Starting phenix.real_space_refine on Fri Sep 19 12:58:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kf3_9960/09_2025/6kf3_9960.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kf3_9960/09_2025/6kf3_9960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kf3_9960/09_2025/6kf3_9960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kf3_9960/09_2025/6kf3_9960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kf3_9960/09_2025/6kf3_9960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kf3_9960/09_2025/6kf3_9960.map" } resolution = 3.9 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= 0.001 sd= 0.024 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 Zn 5 6.06 5 Mg 1 5.21 5 S 116 5.16 5 C 16735 2.51 5 N 4621 2.21 5 O 4897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26375 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7181 Classifications: {'peptide': 900} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 50, 'TRANS': 845} Chain: "B" Number of atoms: 8892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8892 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 3, 'PTRANS': 58, 'TRANS': 1052} Chain: "C" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3037 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 370} Chain: "D" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2058 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 241} Chain: "E" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1465 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "F" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1020 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 113} Chain: "H" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 627 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "K" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Chain: "L" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 775 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "N" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 529 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 426 SG CYS A 60 72.360 54.169 43.545 1.00 80.67 S ATOM 752 SG CYS A 103 85.940 15.620 70.103 1.00 86.02 S ATOM 1114 SG CYS A 147 87.237 13.399 74.472 1.00 85.54 S ATOM 15757 SG CYS B1083 64.438 40.792 53.175 1.00 81.07 S ATOM 15777 SG CYS B1086 63.164 36.883 53.759 1.00 78.05 S ATOM 25542 SG CYS N 7 87.561 119.142 80.286 1.00 11.70 S ATOM 25566 SG CYS N 10 85.747 121.623 82.462 1.00 11.70 S ATOM 26066 SG CYS P 11 105.693 106.155 42.626 1.00 31.51 S ATOM 26189 SG CYS P 27 108.450 104.997 39.939 1.00 48.40 S ATOM 26214 SG CYS P 30 110.186 106.736 43.197 1.00 54.91 S Time building chain proxies: 5.32, per 1000 atoms: 0.20 Number of scatterers: 26375 At special positions: 0 Unit cell: (159.6, 156.8, 145.6, 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) Zn 5 29.99 S 116 16.00 Mg 1 11.99 O 4897 8.00 N 4621 7.00 C 16735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.85 Conformation dependent library (CDL) restraints added in 829.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 73 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 60 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 149 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 147 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 103 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1086 " pdb=" ZN N1401 " pdb="ZN ZN N1401 " - pdb=" SG CYS N 10 " pdb="ZN ZN N1401 " - pdb=" SG CYS N 7 " pdb=" ZN P1501 " pdb="ZN ZN P1501 " - pdb=" SG CYS P 11 " pdb="ZN ZN P1501 " - pdb=" SG CYS P 30 " pdb="ZN ZN P1501 " - pdb=" SG CYS P 27 " 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6112 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 41 sheets defined 34.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.558A pdb=" N ARG A 22 " --> pdb=" O PRO A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.783A pdb=" N ARG A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.826A pdb=" N GLN A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 143 removed outlier: 3.742A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.561A pdb=" N ASP A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 193 No H-bonds generated for 'chain 'A' and resid 192 through 193' Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 239 through 261 removed outlier: 3.611A pdb=" N LYS A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 removed outlier: 3.574A pdb=" N ASP A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.652A pdb=" N LYS A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.712A pdb=" N MET A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.955A pdb=" N GLN A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 485 removed outlier: 3.880A pdb=" N ALA A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.808A pdb=" N ILE A 491 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.845A pdb=" N SER A 509 " --> pdb=" O GLN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.684A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 533 removed outlier: 3.790A pdb=" N MET A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.623A pdb=" N PHE A 559 " --> pdb=" O GLY A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 592 removed outlier: 3.873A pdb=" N CYS A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.552A pdb=" N VAL A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 639 " --> pdb=" O ASP A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 639' Processing helix chain 'A' and resid 645 through 663 removed outlier: 3.766A pdb=" N LEU A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 652 " --> pdb=" O GLN A 648 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 660 " --> pdb=" O LEU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.975A pdb=" N ASP A 672 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 673 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 703 removed outlier: 3.760A pdb=" N ILE A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 741 removed outlier: 3.651A pdb=" N GLU A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 724 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 736 " --> pdb=" O ASN A 732 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.720A pdb=" N THR A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 850 removed outlier: 3.669A pdb=" N MET A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 823 " --> pdb=" O PHE A 819 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 826 " --> pdb=" O MET A 822 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 828 " --> pdb=" O GLY A 824 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 844 " --> pdb=" O TYR A 840 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 904 removed outlier: 3.580A pdb=" N VAL A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 removed outlier: 4.104A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.554A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.745A pdb=" N VAL B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.821A pdb=" N ARG B 93 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 94 " --> pdb=" O ASP B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 94' Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.560A pdb=" N ILE B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 4.239A pdb=" N GLY B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 248 Processing helix chain 'B' and resid 250 through 266 removed outlier: 4.375A pdb=" N VAL B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.011A pdb=" N GLY B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 302 removed outlier: 3.591A pdb=" N LEU B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 333 removed outlier: 4.060A pdb=" N TYR B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 4.129A pdb=" N LYS B 346 " --> pdb=" O TYR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 376 removed outlier: 3.625A pdb=" N LEU B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 397 removed outlier: 4.518A pdb=" N ILE B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG B 395 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 4.211A pdb=" N SER B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 459 through 463 removed outlier: 3.676A pdb=" N TRP B 463 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 removed outlier: 4.336A pdb=" N VAL B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 547 removed outlier: 3.531A pdb=" N LEU B 538 " --> pdb=" O ASP B 534 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 601 Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.726A pdb=" N ILE B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 664 through 672 removed outlier: 3.662A pdb=" N ASN B 668 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 3.953A pdb=" N PHE B 686 " --> pdb=" O TRP B 683 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG B 687 " --> pdb=" O ALA B 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 683 through 687' Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.766A pdb=" N ARG B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 834 removed outlier: 3.951A pdb=" N LEU B 833 " --> pdb=" O GLY B 829 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 834 " --> pdb=" O SER B 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 829 through 834' Processing helix chain 'B' and resid 918 through 923 removed outlier: 3.609A pdb=" N ARG B 922 " --> pdb=" O GLY B 918 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 923 " --> pdb=" O ILE B 919 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 918 through 923' Processing helix chain 'B' and resid 924 through 940 removed outlier: 4.135A pdb=" N LEU B 928 " --> pdb=" O THR B 924 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 935 " --> pdb=" O ALA B 931 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 939 " --> pdb=" O LYS B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 961 removed outlier: 4.095A pdb=" N LEU B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 958 " --> pdb=" O GLU B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1004 Processing helix chain 'B' and resid 1034 through 1042 removed outlier: 3.836A pdb=" N ASP B1038 " --> pdb=" O GLU B1034 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B1040 " --> pdb=" O GLU B1036 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B1041 " --> pdb=" O ARG B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1054 removed outlier: 3.549A pdb=" N ILE B1050 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1111 removed outlier: 3.991A pdb=" N MET B1111 " --> pdb=" O GLU B1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.503A pdb=" N MET C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.701A pdb=" N LEU C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 56 removed outlier: 3.745A pdb=" N GLN C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.767A pdb=" N ALA C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.855A pdb=" N ILE C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 140 removed outlier: 3.584A pdb=" N LEU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 removed outlier: 4.086A pdb=" N VAL C 179 " --> pdb=" O MET C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 4.270A pdb=" N ILE C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.725A pdb=" N ALA C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 274 " --> pdb=" O TRP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.630A pdb=" N ASN C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 removed outlier: 3.939A pdb=" N ILE C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 310 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 373 through 378 removed outlier: 3.843A pdb=" N GLY C 376 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 377 " --> pdb=" O GLY C 374 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 378 " --> pdb=" O THR C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 373 through 378' Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.747A pdb=" N ASN D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 28 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 removed outlier: 3.671A pdb=" N ALA D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 168 through 178 removed outlier: 3.512A pdb=" N LYS D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 removed outlier: 3.614A pdb=" N GLU D 204 " --> pdb=" O ARG D 201 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 205 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 258 removed outlier: 4.046A pdb=" N PHE D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 35 removed outlier: 3.695A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 33 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU E 35 " --> pdb=" O ARG E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 179 removed outlier: 3.628A pdb=" N LYS E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 26 removed outlier: 4.436A pdb=" N GLU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 removed outlier: 3.549A pdb=" N ALA F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.651A pdb=" N ARG F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 85 removed outlier: 3.568A pdb=" N LYS F 80 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 96 removed outlier: 3.877A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 99 No H-bonds generated for 'chain 'F' and resid 97 through 99' Processing helix chain 'F' and resid 104 through 115 removed outlier: 3.596A pdb=" N ILE F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 34 removed outlier: 3.596A pdb=" N GLU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 20 removed outlier: 3.589A pdb=" N LYS K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG K 11 " --> pdb=" O PHE K 7 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE K 13 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU K 18 " --> pdb=" O GLY K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 46 removed outlier: 3.606A pdb=" N ALA K 40 " --> pdb=" O PRO K 36 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 34 removed outlier: 3.726A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU L 30 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 91 removed outlier: 3.706A pdb=" N LYS L 77 " --> pdb=" O GLU L 73 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU L 87 " --> pdb=" O ARG L 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 17 Processing helix chain 'N' and resid 18 through 23 removed outlier: 3.912A pdb=" N LYS N 23 " --> pdb=" O TYR N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 38 removed outlier: 3.926A pdb=" N ASP N 36 " --> pdb=" O GLY N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 49 removed outlier: 3.769A pdb=" N THR N 48 " --> pdb=" O CYS N 45 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU N 49 " --> pdb=" O ARG N 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 45 through 49' Processing helix chain 'N' and resid 55 through 62 removed outlier: 3.930A pdb=" N VAL N 59 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL N 61 " --> pdb=" O ASP N 57 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR N 62 " --> pdb=" O GLN N 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1113 through 1120 removed outlier: 6.430A pdb=" N ARG B1114 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE A 13 " --> pdb=" O ARG B1114 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER B1116 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE A 11 " --> pdb=" O SER B1116 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG B1118 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU C 354 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.584A pdb=" N ALA A 27 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLU A 78 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR A 216 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N ARG A 81 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N VAL A 214 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.073A pdb=" N ARG A 169 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR A 177 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 334 removed outlier: 3.973A pdb=" N LEU A 450 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 345 removed outlier: 5.580A pdb=" N VAL A 343 " --> pdb=" O ARG A 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 removed outlier: 6.733A pdb=" N THR A 411 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL A 384 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU A 413 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 572 removed outlier: 3.599A pdb=" N SER A 618 " --> pdb=" O TYR A 610 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN A 612 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 859 through 861 removed outlier: 7.032A pdb=" N VAL A 860 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 63 through 72 removed outlier: 3.580A pdb=" N LYS B 64 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU B 106 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE B 70 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 104 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE B 72 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 63 through 72 removed outlier: 3.580A pdb=" N LYS B 64 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU B 106 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE B 70 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 104 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE B 72 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 101 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU B 125 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 103 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.563A pdb=" N ARG B 85 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.399A pdb=" N SER B 170 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 195 through 197 removed outlier: 3.717A pdb=" N SER B 196 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 203 " --> pdb=" O SER B 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB9, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AC1, first strand: chain 'B' and resid 588 through 589 Processing sheet with id=AC2, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AC3, first strand: chain 'B' and resid 556 through 561 removed outlier: 4.286A pdb=" N ASN B 556 " --> pdb=" O ASN B 571 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN B 571 " --> pdb=" O ASN B 556 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 567 " --> pdb=" O TYR B 560 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 693 through 697 Processing sheet with id=AC5, first strand: chain 'B' and resid 913 through 914 removed outlier: 6.307A pdb=" N ALA B 727 " --> pdb=" O VAL B 914 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE B 988 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AC7, first strand: chain 'B' and resid 763 through 764 removed outlier: 4.169A pdb=" N LYS B 864 " --> pdb=" O GLU B 764 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 811 through 815 removed outlier: 7.387A pdb=" N VAL B 841 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY B 814 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR B 839 " --> pdb=" O GLY B 814 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 868 through 871 removed outlier: 7.057A pdb=" N THR B 869 " --> pdb=" O ASP B 852 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 854 " --> pdb=" O LYS P 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS P 10 " --> pdb=" O TYR P 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AD2, first strand: chain 'B' and resid 903 through 904 Processing sheet with id=AD3, first strand: chain 'B' and resid 1059 through 1065 removed outlier: 3.523A pdb=" N MET B1097 " --> pdb=" O THR B1060 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 233 through 237 removed outlier: 3.541A pdb=" N ILE C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 380 through 381 removed outlier: 3.589A pdb=" N THR K 52 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.956A pdb=" N LYS D 15 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS D 9 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 12.324A pdb=" N GLU D 213 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 12.453A pdb=" N SER D 162 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N ILE D 215 " --> pdb=" O HIS D 160 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N HIS D 160 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N LYS D 158 " --> pdb=" O PRO D 217 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER D 219 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 105 through 106 removed outlier: 6.787A pdb=" N ARG D 128 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU D 49 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR D 130 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N PHE D 47 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN D 132 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL D 45 " --> pdb=" O ASN D 132 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR D 134 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 97 through 100 removed outlier: 7.082A pdb=" N GLY D 97 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS D 122 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL D 99 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 37 through 38 removed outlier: 4.052A pdb=" N ILE E 37 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 45 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL E 45 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP E 77 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 47 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN E 73 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL E 51 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 71 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 37 through 38 removed outlier: 4.052A pdb=" N ILE E 37 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 45 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL E 45 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP E 77 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 47 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN E 73 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL E 51 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 71 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 9 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE E 72 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU F 8 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LYS E 8 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS F 6 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 171 through 172 removed outlier: 5.601A pdb=" N ILE E 146 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR E 164 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 160 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 161 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HIS E 109 " --> pdb=" O MET E 163 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 144 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 118 through 121 removed outlier: 3.865A pdb=" N VAL E 119 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 128 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 121 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN E 126 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AE5, first strand: chain 'L' and resid 3 through 8 removed outlier: 6.767A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG L 8 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU L 12 " --> pdb=" O ARG L 8 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 1980 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: 4.05 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7103 1.33 - 1.45: 4479 1.45 - 1.57: 15081 1.57 - 1.69: 2 1.69 - 1.81: 207 Bond restraints: 26872 Sorted by residual: bond pdb=" CB ILE B 688 " pdb=" CG2 ILE B 688 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.82e+00 bond pdb=" CB PHE D 150 " pdb=" CG PHE D 150 " ideal model delta sigma weight residual 1.502 1.432 0.070 2.30e-02 1.89e+03 9.27e+00 bond pdb=" C PRO B 818 " pdb=" N PRO B 819 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.67e+00 bond pdb=" CA ARG E 125 " pdb=" CB ARG E 125 " ideal model delta sigma weight residual 1.539 1.669 -0.129 4.88e-02 4.20e+02 7.03e+00 bond pdb=" CB VAL A 804 " pdb=" CG2 VAL A 804 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.90e+00 ... (remaining 26867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 35274 3.47 - 6.93: 846 6.93 - 10.40: 138 10.40 - 13.86: 21 13.86 - 17.33: 3 Bond angle restraints: 36282 Sorted by residual: angle pdb=" C VAL B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta sigma weight residual 127.00 144.33 -17.33 2.40e+00 1.74e-01 5.21e+01 angle pdb=" C LYS P 13 " pdb=" N GLU P 14 " pdb=" CA GLU P 14 " ideal model delta sigma weight residual 121.54 134.77 -13.23 1.91e+00 2.74e-01 4.80e+01 angle pdb=" C VAL B 57 " pdb=" N PRO B 58 " pdb=" CD PRO B 58 " ideal model delta sigma weight residual 120.60 105.70 14.90 2.20e+00 2.07e-01 4.59e+01 angle pdb=" C LEU B 12 " pdb=" N THR B 13 " pdb=" CA THR B 13 " ideal model delta sigma weight residual 121.80 138.22 -16.42 2.44e+00 1.68e-01 4.53e+01 angle pdb=" C GLY F 28 " pdb=" N LEU F 29 " pdb=" CA LEU F 29 " ideal model delta sigma weight residual 121.70 133.62 -11.92 1.80e+00 3.09e-01 4.38e+01 ... (remaining 36277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15301 17.93 - 35.86: 976 35.86 - 53.78: 226 53.78 - 71.71: 33 71.71 - 89.64: 8 Dihedral angle restraints: 16544 sinusoidal: 7026 harmonic: 9518 Sorted by residual: dihedral pdb=" CA GLN A 427 " pdb=" C GLN A 427 " pdb=" N PRO A 428 " pdb=" CA PRO A 428 " ideal model delta harmonic sigma weight residual 180.00 100.05 79.95 0 5.00e+00 4.00e-02 2.56e+02 dihedral pdb=" CA ASN C 110 " pdb=" C ASN C 110 " pdb=" N PRO C 111 " pdb=" CA PRO C 111 " ideal model delta harmonic sigma weight residual -180.00 -128.99 -51.01 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA VAL K 30 " pdb=" C VAL K 30 " pdb=" N PRO K 31 " pdb=" CA PRO K 31 " ideal model delta harmonic sigma weight residual -180.00 -135.05 -44.95 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 16541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3556 0.111 - 0.221: 426 0.221 - 0.332: 27 0.332 - 0.443: 5 0.443 - 0.553: 1 Chirality restraints: 4015 Sorted by residual: chirality pdb=" CB ILE B 652 " pdb=" CA ILE B 652 " pdb=" CG1 ILE B 652 " pdb=" CG2 ILE B 652 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ASN B 431 " pdb=" N ASN B 431 " pdb=" C ASN B 431 " pdb=" CB ASN B 431 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CB ILE B 895 " pdb=" CA ILE B 895 " pdb=" CG1 ILE B 895 " pdb=" CG2 ILE B 895 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 4012 not shown) Planarity restraints: 4722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 455 " 0.093 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO A 456 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 427 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 428 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 110 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 111 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.056 5.00e-02 4.00e+02 ... (remaining 4719 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 455 2.66 - 3.22: 22507 3.22 - 3.78: 37071 3.78 - 4.34: 48839 4.34 - 4.90: 81067 Nonbonded interactions: 189939 Sorted by model distance: nonbonded pdb=" OD1 ASP A 465 " pdb="MG MG A1001 " model vdw 2.102 2.170 nonbonded pdb=" O CYS N 44 " pdb="ZN ZN N1401 " model vdw 2.162 2.230 nonbonded pdb=" OG1 THR B 13 " pdb=" OE1 GLU B 16 " model vdw 2.184 3.040 nonbonded pdb=" O GLU B 150 " pdb=" OH TYR N 62 " model vdw 2.224 3.040 nonbonded pdb=" C CYS N 44 " pdb="ZN ZN N1401 " model vdw 2.258 2.460 ... (remaining 189934 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.012 0.697 26884 Z= 0.446 Angle : 1.330 17.327 36282 Z= 0.713 Chirality : 0.072 0.553 4015 Planarity : 0.009 0.140 4722 Dihedral : 12.715 89.641 10432 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.71 % Favored : 85.53 % Rotamer: Outliers : 4.74 % Allowed : 6.98 % Favored : 88.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.82 % Twisted General : 0.35 % 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: -5.00 (0.11), residues: 3275 helix: -3.96 (0.09), residues: 996 sheet: -2.32 (0.24), residues: 378 loop : -3.28 (0.12), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 601 TYR 0.045 0.004 TYR P 29 PHE 0.059 0.004 PHE B1032 TRP 0.056 0.005 TRP A 272 HIS 0.014 0.003 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00838 (26872) covalent geometry : angle 1.33047 (36282) hydrogen bonds : bond 0.33342 ( 700) hydrogen bonds : angle 9.60274 ( 1980) metal coordination : bond 0.38531 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 717 time to evaluate : 1.197 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: A 108 LEU cc_start: 0.4713 (mm) cc_final: 0.4296 (mt) REVERT: A 207 LYS cc_start: 0.6657 (mttt) cc_final: 0.6302 (mmtt) REVERT: A 266 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6142 (tt) REVERT: A 274 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6306 (tp) REVERT: A 325 ASN cc_start: 0.6799 (m-40) cc_final: 0.6527 (t0) REVERT: A 337 MET cc_start: 0.7702 (mmm) cc_final: 0.7488 (tpp) REVERT: A 358 LYS cc_start: 0.8186 (tptt) cc_final: 0.7920 (tttp) REVERT: A 422 VAL cc_start: 0.9621 (p) cc_final: 0.9368 (m) REVERT: A 463 ASP cc_start: 0.8946 (p0) cc_final: 0.8658 (p0) REVERT: A 475 GLU cc_start: 0.6389 (mp0) cc_final: 0.5999 (mp0) REVERT: A 847 ASN cc_start: 0.8115 (t0) cc_final: 0.7371 (t0) REVERT: A 889 ASP cc_start: 0.6597 (m-30) cc_final: 0.5744 (p0) REVERT: A 899 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8703 (mm) REVERT: B 14 PRO cc_start: 0.7517 (Cg_exo) cc_final: 0.7296 (Cg_endo) REVERT: B 89 PRO cc_start: 0.9062 (Cg_exo) cc_final: 0.8693 (Cg_endo) REVERT: B 129 MET cc_start: 0.7483 (ttm) cc_final: 0.7175 (ttm) REVERT: B 289 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.4595 (m-80) REVERT: B 458 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8428 (tp) REVERT: B 674 MET cc_start: 0.7937 (mtt) cc_final: 0.7693 (mtp) REVERT: B 765 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7330 (mttp) REVERT: B 873 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8696 (tp) REVERT: C 27 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7475 (tptm) REVERT: C 164 ASP cc_start: 0.3340 (OUTLIER) cc_final: 0.2484 (m-30) REVERT: C 287 ASP cc_start: 0.7360 (t70) cc_final: 0.7095 (t0) REVERT: C 358 LEU cc_start: 0.7024 (mt) cc_final: 0.6628 (mt) REVERT: D 145 LYS cc_start: 0.8849 (ptpt) cc_final: 0.8647 (ptmt) REVERT: E 5 LEU cc_start: 0.5042 (mm) cc_final: 0.4419 (mm) REVERT: E 17 MET cc_start: 0.7220 (pmm) cc_final: 0.6975 (pmm) REVERT: H 35 ILE cc_start: 0.8452 (pt) cc_final: 0.8243 (pt) REVERT: L 51 MET cc_start: 0.8476 (ptp) cc_final: 0.8249 (ptm) REVERT: P 13 LYS cc_start: 0.6463 (OUTLIER) cc_final: 0.5965 (mptt) outliers start: 135 outliers final: 30 residues processed: 813 average time/residue: 0.2071 time to fit residues: 248.7241 Evaluate side-chains 444 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 405 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 29 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 252 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN A 732 ASN A 790 HIS A 815 GLN B 260 ASN B 312 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN B 662 HIS B 968 HIS B1014 GLN C 19 ASN D 117 ASN D 206 HIS E 162 ASN F 32 ASN K 38 GLN L 22 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.215218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198217 restraints weight = 34494.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188714 restraints weight = 68796.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.185877 restraints weight = 52124.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.183553 restraints weight = 57028.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184151 restraints weight = 51014.412| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26884 Z= 0.149 Angle : 0.796 13.080 36282 Z= 0.412 Chirality : 0.049 0.300 4015 Planarity : 0.007 0.126 4722 Dihedral : 7.502 69.060 3729 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.87 % Favored : 88.98 % Rotamer: Outliers : 4.04 % Allowed : 14.25 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.23 % 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: -3.81 (0.13), residues: 3275 helix: -2.47 (0.13), residues: 1053 sheet: -1.27 (0.26), residues: 360 loop : -2.93 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 696 TYR 0.019 0.001 TYR A 740 PHE 0.024 0.001 PHE B 821 TRP 0.025 0.002 TRP B 683 HIS 0.007 0.001 HIS B 595 Details of bonding type rmsd covalent geometry : bond 0.00321 (26872) covalent geometry : angle 0.79612 (36282) hydrogen bonds : bond 0.05867 ( 700) hydrogen bonds : angle 5.79700 ( 1980) metal coordination : bond 0.01851 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 493 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8437 (mmm) cc_final: 0.8052 (tpp) REVERT: A 66 ARG cc_start: 0.6939 (mmm-85) cc_final: 0.5454 (mpt90) REVERT: A 108 LEU cc_start: 0.4945 (mm) cc_final: 0.3990 (mt) REVERT: A 123 MET cc_start: 0.4400 (ttm) cc_final: 0.4039 (mpp) REVERT: A 225 MET cc_start: 0.5162 (tmm) cc_final: 0.4410 (ttt) REVERT: A 274 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.5828 (tp) REVERT: A 337 MET cc_start: 0.7987 (mmm) cc_final: 0.7511 (tpp) REVERT: A 422 VAL cc_start: 0.9461 (p) cc_final: 0.9182 (m) REVERT: A 466 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 475 GLU cc_start: 0.6209 (mp0) cc_final: 0.5986 (mp0) REVERT: A 585 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 633 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9102 (tp) REVERT: A 774 ILE cc_start: 0.8443 (tt) cc_final: 0.7869 (pt) REVERT: A 899 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8608 (mm) REVERT: B 89 PRO cc_start: 0.9006 (Cg_exo) cc_final: 0.8683 (Cg_endo) REVERT: B 90 MET cc_start: 0.8357 (tpp) cc_final: 0.7933 (tpp) REVERT: B 365 GLN cc_start: 0.7388 (pp30) cc_final: 0.5889 (mp10) REVERT: B 372 TYR cc_start: 0.7417 (t80) cc_final: 0.6991 (t80) REVERT: B 674 MET cc_start: 0.7783 (mtt) cc_final: 0.7575 (mtp) REVERT: B 873 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B 915 ASN cc_start: 0.7405 (t0) cc_final: 0.7118 (m-40) REVERT: B 1032 PHE cc_start: 0.3281 (OUTLIER) cc_final: 0.2906 (m-10) REVERT: C 53 TYR cc_start: 0.8375 (t80) cc_final: 0.7875 (t80) REVERT: C 293 MET cc_start: 0.7291 (mmp) cc_final: 0.7055 (ptt) REVERT: C 358 LEU cc_start: 0.7293 (mt) cc_final: 0.6889 (mt) REVERT: F 102 MET cc_start: 0.3920 (tpt) cc_final: 0.3399 (tpt) REVERT: H 34 ARG cc_start: 0.7547 (mpt-90) cc_final: 0.7345 (mmt90) REVERT: L 72 GLU cc_start: 0.7290 (tp30) cc_final: 0.7076 (tm-30) REVERT: L 76 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7377 (tm-30) outliers start: 115 outliers final: 48 residues processed: 566 average time/residue: 0.1961 time to fit residues: 168.9120 Evaluate side-chains 414 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 359 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 15 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 19 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 305 HIS ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 586 ASN D 117 ASN E 68 HIS E 82 GLN E 124 ASN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.201671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.184390 restraints weight = 34914.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177838 restraints weight = 84127.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174166 restraints weight = 64678.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172086 restraints weight = 61369.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172556 restraints weight = 49074.404| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 26884 Z= 0.289 Angle : 0.894 13.999 36282 Z= 0.462 Chirality : 0.054 0.261 4015 Planarity : 0.007 0.126 4722 Dihedral : 7.307 74.150 3692 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.92 % Favored : 86.87 % Rotamer: Outliers : 5.62 % Allowed : 15.65 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.16 % 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: -3.55 (0.13), residues: 3275 helix: -1.95 (0.14), residues: 1078 sheet: -1.37 (0.26), residues: 372 loop : -2.93 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 579 TYR 0.026 0.003 TYR B 993 PHE 0.027 0.003 PHE F 38 TRP 0.024 0.002 TRP B 683 HIS 0.011 0.002 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00698 (26872) covalent geometry : angle 0.89398 (36282) hydrogen bonds : bond 0.06120 ( 700) hydrogen bonds : angle 5.71014 ( 1980) metal coordination : bond 0.01224 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 363 time to evaluate : 1.093 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: A 108 LEU cc_start: 0.4702 (mm) cc_final: 0.3841 (mt) REVERT: A 268 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6523 (tt) REVERT: A 274 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6274 (tp) REVERT: A 325 ASN cc_start: 0.7877 (m-40) cc_final: 0.7356 (t0) REVERT: A 337 MET cc_start: 0.8000 (mmm) cc_final: 0.7483 (tpp) REVERT: A 422 VAL cc_start: 0.9680 (p) cc_final: 0.9461 (m) REVERT: A 585 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 587 LYS cc_start: 0.8124 (tppt) cc_final: 0.7869 (mmmt) REVERT: A 650 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8651 (tp) REVERT: A 651 ASP cc_start: 0.8636 (t70) cc_final: 0.7664 (t0) REVERT: A 697 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8063 (tp) REVERT: B 13 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6536 (p) REVERT: B 89 PRO cc_start: 0.9117 (Cg_exo) cc_final: 0.8860 (Cg_endo) REVERT: B 90 MET cc_start: 0.8633 (tpp) cc_final: 0.7941 (tpp) REVERT: B 306 MET cc_start: 0.7103 (mmm) cc_final: 0.6861 (mmt) REVERT: B 320 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 372 TYR cc_start: 0.7325 (t80) cc_final: 0.7124 (t80) REVERT: B 429 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7922 (tpp-160) REVERT: B 559 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7403 (tt) REVERT: B 624 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8052 (mm-30) REVERT: B 696 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8647 (tm) REVERT: B 761 GLU cc_start: 0.7470 (pp20) cc_final: 0.7262 (pp20) REVERT: B 873 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 1005 MET cc_start: 0.8262 (ttp) cc_final: 0.7790 (ptm) REVERT: B 1032 PHE cc_start: 0.4566 (OUTLIER) cc_final: 0.3721 (m-10) REVERT: B 1035 MET cc_start: 0.7941 (mmm) cc_final: 0.7647 (mmt) REVERT: C 293 MET cc_start: 0.7835 (mmp) cc_final: 0.7536 (ptt) REVERT: C 358 LEU cc_start: 0.7506 (mt) cc_final: 0.7230 (mt) REVERT: D 167 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7882 (t70) REVERT: H 30 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8481 (mm) REVERT: H 34 ARG cc_start: 0.7806 (mpt-90) cc_final: 0.7583 (mmt90) REVERT: H 63 ILE cc_start: 0.8283 (tt) cc_final: 0.7802 (mt) REVERT: K 46 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7587 (mtmt) REVERT: L 72 GLU cc_start: 0.7250 (tp30) cc_final: 0.7029 (tm-30) REVERT: N 16 ASP cc_start: 0.8039 (p0) cc_final: 0.7727 (p0) REVERT: P 33 LYS cc_start: 0.8648 (pttt) cc_final: 0.8102 (pttt) outliers start: 160 outliers final: 90 residues processed: 486 average time/residue: 0.1764 time to fit residues: 135.5352 Evaluate side-chains 432 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 328 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 312 optimal weight: 7.9990 chunk 120 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 365 GLN B 556 ASN E 124 ASN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.210350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.193601 restraints weight = 34568.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.184268 restraints weight = 76183.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182131 restraints weight = 59543.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.179658 restraints weight = 52635.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.180150 restraints weight = 48581.218| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26884 Z= 0.125 Angle : 0.709 14.018 36282 Z= 0.362 Chirality : 0.047 0.233 4015 Planarity : 0.006 0.123 4722 Dihedral : 6.548 67.097 3690 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.38 % Favored : 89.56 % Rotamer: Outliers : 4.42 % Allowed : 16.99 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -3.07 (0.14), residues: 3275 helix: -1.37 (0.15), residues: 1078 sheet: -1.05 (0.27), residues: 355 loop : -2.77 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 265 TYR 0.022 0.001 TYR C 53 PHE 0.018 0.001 PHE B 821 TRP 0.017 0.001 TRP B 683 HIS 0.004 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00275 (26872) covalent geometry : angle 0.70911 (36282) hydrogen bonds : bond 0.04141 ( 700) hydrogen bonds : angle 5.05596 ( 1980) metal coordination : bond 0.00822 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 373 time to evaluate : 0.880 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: A 66 ARG cc_start: 0.6654 (mmm-85) cc_final: 0.5446 (mpt90) REVERT: A 108 LEU cc_start: 0.4741 (mm) cc_final: 0.3904 (mt) REVERT: A 268 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6521 (tt) REVERT: A 325 ASN cc_start: 0.7605 (m-40) cc_final: 0.7018 (t0) REVERT: A 337 MET cc_start: 0.7979 (mmm) cc_final: 0.7455 (tpp) REVERT: A 358 LYS cc_start: 0.8408 (tttp) cc_final: 0.7335 (mttt) REVERT: A 422 VAL cc_start: 0.9450 (p) cc_final: 0.9180 (m) REVERT: A 542 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6603 (mm-30) REVERT: A 626 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: A 632 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8226 (mttm) REVERT: A 651 ASP cc_start: 0.8554 (t70) cc_final: 0.7720 (t0) REVERT: B 89 PRO cc_start: 0.8987 (Cg_exo) cc_final: 0.8779 (Cg_endo) REVERT: B 90 MET cc_start: 0.8455 (tpp) cc_final: 0.7777 (tpp) REVERT: B 374 MET cc_start: 0.7221 (tmm) cc_final: 0.6979 (tmm) REVERT: B 471 THR cc_start: 0.8303 (m) cc_final: 0.8012 (p) REVERT: B 555 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7677 (mt) REVERT: B 696 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8384 (tp) REVERT: B 761 GLU cc_start: 0.7500 (pp20) cc_final: 0.7264 (pp20) REVERT: B 873 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8633 (tp) REVERT: B 880 ASP cc_start: 0.8748 (m-30) cc_final: 0.8293 (m-30) REVERT: B 1005 MET cc_start: 0.8125 (ttp) cc_final: 0.7659 (ptm) REVERT: C 35 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.6138 (p90) REVERT: C 293 MET cc_start: 0.7578 (mmp) cc_final: 0.7070 (ptt) REVERT: C 358 LEU cc_start: 0.7366 (mt) cc_final: 0.6789 (mt) REVERT: C 377 ILE cc_start: 0.8099 (tp) cc_final: 0.7881 (tp) REVERT: C 384 LEU cc_start: 0.7759 (tp) cc_final: 0.7491 (tt) REVERT: D 167 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7880 (t70) REVERT: E 20 MET cc_start: 0.7034 (ttm) cc_final: 0.6825 (ttm) REVERT: F 24 ARG cc_start: 0.5574 (tpt170) cc_final: 0.4747 (tpt170) REVERT: H 30 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8465 (mm) REVERT: K 8 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5063 (mt-10) REVERT: K 46 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7409 (mtmt) REVERT: L 72 GLU cc_start: 0.7145 (tp30) cc_final: 0.6818 (tm-30) REVERT: L 76 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: P 19 LEU cc_start: 0.2914 (OUTLIER) cc_final: 0.2590 (pp) outliers start: 126 outliers final: 71 residues processed: 464 average time/residue: 0.1748 time to fit residues: 127.9321 Evaluate side-chains 414 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 331 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 46 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 3 optimal weight: 0.0670 chunk 66 optimal weight: 8.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 556 ASN C 70 GLN C 124 HIS C 296 GLN E 82 GLN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.208580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.192306 restraints weight = 34379.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.180596 restraints weight = 75438.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178174 restraints weight = 63996.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176698 restraints weight = 55620.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176581 restraints weight = 43360.610| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26884 Z= 0.136 Angle : 0.704 17.584 36282 Z= 0.358 Chirality : 0.047 0.364 4015 Planarity : 0.006 0.121 4722 Dihedral : 6.108 67.070 3677 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.21 % Favored : 88.73 % Rotamer: Outliers : 4.00 % Allowed : 18.81 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.83 (0.14), residues: 3275 helix: -1.03 (0.15), residues: 1072 sheet: -1.04 (0.27), residues: 371 loop : -2.69 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 24 TYR 0.018 0.001 TYR A 740 PHE 0.019 0.001 PHE B 821 TRP 0.010 0.001 TRP B 683 HIS 0.011 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00312 (26872) covalent geometry : angle 0.70443 (36282) hydrogen bonds : bond 0.04067 ( 700) hydrogen bonds : angle 4.91060 ( 1980) metal coordination : bond 0.00712 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 357 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.6723 (mmm-85) cc_final: 0.5473 (mpt90) REVERT: A 108 LEU cc_start: 0.4823 (mm) cc_final: 0.3943 (mt) REVERT: A 325 ASN cc_start: 0.7749 (m-40) cc_final: 0.7266 (m-40) REVERT: A 337 MET cc_start: 0.8263 (mmm) cc_final: 0.7802 (tpp) REVERT: A 358 LYS cc_start: 0.8375 (tttp) cc_final: 0.7298 (mtmt) REVERT: A 422 VAL cc_start: 0.9499 (p) cc_final: 0.9262 (m) REVERT: A 542 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6727 (mm-30) REVERT: A 567 LEU cc_start: 0.8741 (mm) cc_final: 0.8480 (mm) REVERT: A 626 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: A 632 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8440 (mptt) REVERT: A 650 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8441 (tt) REVERT: A 651 ASP cc_start: 0.8565 (t70) cc_final: 0.7508 (t0) REVERT: A 697 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7940 (tp) REVERT: B 89 PRO cc_start: 0.8969 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: B 90 MET cc_start: 0.8454 (tpp) cc_final: 0.7728 (tpp) REVERT: B 471 THR cc_start: 0.8507 (m) cc_final: 0.8029 (p) REVERT: B 674 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7251 (mtm) REVERT: B 696 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8523 (tp) REVERT: B 856 VAL cc_start: 0.7224 (OUTLIER) cc_final: 0.6944 (m) REVERT: B 873 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8715 (tp) REVERT: B 880 ASP cc_start: 0.8582 (m-30) cc_final: 0.8306 (m-30) REVERT: B 915 ASN cc_start: 0.7464 (t0) cc_final: 0.7239 (m-40) REVERT: B 1005 MET cc_start: 0.8198 (ttp) cc_final: 0.7686 (ptm) REVERT: B 1052 ARG cc_start: 0.8574 (tpp-160) cc_final: 0.8216 (tpp-160) REVERT: C 25 TYR cc_start: 0.7509 (t80) cc_final: 0.7231 (t80) REVERT: C 293 MET cc_start: 0.7429 (mmp) cc_final: 0.7033 (ptt) REVERT: C 307 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7535 (tp) REVERT: C 358 LEU cc_start: 0.7189 (mt) cc_final: 0.6700 (mt) REVERT: C 377 ILE cc_start: 0.8144 (tp) cc_final: 0.7921 (tp) REVERT: C 384 LEU cc_start: 0.7877 (tp) cc_final: 0.7488 (tt) REVERT: D 167 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7958 (t70) REVERT: E 20 MET cc_start: 0.6726 (ttm) cc_final: 0.6468 (ttm) REVERT: F 24 ARG cc_start: 0.5644 (tpt170) cc_final: 0.4628 (tpt170) REVERT: H 25 GLU cc_start: 0.7262 (mp0) cc_final: 0.7057 (mp0) REVERT: H 30 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (mm) REVERT: K 46 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7463 (mtmt) REVERT: L 76 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: P 19 LEU cc_start: 0.2441 (OUTLIER) cc_final: 0.2209 (pp) outliers start: 114 outliers final: 78 residues processed: 441 average time/residue: 0.1668 time to fit residues: 118.7190 Evaluate side-chains 416 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 325 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 309 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 ASN A 850 GLN B 365 GLN B 431 ASN B 556 ASN C 19 ASN E 82 GLN E 124 ASN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.203535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.187017 restraints weight = 34680.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177264 restraints weight = 83801.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174161 restraints weight = 66141.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172167 restraints weight = 58189.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.172493 restraints weight = 47115.735| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 26884 Z= 0.200 Angle : 0.765 16.002 36282 Z= 0.390 Chirality : 0.049 0.333 4015 Planarity : 0.006 0.122 4722 Dihedral : 6.335 69.126 3677 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.70 % Favored : 87.21 % Rotamer: Outliers : 4.95 % Allowed : 19.02 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.91 (0.14), residues: 3275 helix: -1.04 (0.15), residues: 1074 sheet: -1.16 (0.27), residues: 364 loop : -2.77 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1031 TYR 0.023 0.002 TYR A 740 PHE 0.019 0.002 PHE B 821 TRP 0.012 0.002 TRP L 89 HIS 0.011 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00480 (26872) covalent geometry : angle 0.76538 (36282) hydrogen bonds : bond 0.04627 ( 700) hydrogen bonds : angle 5.07408 ( 1980) metal coordination : bond 0.00705 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 343 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.6788 (mmm-85) cc_final: 0.5553 (mpt90) REVERT: A 108 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.3940 (mt) REVERT: A 123 MET cc_start: 0.5846 (tpt) cc_final: 0.5184 (mpp) REVERT: A 325 ASN cc_start: 0.8048 (m-40) cc_final: 0.7656 (m-40) REVERT: A 337 MET cc_start: 0.7960 (mmm) cc_final: 0.7401 (tpp) REVERT: A 422 VAL cc_start: 0.9624 (p) cc_final: 0.9421 (m) REVERT: A 542 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 623 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7859 (ttmt) REVERT: A 626 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: A 650 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 651 ASP cc_start: 0.8638 (t70) cc_final: 0.7615 (t0) REVERT: A 697 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8057 (tp) REVERT: B 90 MET cc_start: 0.8498 (tpp) cc_final: 0.7579 (tpp) REVERT: B 320 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7865 (tt) REVERT: B 411 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7489 (tt) REVERT: B 471 THR cc_start: 0.8577 (m) cc_final: 0.8068 (p) REVERT: B 674 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7564 (mtm) REVERT: B 696 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8536 (tp) REVERT: B 856 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7445 (m) REVERT: B 873 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 880 ASP cc_start: 0.8647 (m-30) cc_final: 0.8398 (m-30) REVERT: B 915 ASN cc_start: 0.7824 (t0) cc_final: 0.7562 (m-40) REVERT: B 1005 MET cc_start: 0.8250 (ttp) cc_final: 0.7843 (ptm) REVERT: B 1114 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6876 (ptm-80) REVERT: C 157 MET cc_start: 0.1640 (OUTLIER) cc_final: 0.0822 (tpt) REVERT: C 293 MET cc_start: 0.7350 (mmp) cc_final: 0.7058 (ptt) REVERT: C 358 LEU cc_start: 0.7366 (mt) cc_final: 0.6844 (mt) REVERT: C 384 LEU cc_start: 0.7833 (tp) cc_final: 0.7421 (tt) REVERT: E 20 MET cc_start: 0.6902 (ttm) cc_final: 0.6628 (ttm) REVERT: E 93 MET cc_start: 0.4535 (ttp) cc_final: 0.4256 (ttp) REVERT: H 25 GLU cc_start: 0.7281 (mp0) cc_final: 0.7057 (mp0) REVERT: H 30 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8582 (mm) REVERT: H 78 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7010 (mt) REVERT: L 72 GLU cc_start: 0.7128 (tp30) cc_final: 0.6740 (tm-30) REVERT: P 19 LEU cc_start: 0.2837 (OUTLIER) cc_final: 0.2468 (pp) outliers start: 141 outliers final: 102 residues processed: 445 average time/residue: 0.1778 time to fit residues: 127.3627 Evaluate side-chains 440 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 322 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 154 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 283 optimal weight: 0.0980 chunk 108 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 431 ASN B 556 ASN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.207012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.190613 restraints weight = 34593.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.180763 restraints weight = 79665.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178659 restraints weight = 62692.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.176229 restraints weight = 51151.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.176386 restraints weight = 46309.461| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26884 Z= 0.135 Angle : 0.702 15.216 36282 Z= 0.356 Chirality : 0.047 0.309 4015 Planarity : 0.006 0.121 4722 Dihedral : 6.005 66.687 3677 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.99 % Favored : 88.95 % Rotamer: Outliers : 4.14 % Allowed : 19.83 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.68 (0.14), residues: 3275 helix: -0.71 (0.16), residues: 1065 sheet: -1.12 (0.27), residues: 372 loop : -2.70 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 166 TYR 0.019 0.001 TYR B 432 PHE 0.017 0.001 PHE B 821 TRP 0.012 0.001 TRP A 272 HIS 0.008 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00311 (26872) covalent geometry : angle 0.70247 (36282) hydrogen bonds : bond 0.03917 ( 700) hydrogen bonds : angle 4.84947 ( 1980) metal coordination : bond 0.00659 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 349 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.6808 (mmm-85) cc_final: 0.5627 (mpt90) REVERT: A 108 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.3961 (mt) REVERT: A 123 MET cc_start: 0.5702 (tpt) cc_final: 0.5170 (mpp) REVERT: A 325 ASN cc_start: 0.7808 (m-40) cc_final: 0.7505 (m-40) REVERT: A 337 MET cc_start: 0.7913 (mmm) cc_final: 0.7354 (tpp) REVERT: A 422 VAL cc_start: 0.9502 (p) cc_final: 0.9272 (m) REVERT: A 542 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 567 LEU cc_start: 0.8903 (mm) cc_final: 0.8624 (mm) REVERT: A 626 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: A 632 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8248 (mttm) REVERT: A 651 ASP cc_start: 0.8574 (t70) cc_final: 0.7497 (t0) REVERT: A 697 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 874 GLU cc_start: 0.8159 (mp0) cc_final: 0.7837 (mp0) REVERT: B 90 MET cc_start: 0.8427 (tpp) cc_final: 0.7538 (tpp) REVERT: B 320 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7803 (tt) REVERT: B 326 LYS cc_start: 0.8278 (tptt) cc_final: 0.8054 (tptt) REVERT: B 471 THR cc_start: 0.8460 (m) cc_final: 0.7976 (p) REVERT: B 696 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 856 VAL cc_start: 0.7676 (OUTLIER) cc_final: 0.7431 (m) REVERT: B 873 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8747 (tp) REVERT: B 915 ASN cc_start: 0.7810 (t0) cc_final: 0.7578 (m-40) REVERT: B 1005 MET cc_start: 0.8166 (ttp) cc_final: 0.7751 (ptm) REVERT: B 1114 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.7011 (ptm-80) REVERT: C 157 MET cc_start: 0.1328 (OUTLIER) cc_final: 0.0611 (tpt) REVERT: C 293 MET cc_start: 0.7212 (mmp) cc_final: 0.6933 (ptt) REVERT: C 307 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7665 (tp) REVERT: C 358 LEU cc_start: 0.7302 (mt) cc_final: 0.6819 (mt) REVERT: C 384 LEU cc_start: 0.7747 (tp) cc_final: 0.7279 (tt) REVERT: D 150 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6833 (t80) REVERT: E 20 MET cc_start: 0.6866 (ttm) cc_final: 0.6550 (ttm) REVERT: E 93 MET cc_start: 0.4754 (ttp) cc_final: 0.4469 (ttp) REVERT: F 21 LEU cc_start: 0.6408 (tp) cc_final: 0.6207 (tp) REVERT: H 25 GLU cc_start: 0.7393 (mp0) cc_final: 0.7147 (mp0) REVERT: H 30 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8513 (mm) REVERT: H 74 TYR cc_start: 0.8644 (m-10) cc_final: 0.8264 (m-80) REVERT: K 8 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5419 (mt-10) REVERT: L 14 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6225 (mt-10) REVERT: L 76 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7044 (tm-30) outliers start: 118 outliers final: 80 residues processed: 433 average time/residue: 0.1788 time to fit residues: 124.4728 Evaluate side-chains 420 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 325 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 150 PHE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 15 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 195 optimal weight: 6.9990 chunk 259 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 73 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 200 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 556 ASN C 364 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.208817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182325 restraints weight = 34831.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178041 restraints weight = 42061.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.177879 restraints weight = 41881.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178438 restraints weight = 34013.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178539 restraints weight = 29083.322| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26884 Z= 0.121 Angle : 0.697 14.680 36282 Z= 0.352 Chirality : 0.046 0.286 4015 Planarity : 0.006 0.120 4722 Dihedral : 5.782 65.245 3675 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.08 % Favored : 88.85 % Rotamer: Outliers : 3.86 % Allowed : 20.64 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.49 (0.14), residues: 3275 helix: -0.50 (0.16), residues: 1064 sheet: -1.01 (0.26), residues: 411 loop : -2.65 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 166 TYR 0.018 0.001 TYR B 432 PHE 0.017 0.001 PHE B 821 TRP 0.008 0.001 TRP A 272 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00273 (26872) covalent geometry : angle 0.69747 (36282) hydrogen bonds : bond 0.03575 ( 700) hydrogen bonds : angle 4.71553 ( 1980) metal coordination : bond 0.00587 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 351 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8365 (tpp) cc_final: 0.8045 (tpt) REVERT: A 66 ARG cc_start: 0.6827 (mmm-85) cc_final: 0.5704 (mpt90) REVERT: A 81 ARG cc_start: 0.4486 (mmm-85) cc_final: 0.4225 (mmm-85) REVERT: A 108 LEU cc_start: 0.4710 (OUTLIER) cc_final: 0.3862 (mt) REVERT: A 123 MET cc_start: 0.5427 (tpt) cc_final: 0.5118 (mpp) REVERT: A 325 ASN cc_start: 0.7728 (m-40) cc_final: 0.7448 (m-40) REVERT: A 337 MET cc_start: 0.8169 (mmm) cc_final: 0.7648 (tpp) REVERT: A 422 VAL cc_start: 0.9437 (p) cc_final: 0.9202 (m) REVERT: A 567 LEU cc_start: 0.8849 (mm) cc_final: 0.8387 (mp) REVERT: A 626 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: A 632 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8334 (mptt) REVERT: A 651 ASP cc_start: 0.8310 (t70) cc_final: 0.7302 (t0) REVERT: A 697 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 90 MET cc_start: 0.8348 (tpp) cc_final: 0.7453 (tpp) REVERT: B 320 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7741 (tt) REVERT: B 471 THR cc_start: 0.8163 (m) cc_final: 0.7705 (p) REVERT: B 696 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8405 (tp) REVERT: B 856 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7086 (m) REVERT: B 873 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 1005 MET cc_start: 0.8215 (ttp) cc_final: 0.7670 (ptm) REVERT: B 1114 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6991 (ptm-80) REVERT: C 54 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: C 157 MET cc_start: 0.1198 (OUTLIER) cc_final: 0.0477 (tpt) REVERT: C 293 MET cc_start: 0.7154 (mmp) cc_final: 0.6871 (ptt) REVERT: C 358 LEU cc_start: 0.7193 (mt) cc_final: 0.6780 (mt) REVERT: C 384 LEU cc_start: 0.7770 (tp) cc_final: 0.7301 (tt) REVERT: F 24 ARG cc_start: 0.6527 (tpt170) cc_final: 0.5088 (tpt170) REVERT: H 25 GLU cc_start: 0.7348 (mp0) cc_final: 0.7092 (mp0) REVERT: H 30 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8423 (mm) REVERT: H 74 TYR cc_start: 0.8604 (m-10) cc_final: 0.8241 (m-80) REVERT: K 8 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5373 (mt-10) REVERT: K 43 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8017 (tp30) REVERT: L 14 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6096 (mt-10) REVERT: L 76 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6867 (tm-30) outliers start: 110 outliers final: 78 residues processed: 426 average time/residue: 0.1802 time to fit residues: 123.5830 Evaluate side-chains 419 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 327 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 15 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 278 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 226 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 0.0000 chunk 97 optimal weight: 8.9990 chunk 127 optimal weight: 0.0030 chunk 88 optimal weight: 0.0570 chunk 235 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 HIS B 556 ASN B 586 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN F 25 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.212698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196011 restraints weight = 34805.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.186589 restraints weight = 73879.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184051 restraints weight = 56354.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.181948 restraints weight = 53383.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.182860 restraints weight = 42774.990| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26884 Z= 0.115 Angle : 0.684 14.222 36282 Z= 0.344 Chirality : 0.046 0.279 4015 Planarity : 0.006 0.117 4722 Dihedral : 5.548 63.278 3675 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.56 % Favored : 89.37 % Rotamer: Outliers : 3.30 % Allowed : 21.48 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.03 % 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: -2.29 (0.14), residues: 3275 helix: -0.26 (0.17), residues: 1060 sheet: -0.90 (0.26), residues: 418 loop : -2.57 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.025 0.001 TYR C 126 PHE 0.016 0.001 PHE B 821 TRP 0.017 0.001 TRP A 272 HIS 0.016 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00254 (26872) covalent geometry : angle 0.68353 (36282) hydrogen bonds : bond 0.03196 ( 700) hydrogen bonds : angle 4.59699 ( 1980) metal coordination : bond 0.00557 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 365 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8278 (tpp) cc_final: 0.7707 (tpt) REVERT: A 66 ARG cc_start: 0.6842 (mmm-85) cc_final: 0.5663 (mpt90) REVERT: A 108 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4106 (mt) REVERT: A 123 MET cc_start: 0.5368 (tpt) cc_final: 0.5142 (mpp) REVERT: A 325 ASN cc_start: 0.7662 (m-40) cc_final: 0.7360 (m-40) REVERT: A 337 MET cc_start: 0.8155 (mmm) cc_final: 0.7531 (tpp) REVERT: A 626 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: A 651 ASP cc_start: 0.8359 (t70) cc_final: 0.7548 (t0) REVERT: A 768 MET cc_start: 0.8279 (mmm) cc_final: 0.7961 (mmm) REVERT: B 90 MET cc_start: 0.8252 (tpp) cc_final: 0.7374 (tpp) REVERT: B 198 ARG cc_start: 0.7245 (tpt-90) cc_final: 0.6973 (tpt170) REVERT: B 320 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7796 (tt) REVERT: B 365 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6387 (tp40) REVERT: B 471 THR cc_start: 0.8000 (m) cc_final: 0.7482 (p) REVERT: B 696 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8386 (tp) REVERT: B 856 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.7085 (m) REVERT: B 873 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8539 (tt) REVERT: B 1005 MET cc_start: 0.8151 (ttp) cc_final: 0.7761 (ptm) REVERT: B 1114 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7099 (ptm-80) REVERT: C 157 MET cc_start: 0.1424 (OUTLIER) cc_final: 0.0772 (tpt) REVERT: C 175 MET cc_start: 0.3355 (tpt) cc_final: 0.0141 (ptm) REVERT: C 293 MET cc_start: 0.7157 (mmp) cc_final: 0.6748 (ptt) REVERT: F 24 ARG cc_start: 0.6420 (tpt170) cc_final: 0.5030 (tpt170) REVERT: H 27 GLU cc_start: 0.6475 (pm20) cc_final: 0.5196 (pm20) REVERT: H 30 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8379 (mm) REVERT: H 46 SER cc_start: 0.6643 (OUTLIER) cc_final: 0.6080 (p) REVERT: H 74 TYR cc_start: 0.8562 (m-10) cc_final: 0.8220 (m-80) REVERT: H 78 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6863 (mt) REVERT: K 8 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5334 (mt-10) REVERT: L 14 GLU cc_start: 0.6391 (mt-10) cc_final: 0.5786 (mt-10) REVERT: L 76 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: N 2 ILE cc_start: 0.8892 (mt) cc_final: 0.8647 (mt) outliers start: 94 outliers final: 64 residues processed: 431 average time/residue: 0.1802 time to fit residues: 125.2028 Evaluate side-chains 409 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 331 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 150 PHE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 241 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 210 optimal weight: 0.0980 chunk 282 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 111 optimal weight: 0.4980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN E 82 GLN F 25 HIS L 33 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.207437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.190658 restraints weight = 34578.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.181264 restraints weight = 79829.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.178818 restraints weight = 60264.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175911 restraints weight = 55618.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176234 restraints weight = 49987.743| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26884 Z= 0.152 Angle : 0.717 13.795 36282 Z= 0.364 Chirality : 0.047 0.281 4015 Planarity : 0.006 0.119 4722 Dihedral : 5.691 65.213 3674 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.63 % Favored : 88.31 % Rotamer: Outliers : 3.12 % Allowed : 21.87 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.31 (0.14), residues: 3275 helix: -0.34 (0.16), residues: 1063 sheet: -0.91 (0.26), residues: 412 loop : -2.54 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 166 TYR 0.021 0.001 TYR B 432 PHE 0.018 0.001 PHE B 821 TRP 0.014 0.001 TRP A 272 HIS 0.010 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00363 (26872) covalent geometry : angle 0.71687 (36282) hydrogen bonds : bond 0.03707 ( 700) hydrogen bonds : angle 4.68172 ( 1980) metal coordination : bond 0.00527 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6550 Ramachandran restraints generated. 3275 Oldfield, 0 Emsley, 3275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 335 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8310 (tpp) cc_final: 0.7566 (tpt) REVERT: A 66 ARG cc_start: 0.6826 (mmm-85) cc_final: 0.5572 (mpt90) REVERT: A 108 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4409 (mt) REVERT: A 337 MET cc_start: 0.8165 (mmm) cc_final: 0.7430 (mmt) REVERT: A 626 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: A 651 ASP cc_start: 0.8609 (t70) cc_final: 0.7566 (t0) REVERT: A 768 MET cc_start: 0.8396 (mmm) cc_final: 0.8146 (mmm) REVERT: B 90 MET cc_start: 0.8366 (tpp) cc_final: 0.7529 (tpp) REVERT: B 198 ARG cc_start: 0.7345 (tpt-90) cc_final: 0.7036 (tpt170) REVERT: B 320 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7849 (tt) REVERT: B 365 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.6101 (mp10) REVERT: B 471 THR cc_start: 0.8189 (m) cc_final: 0.7665 (p) REVERT: B 496 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.6993 (tpm170) REVERT: B 696 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8533 (tp) REVERT: B 856 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7154 (m) REVERT: B 873 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8722 (tp) REVERT: B 1005 MET cc_start: 0.8225 (ttp) cc_final: 0.7821 (ptm) REVERT: B 1114 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7081 (ptm-80) REVERT: C 157 MET cc_start: 0.1702 (OUTLIER) cc_final: 0.1072 (tpt) REVERT: C 175 MET cc_start: 0.2518 (tpt) cc_final: -0.0226 (ptm) REVERT: C 306 MET cc_start: 0.8177 (ptt) cc_final: 0.7787 (ptt) REVERT: C 384 LEU cc_start: 0.7915 (tp) cc_final: 0.7397 (tt) REVERT: D 150 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6817 (t80) REVERT: E 17 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6521 (pmm) REVERT: E 82 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.5723 (tm130) REVERT: F 24 ARG cc_start: 0.6546 (tpt170) cc_final: 0.5159 (tpt170) REVERT: H 30 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (mm) REVERT: H 46 SER cc_start: 0.6557 (OUTLIER) cc_final: 0.6001 (p) REVERT: H 74 TYR cc_start: 0.8635 (m-10) cc_final: 0.8336 (m-80) REVERT: K 8 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.6075 (mt-10) REVERT: L 14 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6274 (mt-10) REVERT: L 76 GLN cc_start: 0.7581 (mm-40) cc_final: 0.6813 (tm-30) outliers start: 89 outliers final: 66 residues processed: 395 average time/residue: 0.1799 time to fit residues: 114.6389 Evaluate side-chains 404 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 323 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 858 GLU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 150 PHE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 112 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 322 optimal weight: 0.0070 chunk 172 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 312 optimal weight: 0.7980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS A 398 ASN A 431 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN F 25 HIS L 33 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.210138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183363 restraints weight = 34635.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178543 restraints weight = 44336.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178433 restraints weight = 43683.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178816 restraints weight = 34684.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.178920 restraints weight = 30470.008| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26884 Z= 0.120 Angle : 0.694 13.722 36282 Z= 0.351 Chirality : 0.046 0.278 4015 Planarity : 0.006 0.118 4722 Dihedral : 5.578 64.307 3674 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.60 % Favored : 89.34 % Rotamer: Outliers : 3.23 % Allowed : 21.83 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.21 (0.15), residues: 3275 helix: -0.23 (0.16), residues: 1066 sheet: -0.83 (0.26), residues: 409 loop : -2.50 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 166 TYR 0.022 0.001 TYR C 126 PHE 0.016 0.001 PHE B 821 TRP 0.014 0.001 TRP A 272 HIS 0.020 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00273 (26872) covalent geometry : angle 0.69389 (36282) hydrogen bonds : bond 0.03357 ( 700) hydrogen bonds : angle 4.57487 ( 1980) metal coordination : bond 0.00530 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.36 seconds wall clock time: 72 minutes 48.43 seconds (4368.43 seconds total)