" N ILE A 38 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 133 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP A 106 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 236 Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.151A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.595A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 removed outlier: 3.962A pdb=" N PHE A 382 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 434 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 433 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 462 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N CYS A 435 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU A 460 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 463 " --> pdb=" O TRP A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 803 removed outlier: 3.768A pdb=" N PHE A 815 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 833 " --> pdb=" O GLY A 877 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY A 877 " --> pdb=" O LYS A 833 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 292 removed outlier: 8.675A pdb=" N TYR B 289 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 162 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR B 291 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU B 164 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER B 159 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG B 516 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL B 161 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL B 518 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 163 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE B 520 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU B 165 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 684 through 688 removed outlier: 7.298A pdb=" N GLN B 673 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL B 832 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU B 675 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 830 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 677 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 801 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 691 through 694 removed outlier: 3.637A pdb=" N SER B 750 " --> pdb=" O THR B 775 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 754 " --> pdb=" O THR B 771 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 770 " --> pdb=" O VAL B 799 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.492A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.984A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.843A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.535A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.681A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.695A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.136A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1896 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: 11.58 Time building geometry restraints manager: 8.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14830 1.03 - 1.22: 52 1.22 - 1.42: 6274 1.42 - 1.61: 8785 1.61 - 1.81: 119 Bond restraints: 30060 Sorted by residual: bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " ideal model delta sigma weight residual 1.458 1.440 0.018 1.40e-02 5.10e+03 1.57e+00 bond pdb=" CB TRP A 413 " pdb=" CG TRP A 413 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB PHE A 832 " pdb=" CG PHE A 832 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.79e-01 bond pdb=" CA VAL C 133 " pdb=" CB VAL C 133 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 8.74e-01 ... (remaining 30055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 52152 1.25 - 2.50: 2027 2.50 - 3.76: 139 3.76 - 5.01: 27 5.01 - 6.26: 8 Bond angle restraints: 54353 Sorted by residual: angle pdb=" N ASN A 430 " pdb=" CA ASN A 430 " pdb=" C ASN A 430 " ideal model delta sigma weight residual 109.24 113.73 -4.49 1.63e+00 3.76e-01 7.57e+00 angle pdb=" N LEU A 429 " pdb=" CA LEU A 429 " pdb=" C LEU A 429 " ideal model delta sigma weight residual 109.15 106.01 3.14 1.44e+00 4.82e-01 4.77e+00 angle pdb=" C1' ADP A1201 " pdb=" C2' ADP A1201 " pdb=" C3' ADP A1201 " ideal model delta sigma weight residual 111.00 104.74 6.26 3.00e+00 1.11e-01 4.35e+00 angle pdb=" CA ILE A1029 " pdb=" CB ILE A1029 " pdb=" CG2 ILE A1029 " ideal model delta sigma weight residual 110.50 113.78 -3.28 1.70e+00 3.46e-01 3.72e+00 angle pdb=" O1B ADP A1201 " pdb=" PB ADP A1201 " pdb=" O2B ADP A1201 " ideal model delta sigma weight residual 119.90 114.19 5.71 3.00e+00 1.11e-01 3.62e+00 ... (remaining 54348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.02: 13757 32.02 - 64.05: 313 64.05 - 96.07: 19 96.07 - 128.10: 0 128.10 - 160.12: 1 Dihedral angle restraints: 14090 sinusoidal: 7700 harmonic: 6390 Sorted by residual: dihedral pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " pdb=" CZ ARG A 294 " pdb=" NH1 ARG A 294 " ideal model delta sinusoidal sigma weight residual 0.00 65.39 -65.39 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 100.12 -160.12 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" CD ARG A 712 " pdb=" NE ARG A 712 " pdb=" CZ ARG A 712 " pdb=" NH1 ARG A 712 " ideal model delta sinusoidal sigma weight residual 0.00 -40.24 40.24 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 14087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1528 0.032 - 0.065: 565 0.065 - 0.097: 152 0.097 - 0.130: 83 0.130 - 0.162: 14 Chirality restraints: 2342 Sorted by residual: chirality pdb=" CA ILE A 879 " pdb=" N ILE A 879 " pdb=" C ILE A 879 " pdb=" CB ILE A 879 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CB ILE A1029 " pdb=" CA ILE A1029 " pdb=" CG1 ILE A1029 " pdb=" CG2 ILE A1029 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE A 387 " pdb=" N ILE A 387 " pdb=" C ILE A 387 " pdb=" CB ILE A 387 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 2339 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 294 " 0.901 9.50e-02 1.11e+02 3.01e-01 1.04e+02 pdb=" NE ARG A 294 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 294 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 294 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG A 294 " -0.019 2.00e-02 2.50e+03 pdb="HH11 ARG A 294 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 294 " 0.015 2.00e-02 2.50e+03 pdb="HH21 ARG A 294 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 294 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 712 " 0.595 9.50e-02 1.11e+02 2.00e-01 5.04e+01 pdb=" NE ARG A 712 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 712 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 712 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 712 " -0.019 2.00e-02 2.50e+03 pdb="HH11 ARG A 712 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 712 " 0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 712 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 712 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 184 " 0.564 9.50e-02 1.11e+02 1.89e-01 4.47e+01 pdb=" NE ARG A 184 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 184 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG A 184 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 184 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG A 184 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 184 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG A 184 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 184 " 0.017 2.00e-02 2.50e+03 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 397 2.05 - 2.69: 47619 2.69 - 3.33: 85142 3.33 - 3.96: 106558 3.96 - 4.60: 170300 Nonbonded interactions: 410016 Sorted by model distance: nonbonded pdb=" OD1 ASN A 688 " pdb=" H ILE A 691 " model vdw 1.418 2.450 nonbonded pdb=" HD1 HIS B 94 " pdb=" O ALA B 203 " model vdw 1.453 2.450 nonbonded pdb=" O LEU B 166 " pdb=" H TRP B 293 " model vdw 1.480 2.450 nonbonded pdb=" H LEU A 44 " pdb=" O GLU A 55 " model vdw 1.516 2.450 nonbonded pdb="HD21 ASN A 430 " pdb=" OD1 ASN A 465 " model vdw 1.534 2.450 ... (remaining 410011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.170 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: 0.510 Extract box with map and model: 1.140 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 60.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.004 0.044 15179 Z= 0.171 Angle : 0.587 6.260 20569 Z= 0.307 Chirality : 0.041 0.162 2342 Planarity : 0.011 0.388 2612 Dihedral : 12.440 160.121 5609 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 2.13 % Allowed : 5.30 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.42 (0.20), residues: 1818 helix: -0.13 (0.20), residues: 676 sheet: -1.14 (0.28), residues: 339 loop : -1.47 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 413 HIS 0.006 0.001 HIS B 607 PHE 0.020 0.002 PHE B 129 TYR 0.024 0.002 TYR B 658 ARG 0.048 0.001 ARG A 712 Details of bonding type rmsd hydrogen bonds : bond 0.28570 ( 665) hydrogen bonds : angle 9.12432 ( 1896) covalent geometry : bond 0.00378 (15179) covalent geometry : angle 0.58663 (20569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 2.125 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 852 GLU cc_start: 0.8192 (tt0) cc_final: 0.7535 (tp30) REVERT: A 1050 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: C 155 ASN cc_start: 0.7549 (t0) cc_final: 0.7253 (t0) REVERT: C 186 ASP cc_start: 0.6397 (m-30) cc_final: 0.5789 (m-30) REVERT: G 11 GLN cc_start: 0.7513 (tt0) cc_final: 0.7256 (tp40) outliers start: 35 outliers final: 17 residues processed: 359 average time/residue: 0.7055 time to fit residues: 353.1773 Evaluate side-chains 203 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 231 GLN A 554 GLN A 734 GLN A 776 ASN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 258 GLN C 230 ASN C 295 ASN G 4 ASN G 18 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.117300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.083045 restraints weight = 119587.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.086820 restraints weight = 49454.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089120 restraints weight = 29839.556| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15179 Z= 0.203 Angle : 0.675 7.455 20569 Z= 0.356 Chirality : 0.042 0.157 2342 Planarity : 0.005 0.069 2612 Dihedral : 7.856 172.537 2050 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.44 % Allowed : 10.79 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.42 (0.19), residues: 1818 helix: -0.09 (0.18), residues: 714 sheet: -1.13 (0.27), residues: 344 loop : -1.57 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.007 0.001 HIS A 909 PHE 0.022 0.002 PHE A1009 TYR 0.020 0.002 TYR A1067 ARG 0.010 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.06308 ( 665) hydrogen bonds : angle 6.33857 ( 1896) covalent geometry : bond 0.00427 (15179) covalent geometry : angle 0.67498 (20569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 2.282 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 249 PHE cc_start: 0.7665 (m-10) cc_final: 0.7444 (m-10) REVERT: A 628 MET cc_start: 0.7799 (mmm) cc_final: 0.7441 (mmm) REVERT: A 852 GLU cc_start: 0.8078 (tt0) cc_final: 0.7636 (tp30) REVERT: A 1050 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: B 741 TRP cc_start: 0.7429 (m100) cc_final: 0.6877 (m100) REVERT: C 5 ASP cc_start: 0.8291 (m-30) cc_final: 0.7862 (p0) REVERT: C 12 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6569 (mm-30) REVERT: C 188 MET cc_start: 0.5716 (mpp) cc_final: 0.5062 (mpp) REVERT: C 293 ASN cc_start: 0.8269 (m-40) cc_final: 0.7952 (m-40) REVERT: G 11 GLN cc_start: 0.7657 (tt0) cc_final: 0.7043 (tp40) REVERT: G 47 GLU cc_start: 0.8524 (mp0) cc_final: 0.8295 (mp0) outliers start: 40 outliers final: 29 residues processed: 225 average time/residue: 0.6864 time to fit residues: 218.9618 Evaluate side-chains 188 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 67 optimal weight: 0.0870 chunk 145 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.117231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.082716 restraints weight = 119417.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.086628 restraints weight = 48371.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.088962 restraints weight = 28843.977| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15179 Z= 0.155 Angle : 0.600 6.955 20569 Z= 0.309 Chirality : 0.040 0.154 2342 Planarity : 0.004 0.050 2612 Dihedral : 7.503 177.186 2038 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.26 % Allowed : 12.13 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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 (0.19), residues: 1818 helix: 0.17 (0.19), residues: 717 sheet: -0.98 (0.27), residues: 357 loop : -1.49 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.006 0.001 HIS A 909 PHE 0.013 0.001 PHE A1009 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05419 ( 665) hydrogen bonds : angle 5.86079 ( 1896) covalent geometry : bond 0.00337 (15179) covalent geometry : angle 0.59960 (20569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 2.311 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 521 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: A 628 MET cc_start: 0.7769 (mmm) cc_final: 0.7394 (mmm) REVERT: A 852 GLU cc_start: 0.7941 (tt0) cc_final: 0.7547 (tp30) REVERT: A 1050 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: C 5 ASP cc_start: 0.8290 (m-30) cc_final: 0.7875 (p0) REVERT: C 186 ASP cc_start: 0.4800 (m-30) cc_final: 0.4399 (m-30) REVERT: C 188 MET cc_start: 0.5688 (mpp) cc_final: 0.5158 (mpp) REVERT: G 11 GLN cc_start: 0.7583 (tt0) cc_final: 0.6970 (tp40) REVERT: G 40 TYR cc_start: 0.8341 (t80) cc_final: 0.8083 (t80) REVERT: G 47 GLU cc_start: 0.8504 (mp0) cc_final: 0.8258 (mp0) outliers start: 37 outliers final: 29 residues processed: 200 average time/residue: 0.6898 time to fit residues: 201.6465 Evaluate side-chains 189 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 750 LYS Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 54 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 154 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.116141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.081706 restraints weight = 120003.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.085520 restraints weight = 49549.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.087787 restraints weight = 29783.325| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15179 Z= 0.186 Angle : 0.603 6.982 20569 Z= 0.312 Chirality : 0.040 0.158 2342 Planarity : 0.004 0.051 2612 Dihedral : 7.273 179.817 2032 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.50 % Allowed : 12.62 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.28 (0.19), residues: 1818 helix: 0.09 (0.18), residues: 719 sheet: -1.13 (0.27), residues: 345 loop : -1.54 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.008 0.001 HIS A1023 PHE 0.015 0.002 PHE A1009 TYR 0.019 0.002 TYR A1067 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 665) hydrogen bonds : angle 5.66694 ( 1896) covalent geometry : bond 0.00410 (15179) covalent geometry : angle 0.60345 (20569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 2.216 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 521 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: A 628 MET cc_start: 0.7740 (mmm) cc_final: 0.7387 (mmm) REVERT: A 852 GLU cc_start: 0.7888 (tt0) cc_final: 0.7505 (tp30) REVERT: A 1050 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: C 5 ASP cc_start: 0.8354 (m-30) cc_final: 0.7923 (p0) REVERT: C 186 ASP cc_start: 0.4899 (m-30) cc_final: 0.4503 (m-30) REVERT: C 188 MET cc_start: 0.5904 (mpp) cc_final: 0.5352 (mpp) REVERT: G 11 GLN cc_start: 0.7495 (tt0) cc_final: 0.6965 (tp40) REVERT: G 47 GLU cc_start: 0.8483 (mp0) cc_final: 0.8193 (mp0) outliers start: 41 outliers final: 34 residues processed: 189 average time/residue: 0.6761 time to fit residues: 182.7653 Evaluate side-chains 185 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 146 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 HIS A1005 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN C 13 GLN G 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.113985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.079905 restraints weight = 122286.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.083499 restraints weight = 52375.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.085646 restraints weight = 32061.362| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15179 Z= 0.285 Angle : 0.686 8.968 20569 Z= 0.360 Chirality : 0.042 0.230 2342 Planarity : 0.005 0.069 2612 Dihedral : 7.366 178.497 2029 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.11 % Allowed : 12.99 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.78 (0.19), residues: 1818 helix: -0.34 (0.18), residues: 715 sheet: -1.32 (0.27), residues: 347 loop : -1.85 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 697 HIS 0.007 0.002 HIS A 199 PHE 0.017 0.002 PHE B 129 TYR 0.020 0.003 TYR A1067 ARG 0.007 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.05265 ( 665) hydrogen bonds : angle 5.83084 ( 1896) covalent geometry : bond 0.00625 (15179) covalent geometry : angle 0.68577 (20569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 2.196 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 198 MET cc_start: 0.8405 (mpt) cc_final: 0.8133 (mpt) REVERT: A 521 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 852 GLU cc_start: 0.7957 (tt0) cc_final: 0.7589 (tp30) REVERT: A 1050 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: C 5 ASP cc_start: 0.8303 (m-30) cc_final: 0.7873 (p0) REVERT: C 105 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.7159 (t80) REVERT: C 186 ASP cc_start: 0.4945 (m-30) cc_final: 0.4563 (m-30) REVERT: C 188 MET cc_start: 0.6064 (mpp) cc_final: 0.5454 (mpp) REVERT: C 222 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.3442 (m-80) REVERT: G 11 GLN cc_start: 0.7529 (tt0) cc_final: 0.6946 (tp40) outliers start: 51 outliers final: 42 residues processed: 185 average time/residue: 0.6752 time to fit residues: 182.5119 Evaluate side-chains 188 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 750 LYS Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 179 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 56 optimal weight: 0.0980 chunk 142 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 173 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.082484 restraints weight = 119690.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.086295 restraints weight = 49425.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.088575 restraints weight = 29719.188| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15179 Z= 0.118 Angle : 0.567 9.781 20569 Z= 0.288 Chirality : 0.040 0.154 2342 Planarity : 0.004 0.041 2612 Dihedral : 6.873 174.074 2027 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 13.90 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1818 helix: 0.30 (0.19), residues: 726 sheet: -0.98 (0.28), residues: 328 loop : -1.61 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 697 HIS 0.005 0.001 HIS A1022 PHE 0.013 0.001 PHE A 473 TYR 0.018 0.001 TYR G 40 ARG 0.002 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 665) hydrogen bonds : angle 5.24425 ( 1896) covalent geometry : bond 0.00262 (15179) covalent geometry : angle 0.56714 (20569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 2.326 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 198 MET cc_start: 0.8358 (mpt) cc_final: 0.7997 (mpt) REVERT: A 521 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: A 852 GLU cc_start: 0.7852 (tt0) cc_final: 0.7447 (tp30) REVERT: A 1050 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: C 5 ASP cc_start: 0.8339 (m-30) cc_final: 0.7920 (p0) REVERT: C 99 TRP cc_start: 0.5925 (t-100) cc_final: 0.5724 (t-100) REVERT: C 186 ASP cc_start: 0.4588 (m-30) cc_final: 0.4224 (m-30) REVERT: C 188 MET cc_start: 0.5983 (mpp) cc_final: 0.5548 (mpp) REVERT: C 293 ASN cc_start: 0.8508 (t0) cc_final: 0.8300 (t0) REVERT: G 11 GLN cc_start: 0.7522 (tt0) cc_final: 0.6936 (tp40) outliers start: 38 outliers final: 32 residues processed: 181 average time/residue: 0.6966 time to fit residues: 182.1572 Evaluate side-chains 178 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 130 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.115193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.081058 restraints weight = 120680.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.084778 restraints weight = 50832.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.086987 restraints weight = 30894.972| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15179 Z= 0.177 Angle : 0.586 8.936 20569 Z= 0.301 Chirality : 0.040 0.155 2342 Planarity : 0.004 0.044 2612 Dihedral : 6.828 171.493 2025 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.50 % Allowed : 14.15 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.18 (0.19), residues: 1818 helix: 0.33 (0.19), residues: 724 sheet: -1.07 (0.27), residues: 333 loop : -1.69 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 697 HIS 0.005 0.001 HIS A 199 PHE 0.010 0.001 PHE A 473 TYR 0.023 0.002 TYR G 40 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 665) hydrogen bonds : angle 5.28547 ( 1896) covalent geometry : bond 0.00390 (15179) covalent geometry : angle 0.58614 (20569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 2.320 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 198 MET cc_start: 0.8358 (mpt) cc_final: 0.7994 (mpt) REVERT: A 521 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: A 1039 MET cc_start: 0.7056 (ppp) cc_final: 0.6834 (ppp) REVERT: A 1050 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: C 5 ASP cc_start: 0.8210 (m-30) cc_final: 0.7788 (p0) REVERT: C 105 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.7002 (t80) REVERT: C 186 ASP cc_start: 0.4737 (m-30) cc_final: 0.4417 (m-30) REVERT: C 188 MET cc_start: 0.6153 (mpp) cc_final: 0.5635 (mpp) REVERT: C 293 ASN cc_start: 0.8412 (t0) cc_final: 0.8148 (t0) REVERT: G 11 GLN cc_start: 0.7597 (tt0) cc_final: 0.6923 (tp40) outliers start: 41 outliers final: 38 residues processed: 178 average time/residue: 0.6803 time to fit residues: 173.5028 Evaluate side-chains 187 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.115912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081834 restraints weight = 121251.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.085680 restraints weight = 50356.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.087954 restraints weight = 30314.596| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15179 Z= 0.129 Angle : 0.558 9.690 20569 Z= 0.283 Chirality : 0.039 0.153 2342 Planarity : 0.004 0.039 2612 Dihedral : 6.610 166.878 2025 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.50 % Allowed : 14.45 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.92 (0.20), residues: 1818 helix: 0.60 (0.19), residues: 728 sheet: -0.97 (0.27), residues: 336 loop : -1.60 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 PHE 0.011 0.001 PHE A 473 TYR 0.018 0.001 TYR G 40 ARG 0.002 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 665) hydrogen bonds : angle 5.05014 ( 1896) covalent geometry : bond 0.00289 (15179) covalent geometry : angle 0.55847 (20569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 2.214 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 198 MET cc_start: 0.8383 (mpt) cc_final: 0.7960 (mpt) REVERT: A 521 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: A 1039 MET cc_start: 0.6990 (ppp) cc_final: 0.6709 (ppp) REVERT: A 1050 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: C 5 ASP cc_start: 0.8225 (m-30) cc_final: 0.7854 (p0) REVERT: C 57 LYS cc_start: 0.8618 (mttt) cc_final: 0.8314 (mtmt) REVERT: G 11 GLN cc_start: 0.7602 (tt0) cc_final: 0.6924 (tp40) outliers start: 41 outliers final: 35 residues processed: 180 average time/residue: 0.6382 time to fit residues: 166.8612 Evaluate side-chains 180 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 177 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.115482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.081386 restraints weight = 120855.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.085157 restraints weight = 50697.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.087417 restraints weight = 30755.288| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15179 Z= 0.156 Angle : 0.569 8.312 20569 Z= 0.291 Chirality : 0.039 0.153 2342 Planarity : 0.004 0.039 2612 Dihedral : 6.534 163.955 2024 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.38 % Allowed : 14.63 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.88 (0.20), residues: 1818 helix: 0.59 (0.19), residues: 728 sheet: -0.90 (0.27), residues: 335 loop : -1.56 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.005 0.001 HIS A 199 PHE 0.014 0.001 PHE B 550 TYR 0.018 0.002 TYR A1067 ARG 0.004 0.000 ARG A1052 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 665) hydrogen bonds : angle 5.06533 ( 1896) covalent geometry : bond 0.00348 (15179) covalent geometry : angle 0.56944 (20569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 2.147 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 198 MET cc_start: 0.8403 (mpt) cc_final: 0.7944 (mpt) REVERT: A 1039 MET cc_start: 0.7037 (ppp) cc_final: 0.6747 (ppp) REVERT: A 1050 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: C 5 ASP cc_start: 0.8221 (m-30) cc_final: 0.7859 (p0) REVERT: G 11 GLN cc_start: 0.7599 (tt0) cc_final: 0.6923 (tp40) outliers start: 39 outliers final: 37 residues processed: 170 average time/residue: 0.6469 time to fit residues: 158.9099 Evaluate side-chains 180 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 181 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.115606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.081832 restraints weight = 120199.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.085649 restraints weight = 49657.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.087928 restraints weight = 29834.870| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15179 Z= 0.146 Angle : 0.564 8.764 20569 Z= 0.287 Chirality : 0.039 0.151 2342 Planarity : 0.004 0.039 2612 Dihedral : 6.329 159.046 2021 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.38 % Allowed : 14.63 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.80 (0.20), residues: 1818 helix: 0.69 (0.19), residues: 728 sheet: -0.87 (0.27), residues: 335 loop : -1.53 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 697 HIS 0.005 0.001 HIS G 44 PHE 0.011 0.001 PHE A 473 TYR 0.026 0.002 TYR A1067 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 665) hydrogen bonds : angle 4.97092 ( 1896) covalent geometry : bond 0.00326 (15179) covalent geometry : angle 0.56421 (20569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 2.578 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 198 MET cc_start: 0.8389 (mpt) cc_final: 0.7899 (mpt) REVERT: A 1039 MET cc_start: 0.7087 (ppp) cc_final: 0.6770 (ppp) REVERT: C 105 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.7072 (t80) REVERT: G 11 GLN cc_start: 0.7594 (tt0) cc_final: 0.6876 (tp40) outliers start: 39 outliers final: 37 residues processed: 173 average time/residue: 0.7008 time to fit residues: 177.8107 Evaluate side-chains 179 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 166 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.115962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.081907 restraints weight = 120382.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.085751 restraints weight = 50324.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.088037 restraints weight = 30404.321| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15179 Z= 0.132 Angle : 0.552 8.726 20569 Z= 0.279 Chirality : 0.039 0.155 2342 Planarity : 0.004 0.039 2612 Dihedral : 6.173 153.220 2021 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.50 % Allowed : 14.63 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.70 (0.20), residues: 1818 helix: 0.83 (0.19), residues: 728 sheet: -1.00 (0.27), residues: 337 loop : -1.45 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 PHE 0.010 0.001 PHE C 151 TYR 0.026 0.001 TYR A1067 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 665) hydrogen bonds : angle 4.87366 ( 1896) covalent geometry : bond 0.00296 (15179) covalent geometry : angle 0.55172 (20569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11201.14 seconds wall clock time: 193 minutes 26.31 seconds (11606.31 seconds total)