Starting phenix.real_space_refine (version: dev) on Thu Dec 15 15:42:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/12_2022/6kf3_9960.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/12_2022/6kf3_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/12_2022/6kf3_9960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/12_2022/6kf3_9960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/12_2022/6kf3_9960.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/12_2022/6kf3_9960.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ASP 731": "OD1" <-> "OD2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "B TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 820": "NH1" <-> "NH2" Residue "B PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/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: 14.50, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.77 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 1.46 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: 9.00 Time building geometry restraints manager: 11.64 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: 96.69 - 106.22: 907 106.22 - 115.75: 16397 115.75 - 125.27: 18447 125.27 - 134.80: 528 134.80 - 144.33: 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=" CA LYS P 13 " pdb=" CB LYS P 13 " pdb=" CG LYS P 13 " ideal model delta sigma weight residual 114.10 125.54 -11.44 2.00e+00 2.50e-01 3.27e+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 2.440 nonbonded pdb=" O GLU B 150 " pdb=" OH TYR N 62 " model vdw 2.224 2.440 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 ========== 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 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. 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: 0.210 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: 0.030 Extract box with map and model: 4.000 Check model and map are aligned: 0.420 Convert atoms to be neutral: 0.250 Process input model: 69.600 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.008 0.129 26872 Z= 0.553 Angle : 1.330 17.327 36282 Z= 0.712 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 : 4.59 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.71 % Favored : 85.53 % Rotamer Outliers : 4.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.82 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (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 *********************** 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 fitting. rotamer outliers: 135 poor density : 717 time to evaluate : 3.154 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 outliers start: 135 outliers final: 30 residues processed: 813 average time/residue: 0.4406 time to fit residues: 533.4998 Evaluate side-chains 432 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 402 time to evaluate : 3.184 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2357 time to fit residues: 18.1714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 40.0000 chunk 246 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 382 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN A 732 ASN A 790 HIS A 815 GLN B 51 ASN B 260 ASN B 312 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN B 968 HIS C 19 ASN C 82 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 26872 Z= 0.209 Angle : 0.780 13.244 36282 Z= 0.400 Chirality : 0.049 0.349 4015 Planarity : 0.007 0.125 4722 Dihedral : 6.283 68.616 3658 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.63 % Favored : 89.16 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.13), residues: 3275 helix: -2.51 (0.13), residues: 1047 sheet: -1.22 (0.26), residues: 361 loop : -2.95 (0.13), residues: 1867 *********************** 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 597 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 489 time to evaluate : 3.263 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 outliers start: 108 outliers final: 39 residues processed: 556 average time/residue: 0.4086 time to fit residues: 350.5671 Evaluate side-chains 395 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 356 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2386 time to fit residues: 22.1997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 245 optimal weight: 0.5980 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 295 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 382 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN ** 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** D 117 ASN E 82 GLN E 124 ASN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 26872 Z= 0.314 Angle : 0.778 15.141 36282 Z= 0.399 Chirality : 0.050 0.383 4015 Planarity : 0.007 0.124 4722 Dihedral : 6.150 70.967 3658 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.85 % Favored : 87.97 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.13), residues: 3275 helix: -1.86 (0.14), residues: 1077 sheet: -1.25 (0.26), residues: 360 loop : -2.85 (0.13), residues: 1838 *********************** 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 478 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 376 time to evaluate : 3.267 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 outliers start: 102 outliers final: 48 residues processed: 452 average time/residue: 0.3949 time to fit residues: 279.7790 Evaluate side-chains 372 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 324 time to evaluate : 3.116 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2308 time to fit residues: 25.3245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 296 optimal weight: 10.0000 chunk 314 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 305 HIS B 431 ASN B 556 ASN B 662 HIS E 68 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.139 26872 Z= 0.505 Angle : 0.906 15.037 36282 Z= 0.465 Chirality : 0.054 0.395 4015 Planarity : 0.008 0.125 4722 Dihedral : 6.669 73.565 3658 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.95 % Favored : 85.77 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.82 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.13), residues: 3275 helix: -1.85 (0.14), residues: 1075 sheet: -1.40 (0.27), residues: 347 loop : -2.94 (0.13), residues: 1853 *********************** 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 435 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 342 time to evaluate : 3.080 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 outliers start: 93 outliers final: 47 residues processed: 402 average time/residue: 0.4001 time to fit residues: 257.3321 Evaluate side-chains 356 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 309 time to evaluate : 3.165 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2574 time to fit residues: 26.9425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 268 optimal weight: 7.9990 chunk 217 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 281 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 431 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26872 Z= 0.176 Angle : 0.699 15.918 36282 Z= 0.353 Chirality : 0.047 0.347 4015 Planarity : 0.006 0.122 4722 Dihedral : 5.819 66.870 3658 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.96 % Favored : 88.89 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.14), residues: 3275 helix: -1.23 (0.15), residues: 1058 sheet: -1.32 (0.26), residues: 377 loop : -2.74 (0.13), residues: 1840 *********************** 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 417 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 367 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 396 average time/residue: 0.3842 time to fit residues: 242.8791 Evaluate side-chains 343 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 323 time to evaluate : 3.136 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2311 time to fit residues: 13.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 0.0470 chunk 282 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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 473 GLN A 613 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 70 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 26872 Z= 0.309 Angle : 0.759 14.914 36282 Z= 0.384 Chirality : 0.049 0.432 4015 Planarity : 0.006 0.123 4722 Dihedral : 5.942 69.383 3658 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.34 % Favored : 86.53 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.14), residues: 3275 helix: -1.19 (0.15), residues: 1074 sheet: -1.19 (0.27), residues: 349 loop : -2.77 (0.13), residues: 1852 *********************** 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 380 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 329 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 363 average time/residue: 0.3910 time to fit residues: 226.9752 Evaluate side-chains 338 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 311 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2511 time to fit residues: 17.5500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 179 optimal weight: 0.0970 chunk 229 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 264 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 313 optimal weight: 0.8980 chunk 196 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- 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 473 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN E 82 GLN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 26872 Z= 0.247 Angle : 0.725 16.514 36282 Z= 0.365 Chirality : 0.048 0.437 4015 Planarity : 0.006 0.123 4722 Dihedral : 5.831 67.765 3658 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.24 % Favored : 87.60 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.14), residues: 3275 helix: -0.88 (0.16), residues: 1038 sheet: -1.13 (0.27), residues: 368 loop : -2.74 (0.13), residues: 1869 *********************** 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 379 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 334 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 21 residues processed: 364 average time/residue: 0.3919 time to fit residues: 229.4248 Evaluate side-chains 339 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 318 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2404 time to fit residues: 14.5102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 29 optimal weight: 0.0050 chunk 246 optimal weight: 8.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 473 GLN A 548 ASN A 815 GLN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 586 ASN B1014 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 26872 Z= 0.173 Angle : 0.689 16.287 36282 Z= 0.344 Chirality : 0.046 0.360 4015 Planarity : 0.006 0.121 4722 Dihedral : 5.485 65.160 3658 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.45 % Favored : 88.40 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 3275 helix: -0.57 (0.16), residues: 1041 sheet: -1.06 (0.27), residues: 383 loop : -2.62 (0.14), residues: 1851 *********************** 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 367 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 345 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 360 average time/residue: 0.3848 time to fit residues: 223.2781 Evaluate side-chains 338 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 323 time to evaluate : 3.543 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2573 time to fit residues: 12.1776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 30.0000 chunk 300 optimal weight: 1.9990 chunk 273 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.115 26872 Z= 0.446 Angle : 0.857 15.584 36282 Z= 0.434 Chirality : 0.053 0.423 4015 Planarity : 0.007 0.123 4722 Dihedral : 6.257 71.137 3658 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.05 % Favored : 85.80 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 3275 helix: -1.07 (0.15), residues: 1055 sheet: -1.12 (0.29), residues: 309 loop : -2.78 (0.13), residues: 1911 *********************** 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 335 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 306 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 322 average time/residue: 0.4112 time to fit residues: 208.1615 Evaluate side-chains 315 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 296 time to evaluate : 3.246 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2765 time to fit residues: 13.8670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 323 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 26872 Z= 0.209 Angle : 0.726 15.222 36282 Z= 0.363 Chirality : 0.047 0.402 4015 Planarity : 0.006 0.121 4722 Dihedral : 5.779 66.591 3658 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.85 % Favored : 88.03 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.82 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.14), residues: 3275 helix: -0.68 (0.16), residues: 1039 sheet: -1.30 (0.29), residues: 340 loop : -2.60 (0.14), residues: 1896 ********************** 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 333 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 321 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 328 average time/residue: 0.3852 time to fit residues: 204.5719 Evaluate side-chains 321 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 313 time to evaluate : 2.987 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2469 time to fit residues: 7.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 71 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 265 optimal weight: 0.0370 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- 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 473 GLN A 613 ASN ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B1014 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4358 r_free = 0.4358 target = 0.207073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178699 restraints weight = 35088.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.174526 restraints weight = 39724.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174139 restraints weight = 45286.746| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 26872 Z= 0.189 Angle : 0.707 15.467 36282 Z= 0.351 Chirality : 0.046 0.383 4015 Planarity : 0.006 0.119 4722 Dihedral : 5.525 65.397 3658 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.21 % Favored : 87.63 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 3275 helix: -0.46 (0.16), residues: 1046 sheet: -1.27 (0.28), residues: 351 loop : -2.54 (0.14), residues: 1878 =============================================================================== Job complete usr+sys time: 5278.57 seconds wall clock time: 96 minutes 32.34 seconds (5792.34 seconds total)