Starting phenix.real_space_refine on Wed Jun 25 23:28:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soc_40653/06_2025/8soc_40653_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soc_40653/06_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_40653/06_2025/8soc_40653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soc_40653/06_2025/8soc_40653.map" model { file = "/net/cci-nas-00/data/ceres_data/8soc_40653/06_2025/8soc_40653_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soc_40653/06_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-5710/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: 14.32, per 1000 atoms: 0.48 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: 8.03 Conformation dependent library (CDL) restraints added in 2.5 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: 3.12 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: 12.05 Time building geometry restraints manager: 9.44 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: 2.560 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: 0.520 Extract box with map and model: 1.190 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 64.200 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.140 ------------------------------------------------------------------------------- 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 : 2.678 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: 0.7392 time to fit residues: 369.6940 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 : 2.383 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.083046 restraints weight = 119587.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.086832 restraints weight = 49450.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089119 restraints weight = 29803.609| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 2.543 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: 0.7666 (m-10) cc_final: 0.7444 (m-10) REVERT: A 628 MET cc_start: 0.7799 (mmm) cc_final: 0.7440 (mmm) REVERT: A 852 GLU cc_start: 0.8078 (tt0) cc_final: 0.7636 (tp30) REVERT: A 1050 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: B 741 TRP cc_start: 0.7430 (m100) cc_final: 0.6877 (m100) REVERT: C 5 ASP cc_start: 0.8295 (m-30) cc_final: 0.7866 (p0) REVERT: C 12 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6572 (mm-30) REVERT: C 188 MET cc_start: 0.5713 (mpp) cc_final: 0.5060 (mpp) REVERT: C 293 ASN cc_start: 0.8270 (m-40) cc_final: 0.7954 (m-40) REVERT: G 11 GLN cc_start: 0.7655 (tt0) cc_final: 0.7043 (tp40) REVERT: G 47 GLU cc_start: 0.8525 (mp0) cc_final: 0.8296 (mp0) outliers start: 40 outliers final: 29 residues processed: 225 average time/residue: 0.6871 time to fit residues: 219.5218 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 : 2.321 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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** A1022 HIS B 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.117579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.083002 restraints weight = 119329.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.086949 restraints weight = 48191.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.089299 restraints weight = 28770.109| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15179 Z= 0.141 Angle : 0.591 7.982 20569 Z= 0.303 Chirality : 0.040 0.153 2342 Planarity : 0.004 0.047 2612 Dihedral : 7.464 177.788 2038 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.20 % Allowed : 11.95 % Favored : 85.85 % 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: -1.07 (0.19), residues: 1818 helix: 0.25 (0.19), residues: 718 sheet: -0.95 (0.27), residues: 357 loop : -1.45 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 339 HIS 0.006 0.001 HIS A 909 PHE 0.012 0.001 PHE A 87 TYR 0.019 0.001 TYR A1067 ARG 0.015 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 665) hydrogen bonds : angle 5.77042 ( 1896) covalent geometry : bond 0.00312 (15179) covalent geometry : angle 0.59051 (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 207 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 2.596 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: A 521 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: A 628 MET cc_start: 0.7753 (mmm) cc_final: 0.7381 (mmm) REVERT: A 852 GLU cc_start: 0.7922 (tt0) cc_final: 0.7529 (tp30) REVERT: A 1050 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: A 1074 VAL cc_start: 0.8243 (t) cc_final: 0.8006 (p) REVERT: C 5 ASP cc_start: 0.8311 (m-30) cc_final: 0.7899 (p0) REVERT: C 186 ASP cc_start: 0.4819 (m-30) cc_final: 0.4408 (m-30) REVERT: C 188 MET cc_start: 0.5731 (mpp) cc_final: 0.5221 (mpp) REVERT: G 11 GLN cc_start: 0.7581 (tt0) cc_final: 0.6966 (tp40) REVERT: G 40 TYR cc_start: 0.8316 (t80) cc_final: 0.8032 (t80) REVERT: G 47 GLU cc_start: 0.8499 (mp0) cc_final: 0.8253 (mp0) outliers start: 36 outliers final: 28 residues processed: 199 average time/residue: 0.7012 time to fit residues: 204.4254 Evaluate side-chains 185 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 106 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** B 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.116264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.081943 restraints weight = 120028.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.085772 restraints weight = 49243.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.088057 restraints weight = 29493.285| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15179 Z= 0.192 Angle : 0.603 6.734 20569 Z= 0.311 Chirality : 0.040 0.157 2342 Planarity : 0.004 0.051 2612 Dihedral : 7.252 179.260 2032 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.44 % Allowed : 12.74 % Favored : 84.82 % 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: -1.26 (0.19), residues: 1818 helix: 0.09 (0.18), residues: 719 sheet: -1.13 (0.27), residues: 347 loop : -1.52 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.007 0.001 HIS A1023 PHE 0.014 0.002 PHE A1009 TYR 0.021 0.002 TYR A 462 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 665) hydrogen bonds : angle 5.60747 ( 1896) covalent geometry : bond 0.00422 (15179) covalent geometry : angle 0.60320 (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: 40 poor density : 157 time to evaluate : 2.313 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: 0.8359 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: A 628 MET cc_start: 0.7752 (mmm) cc_final: 0.7396 (mmm) REVERT: A 852 GLU cc_start: 0.7833 (tt0) cc_final: 0.7455 (tp30) REVERT: A 1050 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: C 5 ASP cc_start: 0.8343 (m-30) cc_final: 0.7916 (p0) REVERT: C 186 ASP cc_start: 0.4867 (m-30) cc_final: 0.4465 (m-30) REVERT: C 188 MET cc_start: 0.5902 (mpp) cc_final: 0.5337 (mpp) REVERT: G 11 GLN cc_start: 0.7473 (tt0) cc_final: 0.6932 (tp40) REVERT: G 47 GLU cc_start: 0.8486 (mp0) cc_final: 0.8191 (mp0) outliers start: 40 outliers final: 32 residues processed: 189 average time/residue: 0.6660 time to fit residues: 180.5385 Evaluate side-chains 188 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 150 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN C 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.113632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.079494 restraints weight = 122402.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.083040 restraints weight = 52759.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.085141 restraints weight = 32408.504| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 15179 Z= 0.314 Angle : 0.713 8.495 20569 Z= 0.376 Chirality : 0.043 0.169 2342 Planarity : 0.006 0.076 2612 Dihedral : 7.463 178.604 2029 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.41 % Allowed : 13.17 % Favored : 83.41 % 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: -1.94 (0.19), residues: 1818 helix: -0.50 (0.18), residues: 715 sheet: -1.37 (0.27), residues: 329 loop : -1.92 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 697 HIS 0.008 0.002 HIS A 225 PHE 0.018 0.002 PHE B 129 TYR 0.018 0.003 TYR G 40 ARG 0.007 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 665) hydrogen bonds : angle 5.89576 ( 1896) covalent geometry : bond 0.00685 (15179) covalent geometry : angle 0.71298 (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 203 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 5.905 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: A 198 MET cc_start: 0.8418 (mpt) cc_final: 0.8079 (mpt) REVERT: A 521 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: A 852 GLU cc_start: 0.7995 (tt0) cc_final: 0.7659 (tp30) REVERT: A 1050 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: C 5 ASP cc_start: 0.8245 (m-30) cc_final: 0.7804 (p0) REVERT: C 105 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7211 (t80) REVERT: C 186 ASP cc_start: 0.4975 (m-30) cc_final: 0.4625 (m-30) REVERT: C 188 MET cc_start: 0.6199 (mpp) cc_final: 0.5606 (mpp) REVERT: G 11 GLN cc_start: 0.7520 (tt0) cc_final: 0.6939 (tp40) outliers start: 56 outliers final: 45 residues processed: 190 average time/residue: 0.9875 time to fit residues: 281.8870 Evaluate side-chains 186 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 2.719 ------------------------------------------------------------------------------- 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 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 571 ASP Chi-restraints excluded: chain A residue 581 GLU 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 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 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 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 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 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: 8.9990 chunk 49 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.114863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080804 restraints weight = 120851.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.084401 restraints weight = 50766.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.086586 restraints weight = 30858.342| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15179 Z= 0.185 Angle : 0.614 9.155 20569 Z= 0.317 Chirality : 0.041 0.177 2342 Planarity : 0.005 0.054 2612 Dihedral : 7.105 174.460 2027 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.56 % Allowed : 14.57 % 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: -1.55 (0.19), residues: 1818 helix: -0.11 (0.18), residues: 726 sheet: -1.20 (0.27), residues: 327 loop : -1.77 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 697 HIS 0.005 0.001 HIS G 44 PHE 0.014 0.002 PHE A 473 TYR 0.019 0.002 TYR G 40 ARG 0.003 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 665) hydrogen bonds : angle 5.51612 ( 1896) covalent geometry : bond 0.00409 (15179) covalent geometry : angle 0.61391 (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 192 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 3.999 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: 0.8353 (mpt) cc_final: 0.7984 (mpt) REVERT: A 1050 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: C 5 ASP cc_start: 0.8268 (m-30) cc_final: 0.7820 (p0) REVERT: C 105 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.7117 (t80) REVERT: C 186 ASP cc_start: 0.4813 (m-30) cc_final: 0.4503 (m-30) REVERT: C 188 MET cc_start: 0.6158 (mpp) cc_final: 0.5569 (mpp) REVERT: C 293 ASN cc_start: 0.8495 (t0) cc_final: 0.8248 (t0) REVERT: G 11 GLN cc_start: 0.7508 (tt0) cc_final: 0.6915 (tp40) REVERT: G 40 TYR cc_start: 0.7852 (t80) cc_final: 0.7562 (t80) REVERT: G 44 HIS cc_start: 0.7927 (m90) cc_final: 0.7391 (m90) outliers start: 42 outliers final: 38 residues processed: 182 average time/residue: 1.0761 time to fit residues: 295.3981 Evaluate side-chains 181 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 5.770 ------------------------------------------------------------------------------- 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 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 771 LEU 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 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 550 PHE 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 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 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: 5.9990 chunk 49 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 149 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 173 optimal weight: 20.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.114201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.080087 restraints weight = 122011.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.083648 restraints weight = 51767.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.085815 restraints weight = 31722.135| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15179 Z= 0.210 Angle : 0.623 7.744 20569 Z= 0.322 Chirality : 0.041 0.257 2342 Planarity : 0.005 0.054 2612 Dihedral : 7.026 170.846 2027 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.99 % Allowed : 14.39 % Favored : 82.62 % 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: -1.56 (0.19), residues: 1818 helix: -0.05 (0.18), residues: 730 sheet: -1.18 (0.27), residues: 327 loop : -1.88 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 697 HIS 0.006 0.001 HIS A 199 PHE 0.013 0.002 PHE A 473 TYR 0.016 0.002 TYR G 40 ARG 0.004 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 665) hydrogen bonds : angle 5.46749 ( 1896) covalent geometry : bond 0.00463 (15179) covalent geometry : angle 0.62267 (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 196 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 2.600 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: A 198 MET cc_start: 0.8399 (mpt) cc_final: 0.7985 (mpt) REVERT: A 529 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7129 (tt) REVERT: A 1050 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: C 5 ASP cc_start: 0.8183 (m-30) cc_final: 0.7773 (p0) REVERT: C 105 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.7199 (t80) REVERT: C 186 ASP cc_start: 0.4896 (m-30) cc_final: 0.4644 (m-30) REVERT: C 188 MET cc_start: 0.6277 (mpp) cc_final: 0.5829 (mpp) REVERT: C 293 ASN cc_start: 0.8477 (t0) cc_final: 0.8211 (t0) REVERT: G 11 GLN cc_start: 0.7515 (tt0) cc_final: 0.6880 (tp40) outliers start: 49 outliers final: 41 residues processed: 184 average time/residue: 0.6595 time to fit residues: 176.8160 Evaluate side-chains 185 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 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 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 655 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 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 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 296 VAL 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: 1.9990 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.115231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.081354 restraints weight = 121444.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.085085 restraints weight = 50018.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.087320 restraints weight = 30181.142| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15179 Z= 0.149 Angle : 0.579 8.544 20569 Z= 0.295 Chirality : 0.040 0.186 2342 Planarity : 0.004 0.045 2612 Dihedral : 6.804 167.302 2027 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 2.87 % Allowed : 14.63 % Favored : 82.50 % 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: -1.30 (0.19), residues: 1818 helix: 0.21 (0.19), residues: 734 sheet: -1.05 (0.28), residues: 322 loop : -1.81 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 PHE 0.014 0.001 PHE A 473 TYR 0.016 0.001 TYR G 40 ARG 0.003 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 665) hydrogen bonds : angle 5.21326 ( 1896) covalent geometry : bond 0.00330 (15179) covalent geometry : angle 0.57865 (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 195 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 2.692 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: A 198 MET cc_start: 0.8365 (mpt) cc_final: 0.7911 (mpt) REVERT: A 592 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7416 (tp) REVERT: A 1050 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: C 5 ASP cc_start: 0.8113 (m-30) cc_final: 0.7719 (p0) REVERT: C 105 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.7124 (t80) REVERT: C 293 ASN cc_start: 0.8396 (t0) cc_final: 0.8142 (t0) REVERT: G 11 GLN cc_start: 0.7521 (tt0) cc_final: 0.6876 (tp40) REVERT: G 44 HIS cc_start: 0.7699 (m90) cc_final: 0.7498 (m90) outliers start: 47 outliers final: 40 residues processed: 184 average time/residue: 0.7048 time to fit residues: 190.2961 Evaluate side-chains 190 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 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 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 571 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 655 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 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 607 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 177 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 112 optimal weight: 0.0770 chunk 148 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.115260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.081274 restraints weight = 121023.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.085076 restraints weight = 50405.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.087331 restraints weight = 30369.001| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4725 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= 0.149 Angle : 0.572 8.479 20569 Z= 0.291 Chirality : 0.040 0.199 2342 Planarity : 0.004 0.042 2612 Dihedral : 6.566 162.883 2024 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.68 % Allowed : 14.94 % Favored : 82.38 % 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: -1.11 (0.19), residues: 1818 helix: 0.42 (0.19), residues: 728 sheet: -0.99 (0.28), residues: 329 loop : -1.73 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 697 HIS 0.005 0.001 HIS A 199 PHE 0.020 0.001 PHE B 550 TYR 0.013 0.001 TYR A1067 ARG 0.003 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 665) hydrogen bonds : angle 5.10465 ( 1896) covalent geometry : bond 0.00331 (15179) covalent geometry : angle 0.57167 (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 191 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 2.640 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: A 198 MET cc_start: 0.8402 (mpt) cc_final: 0.7924 (mpt) REVERT: A 207 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8030 (tt) REVERT: A 592 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7532 (tp) REVERT: A 1050 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: C 105 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.7137 (t80) REVERT: C 293 ASN cc_start: 0.8333 (t0) cc_final: 0.8067 (t0) REVERT: G 11 GLN cc_start: 0.7521 (tt0) cc_final: 0.6874 (tp40) outliers start: 44 outliers final: 38 residues processed: 181 average time/residue: 0.6644 time to fit residues: 174.9137 Evaluate side-chains 184 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 207 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 592 LEU Chi-restraints excluded: chain A residue 655 ASP 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 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 607 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 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 296 VAL 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: 0.2980 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.115299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.081357 restraints weight = 120972.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.085155 restraints weight = 50246.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.087413 restraints weight = 30294.535| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15179 Z= 0.155 Angle : 0.583 8.496 20569 Z= 0.296 Chirality : 0.040 0.184 2342 Planarity : 0.004 0.039 2612 Dihedral : 6.475 160.217 2023 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.33 % Rotamer: Outliers : 2.74 % Allowed : 15.18 % Favored : 82.07 % 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: -1.10 (0.19), residues: 1818 helix: 0.47 (0.19), residues: 728 sheet: -1.10 (0.28), residues: 336 loop : -1.70 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 697 HIS 0.008 0.001 HIS A1023 PHE 0.012 0.001 PHE A 473 TYR 0.013 0.002 TYR A 210 ARG 0.003 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 665) hydrogen bonds : angle 5.06724 ( 1896) covalent geometry : bond 0.00346 (15179) covalent geometry : angle 0.58289 (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 188 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 2.385 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: A 198 MET cc_start: 0.8375 (mpt) cc_final: 0.7852 (mpt) REVERT: A 592 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7525 (tp) REVERT: A 1050 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: C 105 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.7167 (t80) REVERT: C 293 ASN cc_start: 0.8316 (t0) cc_final: 0.8060 (t0) REVERT: G 11 GLN cc_start: 0.7524 (tt0) cc_final: 0.6873 (tp40) REVERT: G 44 HIS cc_start: 0.7812 (m90) cc_final: 0.7494 (m90) outliers start: 45 outliers final: 41 residues processed: 177 average time/residue: 0.6861 time to fit residues: 176.7600 Evaluate side-chains 186 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 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 571 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 655 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 15 HIS 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 607 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 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 296 VAL 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: 7.9990 chunk 25 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.115751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.081845 restraints weight = 120125.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.085695 restraints weight = 49623.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.087972 restraints weight = 29767.290| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15179 Z= 0.134 Angle : 0.562 8.729 20569 Z= 0.283 Chirality : 0.040 0.183 2342 Planarity : 0.004 0.038 2612 Dihedral : 6.264 153.423 2023 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.44 % Allowed : 15.55 % Favored : 82.01 % 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: -0.89 (0.20), residues: 1818 helix: 0.69 (0.19), residues: 728 sheet: -0.94 (0.27), residues: 331 loop : -1.67 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 697 HIS 0.007 0.001 HIS A1023 PHE 0.013 0.001 PHE B 550 TYR 0.015 0.001 TYR A 210 ARG 0.002 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 665) hydrogen bonds : angle 4.91745 ( 1896) covalent geometry : bond 0.00300 (15179) covalent geometry : angle 0.56155 (20569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12819.49 seconds wall clock time: 226 minutes 41.77 seconds (13601.77 seconds total)