Starting phenix.real_space_refine on Wed Mar 20 04:50:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/03_2024/6kf3_9960.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/03_2024/6kf3_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_9960/03_2024/6kf3_9960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/03_2024/6kf3_9960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/03_2024/6kf3_9960.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kf3_9960/03_2024/6kf3_9960.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 Mg 1 5.21 5 S 116 5.16 5 C 16735 2.51 5 N 4621 2.21 5 O 4897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.46, per 1000 atoms: 0.51 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: 9.03 Conformation dependent library (CDL) restraints added in 4.5 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: 2.98 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: 9.78 Time building geometry restraints manager: 10.01 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=" C GLY F 28 " pdb=" N LEU F 29 " pdb=" CA LEU F 29 " ideal model delta sigma weight residual 121.70 133.62 -11.92 1.80e+00 3.09e-01 4.38e+01 ... (remaining 36277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15301 17.93 - 35.86: 976 35.86 - 53.78: 226 53.78 - 71.71: 33 71.71 - 89.64: 8 Dihedral angle restraints: 16544 sinusoidal: 7026 harmonic: 9518 Sorted by residual: dihedral pdb=" CA GLN A 427 " pdb=" C GLN A 427 " pdb=" N PRO A 428 " pdb=" CA PRO A 428 " ideal model delta harmonic sigma weight residual 180.00 100.05 79.95 0 5.00e+00 4.00e-02 2.56e+02 dihedral pdb=" CA ASN C 110 " pdb=" C ASN C 110 " pdb=" N PRO C 111 " pdb=" CA PRO C 111 " ideal model delta harmonic sigma weight residual -180.00 -128.99 -51.01 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA VAL K 30 " pdb=" C VAL K 30 " pdb=" N PRO K 31 " pdb=" CA PRO K 31 " ideal model delta harmonic sigma weight residual -180.00 -135.05 -44.95 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 16541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3556 0.111 - 0.221: 426 0.221 - 0.332: 27 0.332 - 0.443: 5 0.443 - 0.553: 1 Chirality restraints: 4015 Sorted by residual: chirality pdb=" CB ILE B 652 " pdb=" CA ILE B 652 " pdb=" CG1 ILE B 652 " pdb=" CG2 ILE B 652 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ASN B 431 " pdb=" N ASN B 431 " pdb=" C ASN B 431 " pdb=" CB ASN B 431 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CB ILE B 895 " pdb=" CA ILE B 895 " pdb=" CG1 ILE B 895 " pdb=" CG2 ILE B 895 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 4012 not shown) Planarity restraints: 4722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 455 " 0.093 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO A 456 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 427 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 428 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 110 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 111 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.056 5.00e-02 4.00e+02 ... (remaining 4719 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 455 2.66 - 3.22: 22507 3.22 - 3.78: 37071 3.78 - 4.34: 48839 4.34 - 4.90: 81067 Nonbonded interactions: 189939 Sorted by model distance: nonbonded pdb=" OD1 ASP A 465 " pdb="MG MG A1001 " model vdw 2.102 2.170 nonbonded pdb=" O CYS N 44 " pdb="ZN ZN N1401 " model vdw 2.162 2.230 nonbonded pdb=" OG1 THR B 13 " pdb=" OE1 GLU B 16 " model vdw 2.184 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 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: 0.380 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: 0.020 Extract box with map and model: 2.540 Check model and map are aligned: 0.330 Set scattering table: 0.230 Process input model: 69.990 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.129 26872 Z= 0.553 Angle : 1.330 17.327 36282 Z= 0.713 Chirality : 0.072 0.553 4015 Planarity : 0.009 0.140 4722 Dihedral : 12.715 89.641 10432 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.71 % Favored : 85.53 % Rotamer: Outliers : 4.74 % Allowed : 6.98 % Favored : 88.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.82 % Twisted General : 0.35 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP A 272 HIS 0.014 0.003 HIS A 415 PHE 0.059 0.004 PHE B1032 TYR 0.045 0.004 TYR P 29 ARG 0.018 0.001 ARG A 601 *********************** 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 : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.4713 (mm) cc_final: 0.4295 (mt) REVERT: A 207 LYS cc_start: 0.6657 (mttt) cc_final: 0.6298 (mmtt) REVERT: A 266 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6144 (tt) REVERT: A 274 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6306 (tp) REVERT: A 325 ASN cc_start: 0.6799 (m-40) cc_final: 0.6527 (t0) REVERT: A 337 MET cc_start: 0.7702 (mmm) cc_final: 0.7482 (tpp) REVERT: A 358 LYS cc_start: 0.8186 (tptt) cc_final: 0.7919 (tttp) REVERT: A 422 VAL cc_start: 0.9621 (p) cc_final: 0.9367 (m) REVERT: A 463 ASP cc_start: 0.8946 (p0) cc_final: 0.8661 (p0) REVERT: A 475 GLU cc_start: 0.6389 (mp0) cc_final: 0.6000 (mp0) REVERT: A 847 ASN cc_start: 0.8115 (t0) cc_final: 0.7371 (t0) REVERT: A 889 ASP cc_start: 0.6597 (m-30) cc_final: 0.5743 (p0) REVERT: A 899 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8710 (mm) REVERT: B 14 PRO cc_start: 0.7517 (Cg_exo) cc_final: 0.7299 (Cg_endo) REVERT: B 89 PRO cc_start: 0.9062 (Cg_exo) cc_final: 0.8690 (Cg_endo) REVERT: B 129 MET cc_start: 0.7483 (ttm) cc_final: 0.7172 (ttm) REVERT: B 289 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.4599 (m-80) REVERT: B 458 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8431 (tp) REVERT: B 656 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.6832 (tp) REVERT: B 674 MET cc_start: 0.7937 (mtt) cc_final: 0.7690 (mtp) REVERT: B 765 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7333 (mttp) REVERT: B 873 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8694 (tp) REVERT: B 885 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7244 (ptt90) REVERT: C 27 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7475 (tptm) REVERT: C 164 ASP cc_start: 0.3340 (OUTLIER) cc_final: 0.2482 (m-30) REVERT: C 287 ASP cc_start: 0.7360 (t70) cc_final: 0.7094 (t0) REVERT: C 358 LEU cc_start: 0.7024 (mt) cc_final: 0.6627 (mt) REVERT: D 145 LYS cc_start: 0.8849 (ptpt) cc_final: 0.8637 (ptmt) REVERT: E 5 LEU cc_start: 0.5042 (mm) cc_final: 0.4432 (mm) REVERT: E 17 MET cc_start: 0.7220 (pmm) cc_final: 0.6975 (pmm) REVERT: F 102 MET cc_start: 0.4842 (tpt) cc_final: 0.4634 (tpt) REVERT: H 35 ILE cc_start: 0.8452 (pt) cc_final: 0.8243 (pt) REVERT: L 51 MET cc_start: 0.8476 (ptp) cc_final: 0.8251 (ptm) REVERT: P 13 LYS cc_start: 0.6463 (OUTLIER) cc_final: 0.5959 (mptt) outliers start: 135 outliers final: 30 residues processed: 813 average time/residue: 0.4790 time to fit residues: 578.7568 Evaluate side-chains 447 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 406 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 885 ARG Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 29 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 40.0000 chunk 246 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 252 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN A 732 ASN A 790 HIS A 815 GLN B 260 ASN B 312 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN B 968 HIS C 19 ASN C 82 ASN D 117 ASN D 206 HIS E 124 ASN E 162 ASN F 32 ASN K 38 GLN L 22 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26872 Z= 0.229 Angle : 0.788 12.326 36282 Z= 0.408 Chirality : 0.049 0.311 4015 Planarity : 0.007 0.127 4722 Dihedral : 7.633 69.596 3735 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.93 % Favored : 88.85 % Rotamer: Outliers : 4.63 % Allowed : 14.04 % Favored : 81.33 % 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: -3.87 (0.13), residues: 3275 helix: -2.53 (0.13), residues: 1056 sheet: -1.34 (0.26), residues: 365 loop : -2.96 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 683 HIS 0.007 0.001 HIS B 595 PHE 0.024 0.002 PHE B 821 TYR 0.021 0.002 TYR A 740 ARG 0.006 0.001 ARG D 212 *********************** 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 600 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 468 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.6737 (mmm-85) cc_final: 0.5276 (mpt90) REVERT: A 108 LEU cc_start: 0.4941 (mm) cc_final: 0.3988 (mt) REVERT: A 123 MET cc_start: 0.4432 (ttm) cc_final: 0.4099 (mpp) REVERT: A 274 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.5997 (tp) REVERT: A 337 MET cc_start: 0.7926 (mmm) cc_final: 0.7404 (tpp) REVERT: A 358 LYS cc_start: 0.8172 (tptt) cc_final: 0.7919 (tttp) REVERT: A 422 VAL cc_start: 0.9509 (p) cc_final: 0.9218 (m) REVERT: A 463 ASP cc_start: 0.8995 (p0) cc_final: 0.8709 (p0) REVERT: A 466 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 475 GLU cc_start: 0.6348 (mp0) cc_final: 0.6084 (mp0) REVERT: A 632 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8170 (mptt) REVERT: A 774 ILE cc_start: 0.8431 (tt) cc_final: 0.7998 (pt) REVERT: A 899 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8568 (mm) REVERT: B 89 PRO cc_start: 0.9080 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: B 90 MET cc_start: 0.8578 (tpp) cc_final: 0.7993 (tpp) REVERT: B 107 MET cc_start: 0.6673 (mpp) cc_final: 0.6461 (mpp) REVERT: B 365 GLN cc_start: 0.7375 (pp30) cc_final: 0.5810 (mp10) REVERT: B 371 GLN cc_start: 0.6180 (pp30) cc_final: 0.5921 (tt0) REVERT: B 372 TYR cc_start: 0.7468 (t80) cc_final: 0.7016 (t80) REVERT: B 873 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8642 (tp) REVERT: B 1005 MET cc_start: 0.8089 (ttp) cc_final: 0.7791 (ptm) REVERT: B 1032 PHE cc_start: 0.3129 (OUTLIER) cc_final: 0.2673 (m-10) REVERT: C 53 TYR cc_start: 0.8506 (t80) cc_final: 0.8025 (t80) REVERT: C 293 MET cc_start: 0.7354 (mmp) cc_final: 0.7009 (ptt) REVERT: C 358 LEU cc_start: 0.7069 (mt) cc_final: 0.6649 (mt) REVERT: F 102 MET cc_start: 0.4763 (tpt) cc_final: 0.4276 (tpt) REVERT: L 1 MET cc_start: 0.7293 (mtp) cc_final: 0.7061 (mtp) REVERT: L 72 GLU cc_start: 0.7319 (tp30) cc_final: 0.7115 (tm-30) REVERT: L 76 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7273 (tm-30) outliers start: 132 outliers final: 57 residues processed: 557 average time/residue: 0.3979 time to fit residues: 338.8400 Evaluate side-chains 410 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 347 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 15 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 295 optimal weight: 8.9990 chunk 319 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 100 optimal weight: 0.0370 chunk 237 optimal weight: 6.9990 overall best weight: 3.3864 ------------------------------------------------------------------------------- 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 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN C 82 ASN D 117 ASN E 82 GLN ** 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: 0.7473 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 26872 Z= 0.330 Angle : 0.794 15.088 36282 Z= 0.408 Chirality : 0.050 0.359 4015 Planarity : 0.007 0.125 4722 Dihedral : 6.941 71.218 3689 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.55 % Favored : 87.27 % Rotamer: Outliers : 5.30 % Allowed : 15.69 % Favored : 79.01 % 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: -3.48 (0.13), residues: 3275 helix: -1.94 (0.14), residues: 1080 sheet: -1.29 (0.26), residues: 373 loop : -2.87 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 683 HIS 0.008 0.002 HIS A 490 PHE 0.022 0.002 PHE F 38 TYR 0.021 0.002 TYR A 740 ARG 0.006 0.001 ARG D 212 *********************** 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 516 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 365 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.5144 (mm) cc_final: 0.4383 (mt) REVERT: A 123 MET cc_start: 0.4290 (ttm) cc_final: 0.4037 (mpp) REVERT: A 268 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6547 (tt) REVERT: A 274 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6010 (tp) REVERT: A 337 MET cc_start: 0.7728 (mmm) cc_final: 0.7255 (tpp) REVERT: A 422 VAL cc_start: 0.9632 (p) cc_final: 0.9343 (m) REVERT: A 463 ASP cc_start: 0.9038 (p0) cc_final: 0.8694 (p0) REVERT: A 475 GLU cc_start: 0.6416 (mp0) cc_final: 0.6160 (mp0) REVERT: A 544 ASP cc_start: 0.7800 (m-30) cc_final: 0.7561 (m-30) REVERT: A 650 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8556 (tt) REVERT: A 651 ASP cc_start: 0.8589 (t70) cc_final: 0.7564 (t0) REVERT: A 697 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8123 (tp) REVERT: B 35 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 89 PRO cc_start: 0.9193 (Cg_exo) cc_final: 0.8853 (Cg_endo) REVERT: B 90 MET cc_start: 0.8816 (tpp) cc_final: 0.8036 (tpp) REVERT: B 106 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5213 (tt0) REVERT: B 306 MET cc_start: 0.7893 (mmm) cc_final: 0.7675 (mmt) REVERT: B 371 GLN cc_start: 0.6047 (pp30) cc_final: 0.5771 (tt0) REVERT: B 372 TYR cc_start: 0.7784 (t80) cc_final: 0.7277 (t80) REVERT: B 559 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7249 (tt) REVERT: B 612 MET cc_start: 0.7860 (mtp) cc_final: 0.7547 (mtp) REVERT: B 696 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8564 (tp) REVERT: B 761 GLU cc_start: 0.7331 (pp20) cc_final: 0.7044 (pp20) REVERT: B 873 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8699 (tp) REVERT: B 880 ASP cc_start: 0.8777 (m-30) cc_final: 0.8339 (m-30) REVERT: B 1032 PHE cc_start: 0.4091 (OUTLIER) cc_final: 0.3560 (m-10) REVERT: B 1035 MET cc_start: 0.8100 (mmm) cc_final: 0.7845 (mmt) REVERT: B 1097 MET cc_start: 0.5301 (ptp) cc_final: 0.5054 (ptp) REVERT: C 53 TYR cc_start: 0.8459 (t80) cc_final: 0.8143 (t80) REVERT: C 116 MET cc_start: 0.7913 (ptp) cc_final: 0.7491 (ptp) REVERT: C 157 MET cc_start: 0.0348 (OUTLIER) cc_final: -0.2350 (mmm) REVERT: C 293 MET cc_start: 0.7688 (mmp) cc_final: 0.7126 (ptt) REVERT: C 358 LEU cc_start: 0.6947 (mt) cc_final: 0.6480 (mt) REVERT: F 102 MET cc_start: 0.3945 (tpt) cc_final: 0.3517 (tpt) REVERT: K 49 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7092 (tp) REVERT: L 72 GLU cc_start: 0.7227 (tp30) cc_final: 0.6983 (tm-30) REVERT: L 76 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7110 (tm-30) outliers start: 151 outliers final: 86 residues processed: 478 average time/residue: 0.3777 time to fit residues: 285.7627 Evaluate side-chains 425 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 327 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 30.0000 chunk 222 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 281 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 82 ASN E 68 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26872 Z= 0.250 Angle : 0.720 12.531 36282 Z= 0.369 Chirality : 0.047 0.274 4015 Planarity : 0.006 0.122 4722 Dihedral : 6.548 68.542 3681 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.12 % Favored : 87.76 % Rotamer: Outliers : 4.91 % Allowed : 17.37 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -3.16 (0.14), residues: 3275 helix: -1.49 (0.15), residues: 1072 sheet: -1.11 (0.27), residues: 363 loop : -2.80 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 272 HIS 0.006 0.001 HIS B 462 PHE 0.019 0.002 PHE B1032 TYR 0.019 0.001 TYR A 740 ARG 0.005 0.000 ARG N 24 *********************** 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 490 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 350 time to evaluate : 2.995 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: A 47 MET cc_start: 0.8589 (mmm) cc_final: 0.8308 (tpp) REVERT: A 66 ARG cc_start: 0.6643 (mmm-85) cc_final: 0.5396 (mpt90) REVERT: A 108 LEU cc_start: 0.4845 (mm) cc_final: 0.3992 (mt) REVERT: A 268 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6629 (tp) REVERT: A 274 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5688 (tt) REVERT: A 337 MET cc_start: 0.7819 (mmm) cc_final: 0.7290 (tpp) REVERT: A 422 VAL cc_start: 0.9546 (p) cc_final: 0.9254 (m) REVERT: A 463 ASP cc_start: 0.9017 (p0) cc_final: 0.8715 (p0) REVERT: A 626 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: A 650 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 651 ASP cc_start: 0.8666 (t70) cc_final: 0.7726 (t0) REVERT: A 697 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8008 (tp) REVERT: B 89 PRO cc_start: 0.9095 (Cg_exo) cc_final: 0.8795 (Cg_endo) REVERT: B 90 MET cc_start: 0.8736 (tpp) cc_final: 0.7767 (tpp) REVERT: B 320 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7794 (tt) REVERT: B 477 CYS cc_start: 0.8150 (t) cc_final: 0.7638 (t) REVERT: B 696 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 736 MET cc_start: 0.8124 (tpp) cc_final: 0.7844 (tpp) REVERT: B 761 GLU cc_start: 0.7440 (pp20) cc_final: 0.7238 (pp20) REVERT: B 873 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 880 ASP cc_start: 0.8787 (m-30) cc_final: 0.8457 (m-30) REVERT: B 1032 PHE cc_start: 0.3528 (OUTLIER) cc_final: 0.3038 (m-10) REVERT: B 1114 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6832 (ptm-80) REVERT: C 35 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6225 (p90) REVERT: C 293 MET cc_start: 0.7649 (mmp) cc_final: 0.7043 (ptt) REVERT: C 358 LEU cc_start: 0.7028 (mt) cc_final: 0.6578 (mt) REVERT: C 384 LEU cc_start: 0.7778 (tp) cc_final: 0.7392 (tt) REVERT: F 102 MET cc_start: 0.3991 (tpt) cc_final: 0.3530 (tpt) REVERT: K 8 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5170 (mt-10) REVERT: K 53 VAL cc_start: 0.8770 (t) cc_final: 0.7965 (t) REVERT: L 72 GLU cc_start: 0.7204 (tp30) cc_final: 0.6951 (tm-30) REVERT: L 76 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.6968 (tm-30) REVERT: P 19 LEU cc_start: 0.2966 (OUTLIER) cc_final: 0.2640 (pp) outliers start: 140 outliers final: 97 residues processed: 452 average time/residue: 0.3579 time to fit residues: 258.2294 Evaluate side-chains 436 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 325 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 268 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 281 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 HIS C 70 GLN C 82 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 26872 Z= 0.334 Angle : 0.764 15.545 36282 Z= 0.391 Chirality : 0.049 0.439 4015 Planarity : 0.007 0.123 4722 Dihedral : 6.651 69.952 3681 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.25 % Favored : 86.56 % Rotamer: Outliers : 5.48 % Allowed : 18.67 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -3.14 (0.14), residues: 3275 helix: -1.44 (0.15), residues: 1088 sheet: -1.22 (0.27), residues: 367 loop : -2.78 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 89 HIS 0.008 0.002 HIS A 490 PHE 0.022 0.002 PHE B1032 TYR 0.023 0.002 TYR A 740 ARG 0.008 0.001 ARG K 6 *********************** 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 495 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 339 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8643 (mmm) cc_final: 0.8243 (tpp) REVERT: A 66 ARG cc_start: 0.6614 (mmm-85) cc_final: 0.5293 (mpt90) REVERT: A 178 LYS cc_start: 0.4969 (mtpt) cc_final: 0.4672 (mmmt) REVERT: A 268 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6441 (tp) REVERT: A 274 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5926 (tt) REVERT: A 337 MET cc_start: 0.7998 (mmm) cc_final: 0.7457 (tpp) REVERT: A 422 VAL cc_start: 0.9601 (p) cc_final: 0.9332 (m) REVERT: A 463 ASP cc_start: 0.8822 (p0) cc_final: 0.8359 (p0) REVERT: A 623 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: A 626 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: A 650 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 651 ASP cc_start: 0.8674 (t70) cc_final: 0.7695 (t0) REVERT: A 697 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 723 MET cc_start: 0.8850 (mtp) cc_final: 0.8410 (mtp) REVERT: B 89 PRO cc_start: 0.9029 (Cg_exo) cc_final: 0.8739 (Cg_endo) REVERT: B 90 MET cc_start: 0.8754 (tpp) cc_final: 0.7878 (tpp) REVERT: B 107 MET cc_start: 0.6573 (mpp) cc_final: 0.6361 (mpp) REVERT: B 306 MET cc_start: 0.7476 (mmm) cc_final: 0.7273 (mmt) REVERT: B 320 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7907 (tt) REVERT: B 477 CYS cc_start: 0.8379 (t) cc_final: 0.7753 (t) REVERT: B 653 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8355 (Cg_endo) REVERT: B 696 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8566 (tp) REVERT: B 856 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7250 (m) REVERT: B 873 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 880 ASP cc_start: 0.8815 (m-30) cc_final: 0.8489 (m-30) REVERT: B 1032 PHE cc_start: 0.4223 (OUTLIER) cc_final: 0.3515 (m-10) REVERT: B 1114 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7015 (ptm-80) REVERT: C 35 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6533 (p90) REVERT: C 157 MET cc_start: 0.1265 (OUTLIER) cc_final: 0.0630 (tpt) REVERT: C 175 MET cc_start: 0.4423 (tpp) cc_final: 0.4149 (tpt) REVERT: C 293 MET cc_start: 0.7532 (mmp) cc_final: 0.6944 (ptt) REVERT: C 358 LEU cc_start: 0.6657 (mt) cc_final: 0.6268 (mt) REVERT: C 384 LEU cc_start: 0.7848 (tp) cc_final: 0.7539 (tt) REVERT: D 150 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7090 (t80) REVERT: F 102 MET cc_start: 0.4028 (tpt) cc_final: 0.3415 (tpt) REVERT: H 30 LEU cc_start: 0.8578 (mm) cc_final: 0.8080 (mm) REVERT: H 78 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6969 (mt) REVERT: L 72 GLU cc_start: 0.7277 (tp30) cc_final: 0.6923 (tm-30) REVERT: L 76 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7073 (tm-30) outliers start: 156 outliers final: 113 residues processed: 452 average time/residue: 0.3546 time to fit residues: 258.0150 Evaluate side-chains 451 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 321 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 150 PHE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 0.7980 chunk 282 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 314 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 26872 Z= 0.209 Angle : 0.691 15.361 36282 Z= 0.351 Chirality : 0.047 0.413 4015 Planarity : 0.006 0.121 4722 Dihedral : 6.283 67.390 3681 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.79 % Favored : 88.06 % Rotamer: Outliers : 4.70 % Allowed : 19.55 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.86 (0.14), residues: 3275 helix: -1.06 (0.15), residues: 1069 sheet: -1.06 (0.27), residues: 366 loop : -2.71 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.004 0.001 HIS B 342 PHE 0.017 0.001 PHE B1032 TYR 0.019 0.001 TYR A 740 ARG 0.008 0.000 ARG D 212 *********************** 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 486 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 352 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.6642 (mmm-85) cc_final: 0.5403 (mpt90) REVERT: A 123 MET cc_start: 0.5476 (tpt) cc_final: 0.5175 (mpp) REVERT: A 178 LYS cc_start: 0.5135 (mtpt) cc_final: 0.4913 (mmmt) REVERT: A 268 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6480 (tp) REVERT: A 274 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5717 (tp) REVERT: A 337 MET cc_start: 0.7878 (mmm) cc_final: 0.7301 (tpp) REVERT: A 422 VAL cc_start: 0.9521 (p) cc_final: 0.9230 (m) REVERT: A 463 ASP cc_start: 0.8913 (p0) cc_final: 0.8549 (p0) REVERT: A 542 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6734 (mm-30) REVERT: A 623 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8062 (ttmt) REVERT: A 626 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: A 632 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8380 (mttm) REVERT: A 651 ASP cc_start: 0.8549 (t70) cc_final: 0.7558 (t0) REVERT: A 697 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8025 (tp) REVERT: A 723 MET cc_start: 0.8823 (mtp) cc_final: 0.8365 (mtp) REVERT: B 89 PRO cc_start: 0.8985 (Cg_exo) cc_final: 0.8737 (Cg_endo) REVERT: B 90 MET cc_start: 0.8660 (tpp) cc_final: 0.7802 (tpp) REVERT: B 107 MET cc_start: 0.6572 (mpp) cc_final: 0.6327 (mpp) REVERT: B 320 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7935 (tt) REVERT: B 326 LYS cc_start: 0.7849 (mttm) cc_final: 0.7524 (mttp) REVERT: B 696 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 736 MET cc_start: 0.8100 (tpp) cc_final: 0.7808 (tpp) REVERT: B 856 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7226 (m) REVERT: B 873 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B 880 ASP cc_start: 0.8674 (m-30) cc_final: 0.8442 (m-30) REVERT: B 1032 PHE cc_start: 0.3814 (OUTLIER) cc_final: 0.3239 (m-10) REVERT: B 1114 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6980 (ptm-80) REVERT: C 10 MET cc_start: 0.6589 (mtt) cc_final: 0.6269 (mtm) REVERT: C 157 MET cc_start: 0.1285 (OUTLIER) cc_final: 0.0597 (tpt) REVERT: C 293 MET cc_start: 0.7428 (mmp) cc_final: 0.6899 (ptt) REVERT: C 307 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7505 (tp) REVERT: C 358 LEU cc_start: 0.7191 (mt) cc_final: 0.6687 (mt) REVERT: C 384 LEU cc_start: 0.7737 (tp) cc_final: 0.7267 (tt) REVERT: F 102 MET cc_start: 0.3968 (tpt) cc_final: 0.3419 (tpt) REVERT: H 30 LEU cc_start: 0.8502 (mm) cc_final: 0.7938 (mm) REVERT: K 8 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5728 (mt-10) REVERT: K 46 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7567 (mtmt) REVERT: L 14 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6463 (mt-10) REVERT: L 76 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: N 19 TYR cc_start: 0.7282 (m-80) cc_final: 0.6860 (m-10) REVERT: P 19 LEU cc_start: 0.2487 (OUTLIER) cc_final: 0.2054 (pp) outliers start: 134 outliers final: 94 residues processed: 449 average time/residue: 0.3945 time to fit residues: 287.8465 Evaluate side-chains 433 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 322 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 313 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 124 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN L 33 HIS ** 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: 0.7521 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26872 Z= 0.272 Angle : 0.720 13.850 36282 Z= 0.367 Chirality : 0.048 0.388 4015 Planarity : 0.006 0.123 4722 Dihedral : 6.311 68.204 3680 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.07 % Favored : 86.81 % Rotamer: Outliers : 5.37 % Allowed : 19.66 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.85 (0.14), residues: 3275 helix: -1.00 (0.15), residues: 1063 sheet: -1.02 (0.27), residues: 361 loop : -2.75 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 683 HIS 0.007 0.001 HIS A 490 PHE 0.018 0.002 PHE B1032 TYR 0.021 0.002 TYR A 740 ARG 0.007 0.000 ARG D 212 *********************** 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 490 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 337 time to evaluate : 3.037 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: A 66 ARG cc_start: 0.6675 (mmm-85) cc_final: 0.5417 (mpt90) REVERT: A 123 MET cc_start: 0.5471 (tpt) cc_final: 0.5101 (mpp) REVERT: A 268 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5740 (tp) REVERT: A 274 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5646 (tp) REVERT: A 337 MET cc_start: 0.7955 (mmm) cc_final: 0.7358 (tpp) REVERT: A 422 VAL cc_start: 0.9589 (p) cc_final: 0.9315 (m) REVERT: A 463 ASP cc_start: 0.8793 (p0) cc_final: 0.8399 (p0) REVERT: A 542 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 623 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8085 (ttmt) REVERT: A 626 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: A 651 ASP cc_start: 0.8703 (t70) cc_final: 0.7792 (t0) REVERT: A 697 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8040 (tp) REVERT: A 723 MET cc_start: 0.8832 (mtp) cc_final: 0.8405 (mtp) REVERT: B 89 PRO cc_start: 0.8940 (Cg_exo) cc_final: 0.8711 (Cg_endo) REVERT: B 90 MET cc_start: 0.8688 (tpp) cc_final: 0.7739 (tpp) REVERT: B 107 MET cc_start: 0.6403 (mpp) cc_final: 0.6174 (mpp) REVERT: B 320 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 326 LYS cc_start: 0.7862 (mttm) cc_final: 0.7555 (mttp) REVERT: B 477 CYS cc_start: 0.8247 (t) cc_final: 0.7733 (t) REVERT: B 653 PRO cc_start: 0.8497 (Cg_exo) cc_final: 0.8234 (Cg_endo) REVERT: B 696 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8548 (tp) REVERT: B 736 MET cc_start: 0.8031 (tpp) cc_final: 0.7779 (tpp) REVERT: B 856 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7301 (m) REVERT: B 873 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8722 (tp) REVERT: B 880 ASP cc_start: 0.8716 (m-30) cc_final: 0.8500 (m-30) REVERT: B 1032 PHE cc_start: 0.3754 (OUTLIER) cc_final: 0.3054 (m-10) REVERT: B 1114 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.7077 (ptm-80) REVERT: C 25 TYR cc_start: 0.7010 (t80) cc_final: 0.6761 (t80) REVERT: C 157 MET cc_start: 0.1206 (OUTLIER) cc_final: 0.0582 (tpt) REVERT: C 293 MET cc_start: 0.7386 (mmp) cc_final: 0.6962 (ptt) REVERT: C 307 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7874 (tp) REVERT: C 384 LEU cc_start: 0.7734 (tp) cc_final: 0.7326 (tt) REVERT: F 102 MET cc_start: 0.4135 (tpt) cc_final: 0.3627 (tpt) REVERT: H 30 LEU cc_start: 0.8493 (mm) cc_final: 0.7936 (mm) REVERT: H 74 TYR cc_start: 0.8728 (m-10) cc_final: 0.8382 (m-80) REVERT: H 78 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6722 (mt) REVERT: K 8 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5808 (mt-10) REVERT: L 14 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6684 (mt-10) REVERT: L 76 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: P 19 LEU cc_start: 0.2737 (OUTLIER) cc_final: 0.2310 (pp) outliers start: 153 outliers final: 113 residues processed: 450 average time/residue: 0.3493 time to fit residues: 254.7366 Evaluate side-chains 448 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 318 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 154 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 246 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B1014 GLN C 82 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5175 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= 0.183 Angle : 0.681 15.478 36282 Z= 0.344 Chirality : 0.046 0.364 4015 Planarity : 0.006 0.122 4722 Dihedral : 6.013 65.488 3680 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.24 % Favored : 88.61 % Rotamer: Outliers : 4.56 % Allowed : 20.95 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -2.58 (0.14), residues: 3275 helix: -0.65 (0.16), residues: 1061 sheet: -0.97 (0.28), residues: 372 loop : -2.64 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.005 0.001 HIS B1043 PHE 0.016 0.001 PHE B 821 TYR 0.021 0.001 TYR C 126 ARG 0.008 0.000 ARG D 212 *********************** 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 472 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 342 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.7519 (m-10) cc_final: 0.7276 (m-10) REVERT: A 47 MET cc_start: 0.8300 (tpp) cc_final: 0.7628 (tpt) REVERT: A 66 ARG cc_start: 0.6709 (mmm-85) cc_final: 0.5547 (mpt90) REVERT: A 268 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6228 (tp) REVERT: A 274 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5412 (tp) REVERT: A 337 MET cc_start: 0.7935 (mmm) cc_final: 0.7395 (tpp) REVERT: A 352 GLU cc_start: 0.7754 (tp30) cc_final: 0.7504 (tp30) REVERT: A 422 VAL cc_start: 0.9484 (p) cc_final: 0.9214 (m) REVERT: A 443 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7492 (mtp) REVERT: A 463 ASP cc_start: 0.8868 (p0) cc_final: 0.8599 (p0) REVERT: A 466 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6725 (mt-10) REVERT: A 542 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6870 (mm-30) REVERT: A 626 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: A 632 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8290 (mttm) REVERT: A 651 ASP cc_start: 0.8580 (t70) cc_final: 0.7693 (t0) REVERT: A 723 MET cc_start: 0.8786 (mtp) cc_final: 0.8367 (mtp) REVERT: B 89 PRO cc_start: 0.8855 (Cg_exo) cc_final: 0.8628 (Cg_endo) REVERT: B 90 MET cc_start: 0.8645 (tpp) cc_final: 0.7780 (tpp) REVERT: B 320 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8008 (tt) REVERT: B 470 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6120 (mt-10) REVERT: B 477 CYS cc_start: 0.8039 (t) cc_final: 0.7496 (t) REVERT: B 653 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.7094 (Cg_endo) REVERT: B 696 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 736 MET cc_start: 0.8006 (tpp) cc_final: 0.7762 (tpp) REVERT: B 856 VAL cc_start: 0.7224 (OUTLIER) cc_final: 0.6936 (m) REVERT: B 873 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8672 (tp) REVERT: B 1032 PHE cc_start: 0.3633 (OUTLIER) cc_final: 0.3224 (m-10) REVERT: B 1114 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6944 (ptm-80) REVERT: C 157 MET cc_start: 0.1130 (OUTLIER) cc_final: 0.0555 (tpt) REVERT: C 293 MET cc_start: 0.7322 (mmp) cc_final: 0.6889 (ptt) REVERT: F 102 MET cc_start: 0.4061 (tpt) cc_final: 0.3588 (tpt) REVERT: H 27 GLU cc_start: 0.5888 (pm20) cc_final: 0.5466 (pm20) REVERT: H 30 LEU cc_start: 0.8474 (mm) cc_final: 0.7937 (mm) REVERT: H 74 TYR cc_start: 0.8688 (m-10) cc_final: 0.8368 (m-80) REVERT: K 8 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5805 (mt-10) REVERT: L 14 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6560 (mt-10) REVERT: L 72 GLU cc_start: 0.7356 (tp30) cc_final: 0.6981 (tm-30) REVERT: L 76 GLN cc_start: 0.7509 (mm-40) cc_final: 0.6755 (tm-30) outliers start: 130 outliers final: 92 residues processed: 433 average time/residue: 0.3615 time to fit residues: 253.2569 Evaluate side-chains 436 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 330 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 15 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 20.0000 chunk 300 optimal weight: 0.0170 chunk 273 optimal weight: 6.9990 chunk 291 optimal weight: 30.0000 chunk 175 optimal weight: 0.0980 chunk 127 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 290 optimal weight: 30.0000 overall best weight: 1.4222 ------------------------------------------------------------------------------- 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 470 HIS A 548 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 82 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26872 Z= 0.192 Angle : 0.682 16.604 36282 Z= 0.344 Chirality : 0.046 0.357 4015 Planarity : 0.006 0.120 4722 Dihedral : 5.888 65.391 3679 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.79 % Favored : 88.06 % Rotamer: Outliers : 4.28 % Allowed : 21.13 % Favored : 74.59 % 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: -2.46 (0.14), residues: 3275 helix: -0.53 (0.16), residues: 1058 sheet: -0.93 (0.26), residues: 400 loop : -2.60 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 272 HIS 0.005 0.001 HIS B1043 PHE 0.016 0.001 PHE B 821 TYR 0.020 0.001 TYR C 126 ARG 0.008 0.000 ARG D 212 *********************** 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 464 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 342 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.6767 (mmm-85) cc_final: 0.5589 (mpt90) REVERT: A 108 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4104 (mt) REVERT: A 268 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.6021 (tp) REVERT: A 274 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.5209 (tp) REVERT: A 324 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7137 (p) REVERT: A 337 MET cc_start: 0.7996 (mmm) cc_final: 0.7324 (tpp) REVERT: A 358 LYS cc_start: 0.8046 (tttm) cc_final: 0.7706 (tttm) REVERT: A 422 VAL cc_start: 0.9522 (p) cc_final: 0.9255 (m) REVERT: A 443 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7487 (mtp) REVERT: A 463 ASP cc_start: 0.8802 (p0) cc_final: 0.8556 (p0) REVERT: A 544 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6584 (t0) REVERT: A 603 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7683 (mt) REVERT: A 626 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: A 632 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8334 (mptt) REVERT: A 651 ASP cc_start: 0.8648 (t70) cc_final: 0.7730 (t0) REVERT: A 723 MET cc_start: 0.8800 (mtp) cc_final: 0.8343 (mtp) REVERT: B 89 PRO cc_start: 0.8882 (Cg_exo) cc_final: 0.8639 (Cg_endo) REVERT: B 90 MET cc_start: 0.8623 (tpp) cc_final: 0.7766 (tpp) REVERT: B 320 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7821 (tt) REVERT: B 477 CYS cc_start: 0.8134 (t) cc_final: 0.7527 (t) REVERT: B 489 ILE cc_start: 0.8019 (mm) cc_final: 0.7756 (mm) REVERT: B 696 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8485 (tp) REVERT: B 736 MET cc_start: 0.8101 (tpp) cc_final: 0.7822 (tpp) REVERT: B 856 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.6949 (m) REVERT: B 873 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8664 (tp) REVERT: B 908 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8289 (mt) REVERT: B 1114 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6965 (ptm-80) REVERT: C 157 MET cc_start: 0.1402 (OUTLIER) cc_final: 0.0799 (tpt) REVERT: C 293 MET cc_start: 0.7307 (mmp) cc_final: 0.6889 (ptt) REVERT: F 102 MET cc_start: 0.4097 (tpt) cc_final: 0.3611 (tpt) REVERT: H 30 LEU cc_start: 0.8417 (mm) cc_final: 0.7891 (mm) REVERT: H 74 TYR cc_start: 0.8718 (m-10) cc_final: 0.8353 (m-80) REVERT: K 8 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5842 (mt-10) REVERT: L 14 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6467 (mt-10) REVERT: L 76 GLN cc_start: 0.7588 (mm-40) cc_final: 0.6867 (tm-30) outliers start: 122 outliers final: 88 residues processed: 422 average time/residue: 0.3504 time to fit residues: 239.2225 Evaluate side-chains 435 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 330 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 908 ILE Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 298 optimal weight: 0.5980 chunk 257 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 470 HIS ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN C 82 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26872 Z= 0.288 Angle : 0.742 15.804 36282 Z= 0.376 Chirality : 0.048 0.361 4015 Planarity : 0.006 0.121 4722 Dihedral : 6.170 67.497 3679 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.85 % Favored : 87.05 % Rotamer: Outliers : 3.83 % Allowed : 21.90 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.13 % Twisted Proline : 2.26 % Twisted General : 0.06 % 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: -0.74 (0.16), residues: 1066 sheet: -0.94 (0.28), residues: 350 loop : -2.67 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 272 HIS 0.006 0.001 HIS A 490 PHE 0.020 0.002 PHE B1032 TYR 0.022 0.002 TYR A 740 ARG 0.008 0.000 ARG D 212 ********************** 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 443 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 334 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8554 (tpt) cc_final: 0.8072 (tpp) REVERT: A 66 ARG cc_start: 0.6747 (mmm-85) cc_final: 0.5493 (mpt90) REVERT: A 123 MET cc_start: 0.5701 (tpt) cc_final: 0.5352 (mpp) REVERT: A 268 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6221 (tp) REVERT: A 274 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.5231 (tp) REVERT: A 337 MET cc_start: 0.7925 (mmm) cc_final: 0.7394 (tpp) REVERT: A 422 VAL cc_start: 0.9585 (p) cc_final: 0.9322 (m) REVERT: A 443 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7537 (mtp) REVERT: A 463 ASP cc_start: 0.8743 (p0) cc_final: 0.8381 (p0) REVERT: A 603 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7959 (mt) REVERT: A 626 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: A 651 ASP cc_start: 0.8719 (t70) cc_final: 0.7877 (t0) REVERT: A 723 MET cc_start: 0.8797 (mtp) cc_final: 0.8367 (mtp) REVERT: B 89 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8682 (Cg_endo) REVERT: B 161 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8239 (mt) REVERT: B 320 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8012 (tt) REVERT: B 405 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6843 (mm-30) REVERT: B 477 CYS cc_start: 0.8240 (t) cc_final: 0.7638 (t) REVERT: B 696 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8539 (tp) REVERT: B 736 MET cc_start: 0.8099 (tpp) cc_final: 0.7814 (tpp) REVERT: B 856 VAL cc_start: 0.7300 (OUTLIER) cc_final: 0.6998 (m) REVERT: B 908 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8255 (mt) REVERT: B 1114 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7009 (ptm-80) REVERT: C 157 MET cc_start: 0.1781 (OUTLIER) cc_final: 0.1323 (tpt) REVERT: C 293 MET cc_start: 0.7385 (mmp) cc_final: 0.6957 (ptt) REVERT: D 27 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7894 (m-40) REVERT: E 93 MET cc_start: 0.3495 (tpt) cc_final: 0.3272 (ptt) REVERT: F 102 MET cc_start: 0.4512 (tpt) cc_final: 0.3991 (tpt) REVERT: H 27 GLU cc_start: 0.5963 (pm20) cc_final: 0.5520 (pm20) REVERT: H 30 LEU cc_start: 0.8433 (mm) cc_final: 0.7963 (mm) REVERT: H 74 TYR cc_start: 0.8748 (m-10) cc_final: 0.8405 (m-80) REVERT: K 8 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5931 (mt-10) REVERT: L 14 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6770 (mt-10) REVERT: L 72 GLU cc_start: 0.7423 (tp30) cc_final: 0.7083 (tm-30) REVERT: L 76 GLN cc_start: 0.7718 (mm-40) cc_final: 0.6966 (tm-30) outliers start: 109 outliers final: 84 residues processed: 409 average time/residue: 0.3686 time to fit residues: 240.4320 Evaluate side-chains 421 residues out of total 2849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 323 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 TRP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 908 ILE Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1114 ARG Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain K residue 2 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 0.0050 chunk 274 optimal weight: 30.0000 chunk 78 optimal weight: 2.9990 chunk 237 optimal weight: 0.0170 chunk 38 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.1836 ------------------------------------------------------------------------------- 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** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN E 82 GLN ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.206748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178549 restraints weight = 35123.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175290 restraints weight = 42990.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175231 restraints weight = 37194.612| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26872 Z= 0.182 Angle : 0.688 16.303 36282 Z= 0.346 Chirality : 0.046 0.339 4015 Planarity : 0.006 0.120 4722 Dihedral : 5.887 65.553 3676 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.60 % Favored : 88.31 % Rotamer: Outliers : 3.58 % Allowed : 22.22 % Favored : 74.20 % 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: -2.44 (0.14), residues: 3275 helix: -0.49 (0.16), residues: 1054 sheet: -1.00 (0.27), residues: 390 loop : -2.55 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 272 HIS 0.025 0.001 HIS A 470 PHE 0.015 0.001 PHE B 821 TYR 0.020 0.001 TYR C 126 ARG 0.008 0.000 ARG D 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.86 seconds wall clock time: 102 minutes 55.51 seconds (6175.51 seconds total)