Starting phenix.real_space_refine on Mon Oct 13 03:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soc_40653/10_2025/8soc_40653_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soc_40653/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8soc_40653/10_2025/8soc_40653_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soc_40653/10_2025/8soc_40653_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8soc_40653/10_2025/8soc_40653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soc_40653/10_2025/8soc_40653.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.80, per 1000 atoms: 0.19 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: 2.80 Conformation dependent library (CDL) restraints added in 995.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.07 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: 8.25 Time building geometry restraints manager: 3.85 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 30.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- 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 : 5.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.048 0.001 ARG A 712 TYR 0.024 0.002 TYR B 658 PHE 0.020 0.002 PHE B 129 TRP 0.019 0.002 TRP A 413 HIS 0.006 0.001 HIS B 607 Details of bonding type rmsd covalent geometry : bond 0.00378 (15179) covalent geometry : angle 0.58663 (20569) hydrogen bonds : bond 0.28570 ( 665) hydrogen bonds : angle 9.12432 ( 1896) *********************** 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 : 0.725 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: 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: 0.7762 (m-80) REVERT: C 155 ASN cc_start: 0.7549 (t0) cc_final: 0.7110 (t0) REVERT: C 186 ASP cc_start: 0.6397 (m-30) cc_final: 0.5790 (m-30) REVERT: G 11 GLN cc_start: 0.7513 (tt0) cc_final: 0.7256 (tp40) outliers start: 35 outliers final: 18 residues processed: 359 average time/residue: 0.3226 time to fit residues: 161.4253 Evaluate side-chains 205 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 172 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 258 GLN C 230 ASN C 295 ASN G 4 ASN G 18 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.118411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.083913 restraints weight = 119280.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.087871 restraints weight = 48150.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.090241 restraints weight = 28723.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.091577 restraints weight = 21430.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.092251 restraints weight = 18296.021| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15179 Z= 0.164 Angle : 0.637 7.262 20569 Z= 0.333 Chirality : 0.041 0.155 2342 Planarity : 0.005 0.075 2612 Dihedral : 7.898 171.578 2053 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.20 % Allowed : 10.85 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.19), residues: 1818 helix: 0.05 (0.18), residues: 720 sheet: -0.99 (0.28), residues: 333 loop : -1.46 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 366 TYR 0.021 0.002 TYR A1067 PHE 0.020 0.002 PHE A1009 TRP 0.009 0.001 TRP A 697 HIS 0.007 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00339 (15179) covalent geometry : angle 0.63743 (20569) hydrogen bonds : bond 0.06742 ( 665) hydrogen bonds : angle 6.26109 ( 1896) *********************** 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 236 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.594 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: A 249 PHE cc_start: 0.7584 (m-10) cc_final: 0.7378 (m-10) REVERT: A 852 GLU cc_start: 0.8035 (tt0) cc_final: 0.7560 (tp30) REVERT: A 1050 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: B 741 TRP cc_start: 0.7357 (m100) cc_final: 0.6833 (m100) REVERT: C 5 ASP cc_start: 0.8295 (m-30) cc_final: 0.7861 (p0) REVERT: C 12 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6513 (mm-30) REVERT: C 188 MET cc_start: 0.5540 (mpp) cc_final: 0.4884 (mpp) REVERT: C 293 ASN cc_start: 0.8189 (m-40) cc_final: 0.7832 (m-40) REVERT: G 11 GLN cc_start: 0.7678 (tt0) cc_final: 0.7045 (tp40) REVERT: G 47 GLU cc_start: 0.8382 (mp0) cc_final: 0.8174 (mp0) outliers start: 36 outliers final: 22 residues processed: 229 average time/residue: 0.2908 time to fit residues: 94.2822 Evaluate side-chains 189 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 347 GLU Chi-restraints excluded: chain A residue 626 LEU 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 1034 MET Chi-restraints excluded: chain A residue 1050 TYR 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 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 50 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 834 HIS A1022 HIS B 45 GLN B 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.116210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.081699 restraints weight = 120601.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.085471 restraints weight = 50338.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.087682 restraints weight = 30548.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.088905 restraints weight = 23168.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.089574 restraints weight = 19914.897| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15179 Z= 0.216 Angle : 0.640 8.168 20569 Z= 0.333 Chirality : 0.041 0.151 2342 Planarity : 0.005 0.057 2612 Dihedral : 7.349 177.556 2033 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.38 % Allowed : 12.13 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.19), residues: 1818 helix: 0.05 (0.18), residues: 712 sheet: -1.13 (0.27), residues: 354 loop : -1.57 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 13 TYR 0.020 0.002 TYR A1067 PHE 0.013 0.002 PHE A1009 TRP 0.013 0.002 TRP A 697 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00475 (15179) covalent geometry : angle 0.63988 (20569) hydrogen bonds : bond 0.05645 ( 665) hydrogen bonds : angle 5.95675 ( 1896) *********************** 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: 39 poor density : 168 time to evaluate : 0.817 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: 0.8378 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: A 628 MET cc_start: 0.7791 (mmm) cc_final: 0.7404 (mmm) REVERT: A 852 GLU cc_start: 0.7921 (tt0) cc_final: 0.7559 (tp30) REVERT: A 1050 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: C 5 ASP cc_start: 0.8240 (m-30) cc_final: 0.7812 (p0) REVERT: C 99 TRP cc_start: 0.5965 (t-100) cc_final: 0.5665 (t-100) REVERT: C 186 ASP cc_start: 0.4871 (m-30) cc_final: 0.4470 (m-30) REVERT: C 188 MET cc_start: 0.5848 (mpp) cc_final: 0.5340 (mpp) REVERT: C 222 PHE cc_start: 0.4617 (m-80) cc_final: 0.4400 (m-80) REVERT: C 325 MET cc_start: 0.6090 (tpp) cc_final: 0.5867 (tpp) REVERT: G 11 GLN cc_start: 0.7604 (tt0) cc_final: 0.6969 (tp40) REVERT: G 24 ASN cc_start: 0.8313 (t0) cc_final: 0.8048 (p0) REVERT: G 40 TYR cc_start: 0.8323 (t80) cc_final: 0.7910 (m-10) REVERT: G 47 GLU cc_start: 0.8491 (mp0) cc_final: 0.8249 (mp0) outliers start: 39 outliers final: 31 residues processed: 200 average time/residue: 0.2856 time to fit residues: 81.8985 Evaluate side-chains 190 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 571 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 1025 ASN 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 241 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 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 0 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.113412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.079138 restraints weight = 122339.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.082635 restraints weight = 53026.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.084736 restraints weight = 32795.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.085829 restraints weight = 25041.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.086531 restraints weight = 21736.782| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 15179 Z= 0.338 Angle : 0.744 7.299 20569 Z= 0.396 Chirality : 0.044 0.281 2342 Planarity : 0.006 0.083 2612 Dihedral : 7.697 179.956 2030 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.20 % Favored : 91.75 % Rotamer: Outliers : 3.23 % Allowed : 13.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.18), residues: 1818 helix: -0.76 (0.18), residues: 715 sheet: -1.45 (0.27), residues: 329 loop : -2.00 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 184 TYR 0.032 0.003 TYR G 40 PHE 0.022 0.003 PHE B 129 TRP 0.020 0.002 TRP A 697 HIS 0.008 0.002 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00739 (15179) covalent geometry : angle 0.74381 (20569) hydrogen bonds : bond 0.05804 ( 665) hydrogen bonds : angle 6.15848 ( 1896) *********************** 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 204 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.835 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: A 198 MET cc_start: 0.8410 (mpt) cc_final: 0.8150 (mpt) REVERT: A 521 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: A 628 MET cc_start: 0.7782 (mmm) cc_final: 0.7170 (mmm) REVERT: A 852 GLU cc_start: 0.7941 (tt0) cc_final: 0.7585 (tp30) REVERT: A 1050 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: C 5 ASP cc_start: 0.8312 (m-30) cc_final: 0.7816 (p0) REVERT: C 105 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7209 (t80) REVERT: C 186 ASP cc_start: 0.4998 (m-30) cc_final: 0.4648 (m-30) REVERT: C 188 MET cc_start: 0.6102 (mpp) cc_final: 0.5544 (mpp) REVERT: C 222 PHE cc_start: 0.4857 (m-80) cc_final: 0.4646 (m-80) REVERT: C 325 MET cc_start: 0.6355 (tpp) cc_final: 0.6092 (tpp) REVERT: G 11 GLN cc_start: 0.7404 (tt0) cc_final: 0.6933 (tp40) REVERT: G 24 ASN cc_start: 0.8184 (t0) cc_final: 0.7903 (p0) outliers start: 53 outliers final: 43 residues processed: 193 average time/residue: 0.2910 time to fit residues: 80.4833 Evaluate side-chains 184 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 211 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 339 LEU 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 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 775 GLN 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 542 ASN 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 105 TYR Chi-restraints excluded: chain C residue 108 SER 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 18 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.080721 restraints weight = 121432.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.084367 restraints weight = 51163.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.086561 restraints weight = 31248.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.087740 restraints weight = 23601.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.088471 restraints weight = 20340.742| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4257 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= 0.177 Angle : 0.612 7.451 20569 Z= 0.316 Chirality : 0.041 0.193 2342 Planarity : 0.005 0.055 2612 Dihedral : 7.293 176.053 2028 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.99 % Allowed : 14.57 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.19), residues: 1818 helix: -0.21 (0.18), residues: 718 sheet: -1.31 (0.27), residues: 334 loop : -1.80 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.013 0.002 TYR A1067 PHE 0.015 0.002 PHE A 473 TRP 0.014 0.001 TRP A 697 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00392 (15179) covalent geometry : angle 0.61189 (20569) hydrogen bonds : bond 0.04741 ( 665) hydrogen bonds : angle 5.62392 ( 1896) *********************** 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 196 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.796 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: A 198 MET cc_start: 0.8364 (mpt) cc_final: 0.8036 (mpt) REVERT: A 628 MET cc_start: 0.7779 (mmm) cc_final: 0.7128 (mmm) REVERT: A 852 GLU cc_start: 0.7893 (tt0) cc_final: 0.7529 (tp30) REVERT: A 1050 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: C 5 ASP cc_start: 0.8186 (m-30) cc_final: 0.7728 (p0) REVERT: C 105 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.7022 (t80) REVERT: C 186 ASP cc_start: 0.4796 (m-30) cc_final: 0.4501 (m-30) REVERT: C 188 MET cc_start: 0.6077 (mpp) cc_final: 0.5524 (mpp) REVERT: C 293 ASN cc_start: 0.8254 (t0) cc_final: 0.7992 (t0) REVERT: C 325 MET cc_start: 0.6336 (tpp) cc_final: 0.6009 (tpp) REVERT: G 11 GLN cc_start: 0.7442 (tt0) cc_final: 0.6915 (tp40) REVERT: G 24 ASN cc_start: 0.8213 (t0) cc_final: 0.7921 (p0) REVERT: G 40 TYR cc_start: 0.8494 (t80) cc_final: 0.8072 (t80) outliers start: 49 outliers final: 42 residues processed: 184 average time/residue: 0.3102 time to fit residues: 82.5490 Evaluate side-chains 187 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 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 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 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 110 ASN Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 33 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 HIS ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.113280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.079055 restraints weight = 122834.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.082602 restraints weight = 51914.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.084737 restraints weight = 31782.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.085947 restraints weight = 24083.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.086550 restraints weight = 20738.441| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15179 Z= 0.281 Angle : 0.675 6.818 20569 Z= 0.355 Chirality : 0.042 0.203 2342 Planarity : 0.005 0.067 2612 Dihedral : 7.177 174.467 2022 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.35 % Allowed : 14.39 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.19), residues: 1818 helix: -0.44 (0.18), residues: 715 sheet: -1.45 (0.27), residues: 327 loop : -1.96 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 184 TYR 0.015 0.002 TYR B 141 PHE 0.014 0.002 PHE A 473 TRP 0.019 0.002 TRP A 697 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00617 (15179) covalent geometry : angle 0.67545 (20569) hydrogen bonds : bond 0.05082 ( 665) hydrogen bonds : angle 5.82512 ( 1896) *********************** 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 202 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 0.866 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 529 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7097 (tt) REVERT: A 655 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8269 (t0) REVERT: A 1050 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: C 5 ASP cc_start: 0.8210 (m-30) cc_final: 0.7764 (p0) REVERT: C 105 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7260 (t80) REVERT: C 186 ASP cc_start: 0.4814 (m-30) cc_final: 0.4551 (m-30) REVERT: C 188 MET cc_start: 0.6140 (mpp) cc_final: 0.5618 (mpp) REVERT: C 293 ASN cc_start: 0.8377 (t0) cc_final: 0.8135 (t0) REVERT: C 325 MET cc_start: 0.6443 (tpp) cc_final: 0.6115 (tpp) REVERT: G 11 GLN cc_start: 0.7444 (tt0) cc_final: 0.6902 (tp40) REVERT: G 40 TYR cc_start: 0.8397 (t80) cc_final: 0.7907 (t80) outliers start: 55 outliers final: 46 residues processed: 189 average time/residue: 0.3174 time to fit residues: 87.0446 Evaluate side-chains 193 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 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 717 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 884 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 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 218 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 656 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 156 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 171 optimal weight: 0.0570 chunk 124 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.115558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.081393 restraints weight = 120231.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.085085 restraints weight = 49894.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.087317 restraints weight = 30265.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.088550 restraints weight = 22830.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089286 restraints weight = 19654.558| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15179 Z= 0.128 Angle : 0.572 7.140 20569 Z= 0.292 Chirality : 0.040 0.151 2342 Planarity : 0.004 0.044 2612 Dihedral : 6.768 169.786 2022 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.56 % Allowed : 14.88 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.19), residues: 1818 helix: 0.20 (0.19), residues: 726 sheet: -1.18 (0.28), residues: 325 loop : -1.73 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.013 0.001 TYR A1067 PHE 0.016 0.001 PHE A 473 TRP 0.014 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00287 (15179) covalent geometry : angle 0.57248 (20569) hydrogen bonds : bond 0.04142 ( 665) hydrogen bonds : angle 5.27483 ( 1896) *********************** 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 195 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8340 (mpt) cc_final: 0.7902 (mpt) REVERT: A 521 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: A 1050 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: C 5 ASP cc_start: 0.8192 (m-30) cc_final: 0.7783 (p0) REVERT: C 293 ASN cc_start: 0.8325 (t0) cc_final: 0.8067 (t0) REVERT: C 325 MET cc_start: 0.6316 (tpp) cc_final: 0.5966 (tpp) REVERT: G 11 GLN cc_start: 0.7518 (tt0) cc_final: 0.6895 (tp40) REVERT: G 40 TYR cc_start: 0.8325 (t80) cc_final: 0.7882 (t80) outliers start: 42 outliers final: 34 residues processed: 185 average time/residue: 0.3377 time to fit residues: 90.2369 Evaluate side-chains 180 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1009 PHE Chi-restraints excluded: chain A residue 1025 ASN Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 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 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 204 CYS Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.115899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.081755 restraints weight = 119692.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.085625 restraints weight = 49057.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.087943 restraints weight = 29288.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.089202 restraints weight = 21852.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.089959 restraints weight = 18709.003| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15179 Z= 0.120 Angle : 0.558 7.819 20569 Z= 0.282 Chirality : 0.040 0.226 2342 Planarity : 0.004 0.042 2612 Dihedral : 6.499 164.594 2022 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.38 % Allowed : 15.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.20), residues: 1818 helix: 0.56 (0.19), residues: 723 sheet: -1.04 (0.27), residues: 335 loop : -1.55 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 687 TYR 0.013 0.001 TYR A1067 PHE 0.012 0.001 PHE A 473 TRP 0.013 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00270 (15179) covalent geometry : angle 0.55792 (20569) hydrogen bonds : bond 0.03870 ( 665) hydrogen bonds : angle 5.04819 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.857 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: 0.8369 (mpt) cc_final: 0.7835 (mpt) REVERT: A 207 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7890 (tt) REVERT: A 1039 MET cc_start: 0.7191 (ppp) cc_final: 0.6957 (ppp) REVERT: A 1050 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: C 5 ASP cc_start: 0.8073 (m-30) cc_final: 0.7697 (p0) REVERT: C 293 ASN cc_start: 0.8213 (t0) cc_final: 0.7948 (t0) REVERT: C 325 MET cc_start: 0.6442 (tpp) cc_final: 0.6097 (tpp) REVERT: G 11 GLN cc_start: 0.7548 (tt0) cc_final: 0.6893 (tp40) REVERT: G 24 ASN cc_start: 0.8383 (t0) cc_final: 0.8066 (p0) outliers start: 39 outliers final: 35 residues processed: 180 average time/residue: 0.3220 time to fit residues: 83.8294 Evaluate side-chains 181 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 535 THR Chi-restraints excluded: chain A residue 571 ASP 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 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 204 CYS Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.113830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.079945 restraints weight = 122065.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.083451 restraints weight = 51841.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.085662 restraints weight = 31900.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.086897 restraints weight = 24103.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.087501 restraints weight = 20693.748| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15179 Z= 0.235 Angle : 0.634 8.400 20569 Z= 0.329 Chirality : 0.041 0.195 2342 Planarity : 0.005 0.053 2612 Dihedral : 6.690 163.414 2022 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 2.68 % Allowed : 15.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.19), residues: 1818 helix: 0.19 (0.19), residues: 728 sheet: -1.30 (0.27), residues: 333 loop : -1.77 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.031 0.002 TYR G 40 PHE 0.011 0.002 PHE C 222 TRP 0.016 0.002 TRP A 697 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00517 (15179) covalent geometry : angle 0.63438 (20569) hydrogen bonds : bond 0.04448 ( 665) hydrogen bonds : angle 5.34828 ( 1896) *********************** 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 186 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 207 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8080 (tt) REVERT: A 556 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: A 592 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7442 (tp) REVERT: A 1050 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: C 105 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.7227 (t80) REVERT: C 293 ASN cc_start: 0.8317 (t0) cc_final: 0.8101 (t0) REVERT: C 325 MET cc_start: 0.6463 (tpp) cc_final: 0.6170 (tpp) REVERT: G 11 GLN cc_start: 0.7534 (tt0) cc_final: 0.6859 (tp40) outliers start: 44 outliers final: 38 residues processed: 175 average time/residue: 0.3573 time to fit residues: 88.6950 Evaluate side-chains 180 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 272 LEU 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 535 THR Chi-restraints excluded: chain A residue 556 GLU 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 852 GLU 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 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 204 CYS Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 126 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.115733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.081972 restraints weight = 119467.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.085819 restraints weight = 49247.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.088116 restraints weight = 29538.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.089400 restraints weight = 22131.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.090112 restraints weight = 18956.106| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15179 Z= 0.119 Angle : 0.570 9.122 20569 Z= 0.287 Chirality : 0.040 0.192 2342 Planarity : 0.004 0.098 2612 Dihedral : 6.374 158.397 2021 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.13 % Allowed : 16.04 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1818 helix: 0.63 (0.19), residues: 722 sheet: -1.01 (0.27), residues: 335 loop : -1.57 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 268 TYR 0.022 0.001 TYR G 40 PHE 0.015 0.001 PHE A 473 TRP 0.014 0.001 TRP A 697 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00270 (15179) covalent geometry : angle 0.57048 (20569) hydrogen bonds : bond 0.03802 ( 665) hydrogen bonds : angle 4.98108 ( 1896) ********************** 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 178 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8345 (mpt) cc_final: 0.7820 (mpt) REVERT: A 556 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: A 1050 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: C 293 ASN cc_start: 0.8275 (t0) cc_final: 0.8033 (t0) REVERT: C 325 MET cc_start: 0.6454 (tpp) cc_final: 0.6156 (tpp) REVERT: G 11 GLN cc_start: 0.7549 (tt0) cc_final: 0.6867 (tp40) REVERT: G 24 ASN cc_start: 0.8338 (t0) cc_final: 0.8046 (p0) outliers start: 35 outliers final: 32 residues processed: 169 average time/residue: 0.3296 time to fit residues: 79.7623 Evaluate side-chains 175 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 272 LEU 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 556 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 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 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 204 CYS Chi-restraints excluded: chain C residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.114906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.080954 restraints weight = 121770.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.084668 restraints weight = 50881.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.086913 restraints weight = 30852.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.088097 restraints weight = 23197.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.088860 restraints weight = 20034.532| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15179 Z= 0.158 Angle : 0.580 8.072 20569 Z= 0.296 Chirality : 0.039 0.185 2342 Planarity : 0.004 0.079 2612 Dihedral : 6.313 154.216 2021 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.22 % Favored : 93.73 % Rotamer: Outliers : 2.26 % Allowed : 16.04 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.20), residues: 1818 helix: 0.63 (0.19), residues: 720 sheet: -1.13 (0.27), residues: 342 loop : -1.58 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 268 TYR 0.028 0.002 TYR G 40 PHE 0.011 0.001 PHE C 151 TRP 0.012 0.001 TRP A 697 HIS 0.006 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00357 (15179) covalent geometry : angle 0.57981 (20569) hydrogen bonds : bond 0.03927 ( 665) hydrogen bonds : angle 5.02870 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6396.77 seconds wall clock time: 109 minutes 27.10 seconds (6567.10 seconds total)